^SERIES = GSE174367
!Series_title = Single-nucleus chromatin accessibility and transcriptomic characterization of Alzheimer’s Disease
!Series_geo_accession = GSE174367
!Series_status = Public on May 12 2021
!Series_submission_date = May 12 2021
!Series_last_update_date = Aug 11 2021
!Series_pubmed_id = 34239132
!Series_summary = The gene-regulatory landscape of the brain is highly dynamic in health and disease, coordinating a menagerie of biological processes across¬ distinct cell-types. Here, we present a multi-omic single-nucleus study of 191,890 nuclei in late-stage Alzheimer’s Disease (AD), accessible through our intuitive web portal, profiling chromatin accessibility and gene expression in the same biological samples and uncovering vast cellular heterogeneity. We identified cell-type specific, disease-associated candidate cis-regulatory elements and their candidate target genes, including an oligodendrocyte-associated regulatory module containing links to APOE and CLU. We describe cis-regulatory relationships in specific cell-types at AD risk loci defined by genome wide association studies (GWAS), demonstrating the utility of this multi-omic single-nucleus approach. Trajectory analysis of glial populations identified disease-relevant transcription factors, like SREBF1 and their regulatory targets. Further, we introduce scWGCNA, a co-expression network analysis strategy robust to the sparsity of single-cell data, to perform a systems-level meta-analysis of AD transcriptomics.
!Series_overall_design = A multi-omics analysis of Alzheimer's Disease in human postmortem brain tissue using single-nucleus ATAC-seq and RNA-seq (bulk and single-nucleus).
!Series_type = Expression profiling by high throughput sequencing
!Series_type = Genome binding/occupancy profiling by high throughput sequencing
!Series_contributor = Samuel,,Morabito
!Series_contributor = Emily,,Miyoshi
!Series_contributor = Vivek,,Swarup
!Series_sample_id = GSM5292838
!Series_sample_id = GSM5292839
!Series_sample_id = GSM5292840
!Series_sample_id = GSM5292841
!Series_sample_id = GSM5292842
!Series_sample_id = GSM5292843
!Series_sample_id = GSM5292844
!Series_sample_id = GSM5292845
!Series_sample_id = GSM5292846
!Series_sample_id = GSM5292847
!Series_sample_id = GSM5292848
!Series_sample_id = GSM5292849
!Series_sample_id = GSM5292850
!Series_sample_id = GSM5292851
!Series_sample_id = GSM5292852
!Series_sample_id = GSM5292853
!Series_sample_id = GSM5292854
!Series_sample_id = GSM5292855
!Series_sample_id = GSM5292856
!Series_sample_id = GSM5292857
!Series_sample_id = GSM5292858
!Series_sample_id = GSM5292859
!Series_sample_id = GSM5292860
!Series_sample_id = GSM5292861
!Series_sample_id = GSM5292862
!Series_sample_id = GSM5292863
!Series_sample_id = GSM5292864
!Series_sample_id = GSM5292865
!Series_sample_id = GSM5292866
!Series_sample_id = GSM5292867
!Series_sample_id = GSM5292868
!Series_sample_id = GSM5292869
!Series_sample_id = GSM5292870
!Series_sample_id = GSM5292871
!Series_sample_id = GSM5292872
!Series_sample_id = GSM5292873
!Series_sample_id = GSM5292874
!Series_sample_id = GSM5292875
!Series_sample_id = GSM5292876
!Series_sample_id = GSM5292877
!Series_sample_id = GSM5292878
!Series_sample_id = GSM5292879
!Series_sample_id = GSM5292880
!Series_sample_id = GSM5292881
!Series_sample_id = GSM5292882
!Series_sample_id = GSM5292883
!Series_sample_id = GSM5292884
!Series_sample_id = GSM5292885
!Series_sample_id = GSM5292886
!Series_sample_id = GSM5292887
!Series_sample_id = GSM5292888
!Series_sample_id = GSM5292889
!Series_sample_id = GSM5292890
!Series_sample_id = GSM5292891
!Series_sample_id = GSM5292892
!Series_sample_id = GSM5292893
!Series_sample_id = GSM5292894
!Series_sample_id = GSM5292895
!Series_sample_id = GSM5292896
!Series_sample_id = GSM5292897
!Series_sample_id = GSM5292898
!Series_sample_id = GSM5292899
!Series_sample_id = GSM5292900
!Series_sample_id = GSM5292901
!Series_sample_id = GSM5292902
!Series_sample_id = GSM5292903
!Series_sample_id = GSM5292904
!Series_sample_id = GSM5292905
!Series_sample_id = GSM5292906
!Series_sample_id = GSM5292907
!Series_sample_id = GSM5292908
!Series_sample_id = GSM5292909
!Series_sample_id = GSM5292910
!Series_sample_id = GSM5292911
!Series_sample_id = GSM5292912
!Series_sample_id = GSM5292913
!Series_sample_id = GSM5292914
!Series_sample_id = GSM5292915
!Series_sample_id = GSM5292916
!Series_sample_id = GSM5292917
!Series_sample_id = GSM5292918
!Series_sample_id = GSM5292919
!Series_sample_id = GSM5292920
!Series_sample_id = GSM5292921
!Series_sample_id = GSM5292922
!Series_sample_id = GSM5292923
!Series_sample_id = GSM5292924
!Series_sample_id = GSM5292925
!Series_sample_id = GSM5292926
!Series_sample_id = GSM5292927
!Series_sample_id = GSM5292928
!Series_sample_id = GSM5292929
!Series_sample_id = GSM5292930
!Series_sample_id = GSM5292931
!Series_sample_id = GSM5292932
!Series_sample_id = GSM5292933
!Series_sample_id = GSM5292934
!Series_sample_id = GSM5292935
!Series_sample_id = GSM5292936
!Series_sample_id = GSM5292937
!Series_sample_id = GSM5292938
!Series_sample_id = GSM5292939
!Series_sample_id = GSM5292940
!Series_sample_id = GSM5292941
!Series_sample_id = GSM5292942
!Series_sample_id = GSM5292943
!Series_sample_id = GSM5292944
!Series_sample_id = GSM5292945
!Series_sample_id = GSM5292946
!Series_sample_id = GSM5292947
!Series_sample_id = GSM5292948
!Series_sample_id = GSM5292949
!Series_sample_id = GSM5292950
!Series_sample_id = GSM5292951
!Series_sample_id = GSM5292952
!Series_sample_id = GSM5292953
!Series_sample_id = GSM5292954
!Series_sample_id = GSM5292955
!Series_sample_id = GSM5292956
!Series_sample_id = GSM5292957
!Series_sample_id = GSM5292958
!Series_sample_id = GSM5292959
!Series_sample_id = GSM5292960
!Series_sample_id = GSM5292961
!Series_sample_id = GSM5292962
!Series_sample_id = GSM5292963
!Series_sample_id = GSM5292964
!Series_sample_id = GSM5292965
!Series_sample_id = GSM5292966
!Series_sample_id = GSM5292967
!Series_sample_id = GSM5292968
!Series_sample_id = GSM5292969
!Series_sample_id = GSM5292970
!Series_sample_id = GSM5292971
!Series_sample_id = GSM5292972
!Series_sample_id = GSM5292973
!Series_sample_id = GSM5292974
!Series_sample_id = GSM5292975
!Series_sample_id = GSM5292976
!Series_sample_id = GSM5292977
!Series_sample_id = GSM5292978
!Series_sample_id = GSM5292979
!Series_sample_id = GSM5292980
!Series_sample_id = GSM5292981
!Series_sample_id = GSM5292982
!Series_sample_id = GSM5292983
!Series_sample_id = GSM5292984
!Series_sample_id = GSM5292985
!Series_sample_id = GSM5292986
!Series_sample_id = GSM5292987
!Series_sample_id = GSM5292988
!Series_sample_id = GSM5292989
!Series_sample_id = GSM5292990
!Series_sample_id = GSM5292991
!Series_sample_id = GSM5292992
!Series_sample_id = GSM5292993
!Series_sample_id = GSM5292994
!Series_sample_id = GSM5292995
!Series_sample_id = GSM5292996
!Series_sample_id = GSM5292997
!Series_sample_id = GSM5292998
!Series_sample_id = GSM5292999
!Series_sample_id = GSM5293000
!Series_sample_id = GSM5293001
!Series_sample_id = GSM5293002
!Series_sample_id = GSM5293003
!Series_sample_id = GSM5293004
!Series_sample_id = GSM5293005
!Series_sample_id = GSM5293006
!Series_sample_id = GSM5293007
!Series_sample_id = GSM5293008
!Series_sample_id = GSM5293009
!Series_sample_id = GSM5293010
!Series_sample_id = GSM5293011
!Series_sample_id = GSM5293012
!Series_sample_id = GSM5293013
!Series_sample_id = GSM5293014
!Series_sample_id = GSM5293015
!Series_sample_id = GSM5293016
!Series_sample_id = GSM5293017
!Series_sample_id = GSM5293018
!Series_sample_id = GSM5293019
!Series_sample_id = GSM5293020
!Series_sample_id = GSM5293021
!Series_sample_id = GSM5293022
!Series_sample_id = GSM5293023
!Series_sample_id = GSM5293024
!Series_sample_id = GSM5293025
!Series_sample_id = GSM5293026
!Series_sample_id = GSM5293027
!Series_sample_id = GSM5293028
!Series_sample_id = GSM5293029
!Series_sample_id = GSM5293030
!Series_sample_id = GSM5293031
!Series_sample_id = GSM5293032
!Series_sample_id = GSM5293033
!Series_sample_id = GSM5293034
!Series_sample_id = GSM5293035
!Series_sample_id = GSM5293036
!Series_sample_id = GSM5293037
!Series_sample_id = GSM5293038
!Series_sample_id = GSM5293039
!Series_sample_id = GSM5293040
!Series_sample_id = GSM5293041
!Series_sample_id = GSM5293042
!Series_sample_id = GSM5293043
!Series_sample_id = GSM5293044
!Series_sample_id = GSM5293045
!Series_sample_id = GSM5293046
!Series_sample_id = GSM5293047
!Series_sample_id = GSM5293048
!Series_sample_id = GSM5293049
!Series_sample_id = GSM5293050
!Series_sample_id = GSM5293051
!Series_sample_id = GSM5293052
!Series_sample_id = GSM5293053
!Series_sample_id = GSM5293054
!Series_sample_id = GSM5293055
!Series_sample_id = GSM5293056
!Series_sample_id = GSM5293057
!Series_sample_id = GSM5293058
!Series_sample_id = GSM5293059
!Series_sample_id = GSM5293060
!Series_sample_id = GSM5293061
!Series_sample_id = GSM5293062
!Series_sample_id = GSM5293063
!Series_sample_id = GSM5293064
!Series_sample_id = GSM5293065
!Series_sample_id = GSM5293066
!Series_sample_id = GSM5293067
!Series_contact_name = Vivek,,Swarup
!Series_contact_email = vswarup@uci.edu
!Series_contact_department = Neurobiology and Behavior
!Series_contact_institute = University of California Irvine
!Series_contact_address = 3400 Bio Sci 3
!Series_contact_city = Irvine
!Series_contact_state = CALIFORNIA
!Series_contact_zip/postal_code = 92697
!Series_contact_country = USA
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE174nnn/GSE174367/suppl/GSE174367_bulkRNA_processed.rda.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE174nnn/GSE174367/suppl/GSE174367_snATAC-seq_cell_meta.csv.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE174nnn/GSE174367/suppl/GSE174367_snATAC-seq_filtered_peak_bc_matrix.h5
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE174nnn/GSE174367/suppl/GSE174367_snRNA-seq_cell_meta.csv.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE174nnn/GSE174367/suppl/GSE174367_snRNA-seq_filtered_feature_bc_matrix.h5
!Series_platform_id = GPL24676
!Series_platform_organism = Homo sapiens
!Series_platform_taxid = 9606
!Series_sample_organism = Homo sapiens
!Series_sample_taxid = 9606
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA729525
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP319543

^SAMPLE = GSM5292838
!Sample_title = Sample-100 (snRNA-seq)
!Sample_geo_accession = GSM5292838
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: NA
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snRNA-seq_filtered_feature_bc_matrix.h5
!Sample_description = snRNA-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128610
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859616
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292839
!Sample_title = Sample-101 (snRNA-seq)
!Sample_geo_accession = GSM5292839
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 74
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 7.75
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = Due to low quality, this sample was not part of analysis.
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128609
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859617
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292840
!Sample_title = Sample-17 (snRNA-seq)
!Sample_geo_accession = GSM5292840
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.88
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snRNA-seq_filtered_feature_bc_matrix.h5
!Sample_description = snRNA-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128608
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859618
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292841
!Sample_title = Sample-19 (snRNA-seq)
!Sample_geo_accession = GSM5292841
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.42
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snRNA-seq_filtered_feature_bc_matrix.h5
!Sample_description = snRNA-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128607
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859619
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292842
!Sample_title = Sample-22 (snRNA-seq)
!Sample_geo_accession = GSM5292842
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 86
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.47
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snRNA-seq_filtered_feature_bc_matrix.h5
!Sample_description = snRNA-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128606
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859620
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292843
!Sample_title = Sample-27 (snRNA-seq)
!Sample_geo_accession = GSM5292843
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 81
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 2.87
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snRNA-seq_filtered_feature_bc_matrix.h5
!Sample_description = snRNA-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128605
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859621
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292844
!Sample_title = Sample-33 (snRNA-seq)
!Sample_geo_accession = GSM5292844
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 80
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.75
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snRNA-seq_filtered_feature_bc_matrix.h5
!Sample_description = snRNA-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128611
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859622
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292845
!Sample_title = Sample-37 (snRNA-seq)
!Sample_geo_accession = GSM5292845
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 87
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.25
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snRNA-seq_filtered_feature_bc_matrix.h5
!Sample_description = snRNA-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128604
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859623
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292846
!Sample_title = Sample-43 (snRNA-seq)
!Sample_geo_accession = GSM5292846
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.17
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snRNA-seq_filtered_feature_bc_matrix.h5
!Sample_description = snRNA-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128603
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859624
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292847
!Sample_title = Sample-45 (snRNA-seq)
!Sample_geo_accession = GSM5292847
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 89
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.88
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snRNA-seq_filtered_feature_bc_matrix.h5
!Sample_description = snRNA-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128602
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859625
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292848
!Sample_title = Sample-46 (snRNA-seq)
!Sample_geo_accession = GSM5292848
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.23
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snRNA-seq_filtered_feature_bc_matrix.h5
!Sample_description = snRNA-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128601
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859626
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292849
!Sample_title = Sample-47 (snRNA-seq)
!Sample_geo_accession = GSM5292849
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 5
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snRNA-seq_filtered_feature_bc_matrix.h5
!Sample_description = snRNA-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128600
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859627
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292850
!Sample_title = Sample-50 (snRNA-seq)
!Sample_geo_accession = GSM5292850
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 89
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.08
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snRNA-seq_filtered_feature_bc_matrix.h5
!Sample_description = snRNA-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128599
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859628
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292851
!Sample_title = Sample-52 (snRNA-seq)
!Sample_geo_accession = GSM5292851
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 1.8
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snRNA-seq_filtered_feature_bc_matrix.h5
!Sample_description = snRNA-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128598
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859629
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292852
!Sample_title = Sample-58 (snRNA-seq)
!Sample_geo_accession = GSM5292852
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snRNA-seq_filtered_feature_bc_matrix.h5
!Sample_description = snRNA-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128597
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859630
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292853
!Sample_title = Sample-66 (snRNA-seq)
!Sample_geo_accession = GSM5292853
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 2.92
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snRNA-seq_filtered_feature_bc_matrix.h5
!Sample_description = snRNA-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128596
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859631
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292854
!Sample_title = Sample-82 (snRNA-seq)
!Sample_geo_accession = GSM5292854
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 5
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snRNA-seq_filtered_feature_bc_matrix.h5
!Sample_description = snRNA-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128595
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859632
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292855
!Sample_title = Sample-90 (snRNA-seq)
!Sample_geo_accession = GSM5292855
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.25
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snRNA-seq_filtered_feature_bc_matrix.h5
!Sample_description = snRNA-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128594
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859633
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292856
!Sample_title = Sample-96 (snRNA-seq)
!Sample_geo_accession = GSM5292856
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 7
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex, homogenized in Nuclei EZ Lysis buffer (Sigma).
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell RNA-seq platform (V3)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snRNA-seq_filtered_feature_bc_matrix.h5
!Sample_description = snRNA-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128593
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859634
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292857
!Sample_title = Sample-101 (snATAC-seq)
!Sample_geo_accession = GSM5292857
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 74
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 7.75
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128592
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859635
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292858
!Sample_title = Sample-17 (snATAC-seq)
!Sample_geo_accession = GSM5292858
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.88
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128591
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859636
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292859
!Sample_title = Sample-19 (snATAC-seq)
!Sample_geo_accession = GSM5292859
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.42
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128590
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859637
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292860
!Sample_title = Sample-22 (snATAC-seq)
!Sample_geo_accession = GSM5292860
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 86
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.47
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128589
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859638
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292861
!Sample_title = Sample-27 (snATAC-seq)
!Sample_geo_accession = GSM5292861
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 81
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 2.87
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128588
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859639
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292862
!Sample_title = Sample-33 (snATAC-seq)
!Sample_geo_accession = GSM5292862
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 80
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.75
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128587
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859640
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292863
!Sample_title = Sample-37 (snATAC-seq)
!Sample_geo_accession = GSM5292863
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 87
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.25
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128586
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859641
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292864
!Sample_title = Sample-40 (snATAC-seq)
!Sample_geo_accession = GSM5292864
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.75
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128585
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859642
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292865
!Sample_title = Sample-46 (snATAC-seq)
!Sample_geo_accession = GSM5292865
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.23
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128584
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859643
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292866
!Sample_title = Sample-47 (snATAC-seq)
!Sample_geo_accession = GSM5292866
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 5
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128583
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859644
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292867
!Sample_title = Sample-50 (snATAC-seq)
!Sample_geo_accession = GSM5292867
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 89
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.08
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128582
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859645
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292868
!Sample_title = Sample-52 (snATAC-seq)
!Sample_geo_accession = GSM5292868
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 1.8
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128581
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859646
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292869
!Sample_title = Sample-58 (snATAC-seq)
!Sample_geo_accession = GSM5292869
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128580
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859647
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292870
!Sample_title = Sample-66 (snATAC-seq)
!Sample_geo_accession = GSM5292870
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 2.92
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128579
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859648
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292871
!Sample_title = Sample-82 (snATAC-seq)
!Sample_geo_accession = GSM5292871
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 5
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128578
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859649
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292872
!Sample_title = Sample-90 (snATAC-seq)
!Sample_geo_accession = GSM5292872
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.25
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128577
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859650
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292873
!Sample_title = Sample-100 (snATAC-seq)
!Sample_geo_accession = GSM5292873
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: NA
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128576
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859651
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292874
!Sample_title = Sample-43 (snATAC-seq)
!Sample_geo_accession = GSM5292874
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.17
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128575
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859652
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292875
!Sample_title = Sample-45 (snATAC-seq)
!Sample_geo_accession = GSM5292875
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 89
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.88
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128574
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859653
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292876
!Sample_title = Sample-96 (snATAC-seq)
!Sample_geo_accession = GSM5292876
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 7
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: unbiased total nuclei isolation
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex according to the 10x Genomics Nuclei Isolation with an additional sucrose purification step.
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomicsChromium Single Cell ATAC platform (V1)
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = snATAC-seq_filtered_feature_bc_matrix.h5
!Sample_description = snATAC-seq_cell_meta.csv
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128573
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859654
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292877
!Sample_title = Sample-1 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292877
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.25
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128572
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859655
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292878
!Sample_title = Sample-10 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292878
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.4
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128571
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859656
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292879
!Sample_title = Sample-100 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292879
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: NA
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128570
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859657
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292880
!Sample_title = Sample-101 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292880
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 74
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 7.75
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128569
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859658
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292881
!Sample_title = Sample-102 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292881
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.25
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128568
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859659
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292882
!Sample_title = Sample-103 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292882
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 84
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 1.82
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128567
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859660
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292883
!Sample_title = Sample-104 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292883
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.8
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128566
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859661
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292884
!Sample_title = Sample-105 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292884
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128565
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859662
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292885
!Sample_title = Sample-106 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292885
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: NA
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128564
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859663
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292886
!Sample_title = Sample-107 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292886
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 2.4
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128563
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859664
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292887
!Sample_title = Sample-108 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292887
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 2.9
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128562
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859665
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292888
!Sample_title = Sample-109 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292888
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 6.3
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128625
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859666
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292889
!Sample_title = Sample-11 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292889
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.9
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128624
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859667
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292890
!Sample_title = Sample-110 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292890
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 88
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128623
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859668
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292891
!Sample_title = Sample-111 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292891
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.4
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128622
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859669
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292892
!Sample_title = Sample-112 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292892
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.9
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128621
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859670
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292893
!Sample_title = Sample-113 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292893
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.7
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128620
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859671
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292894
!Sample_title = Sample-114 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292894
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.6
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128619
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859672
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292895
!Sample_title = Sample-115 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292895
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.8
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128618
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859673
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292896
!Sample_title = Sample-116 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292896
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 81
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.3
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128617
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859674
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292897
!Sample_title = Sample-117 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292897
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.7
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128616
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859675
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292898
!Sample_title = Sample-118 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292898
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.88
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128615
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859676
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292899
!Sample_title = Sample-119 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292899
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 5
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128614
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859677
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292900
!Sample_title = Sample-12 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292900
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.7
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128613
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859678
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292901
!Sample_title = Sample-120 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292901
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.42
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128612
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859679
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292902
!Sample_title = Sample-121 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292902
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 7.8
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129694
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859680
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292903
!Sample_title = Sample-122 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292903
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 89
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.67
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129663
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859681
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292904
!Sample_title = Sample-123 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292904
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 86
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.47
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129662
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859682
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292905
!Sample_title = Sample-124 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292905
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 84
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 6.67
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129661
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859683
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292906
!Sample_title = Sample-125 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292906
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 86
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.2
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129660
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859684
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292907
!Sample_title = Sample-126 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292907
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 87
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 6.17
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129659
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859685
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292908
!Sample_title = Sample-128 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292908
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 81
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 2.87
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129658
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859686
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292909
!Sample_title = Sample-129 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292909
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 5.92
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129657
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859687
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292910
!Sample_title = Sample-13 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292910
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.6
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129656
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859688
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292911
!Sample_title = Sample-130 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292911
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 2.67
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129655
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859689
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292912
!Sample_title = Sample-131 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292912
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.75
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129654
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859690
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292913
!Sample_title = Sample-132 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292913
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 78
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 11.78
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129653
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859691
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292914
!Sample_title = Sample-133 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292914
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 89
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 8.3
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129652
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859692
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292915
!Sample_title = Sample-134 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292915
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 80
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.75
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129651
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859693
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292916
!Sample_title = Sample-135 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292916
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 66
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.25
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129650
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859694
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292917
!Sample_title = Sample-136 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292917
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 58
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.83
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129649
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859695
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292918
!Sample_title = Sample-137 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292918
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.43
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129648
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859696
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292919
!Sample_title = Sample-138 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292919
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 87
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.25
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129647
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859697
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292920
!Sample_title = Sample-139 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292920
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 5.63
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129646
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859698
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292921
!Sample_title = Sample-14 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292921
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.8
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129645
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859699
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292922
!Sample_title = Sample-141 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292922
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.75
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129644
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859700
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292923
!Sample_title = Sample-142 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292923
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 86
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.17
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129643
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859701
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292924
!Sample_title = Sample-143 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292924
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 76
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.82
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129642
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859702
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292925
!Sample_title = Sample-144 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292925
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.17
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129641
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859703
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292926
!Sample_title = Sample-145 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292926
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.25
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129640
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859704
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292927
!Sample_title = Sample-146 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292927
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 89
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.88
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129639
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859705
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292928
!Sample_title = Sample-147 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292928
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.23
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129638
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859706
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292929
!Sample_title = Sample-148 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292929
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 5
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129637
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859707
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292930
!Sample_title = Sample-149 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292930
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.58
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129636
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859708
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292931
!Sample_title = Sample-150 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292931
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 77
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.8
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129635
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859709
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292932
!Sample_title = Sample-151 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292932
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 89
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.08
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129634
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859710
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292933
!Sample_title = Sample-152 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292933
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 87
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.5
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129631
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859731
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292934
!Sample_title = Sample-153 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292934
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 1.8
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129630
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859732
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292935
!Sample_title = Sample-154 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292935
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 88
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 5.17
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129629
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859733
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292936
!Sample_title = Sample-155 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292936
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 81
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 7
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129628
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859734
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292937
!Sample_title = Sample-156 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292937
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.8
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129627
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859735
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292938
!Sample_title = Sample-158 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292938
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 5.8
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129626
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859736
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292939
!Sample_title = Sample-159 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292939
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129625
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859737
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292940
!Sample_title = Sample-16 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292940
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.7
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129624
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859738
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292941
!Sample_title = Sample-160 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292941
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.87
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129623
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859739
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292942
!Sample_title = Sample-161 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292942
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.82
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129622
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859740
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292943
!Sample_title = Sample-162 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292943
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 13.5
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129621
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859741
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292944
!Sample_title = Sample-163 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292944
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.42
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129620
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859742
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292945
!Sample_title = Sample-164 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292945
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 86
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 6.17
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129619
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859743
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292946
!Sample_title = Sample-165 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292946
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 86
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 2.92
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129618
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859744
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292947
!Sample_title = Sample-166 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292947
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.33
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129617
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859745
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292948
!Sample_title = Sample-167 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292948
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 2.92
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129616
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859746
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292949
!Sample_title = Sample-168 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292949
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 86
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.42
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129615
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859747
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292950
!Sample_title = Sample-169 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292950
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 87
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.83
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129614
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859748
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292951
!Sample_title = Sample-17 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292951
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.88
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129613
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859749
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292952
!Sample_title = Sample-170 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292952
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 5.5
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129612
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859750
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292953
!Sample_title = Sample-171 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292953
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.17
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128629
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859751
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292954
!Sample_title = Sample-172 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292954
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 52
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.88
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128628
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859752
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292955
!Sample_title = Sample-173 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292955
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 2.2
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128627
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859753
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292956
!Sample_title = Sample-174 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292956
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.92
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19128626
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859754
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292957
!Sample_title = Sample-175 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292957
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 8.75
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129728
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859755
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292958
!Sample_title = Sample-176 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292958
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 87
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.57
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129727
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859756
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292959
!Sample_title = Sample-177 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292959
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 6.32
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129726
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859757
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292960
!Sample_title = Sample-178 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292960
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.18
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129725
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859758
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292961
!Sample_title = Sample-179 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292961
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 80
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.05
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129724
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859759
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292962
!Sample_title = Sample-18 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292962
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 5
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129723
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859760
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292963
!Sample_title = Sample-180 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292963
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 87
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 6.28
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129722
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859761
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292964
!Sample_title = Sample-181 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292964
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 89
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 5.95
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129721
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859762
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292965
!Sample_title = Sample-182 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292965
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 78
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 5.17
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129720
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859763
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292966
!Sample_title = Sample-185 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292966
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 74
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.5
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129719
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859764
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292967
!Sample_title = Sample-186 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292967
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 7.5
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129718
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859765
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292968
!Sample_title = Sample-187 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292968
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 64
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 8
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129717
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859766
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292969
!Sample_title = Sample-188 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292969
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 73
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 10.5
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129716
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859767
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292970
!Sample_title = Sample-189 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292970
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 81
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 6
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129715
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859768
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292971
!Sample_title = Sample-19 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292971
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.42
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129714
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859769
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292972
!Sample_title = Sample-190 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292972
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 71
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.5
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129713
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859770
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292973
!Sample_title = Sample-191 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292973
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.25
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129712
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859771
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292974
!Sample_title = Sample-192 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292974
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 77
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 7.25
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129711
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859772
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292975
!Sample_title = Sample-193 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292975
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 77
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 2.5
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129710
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859773
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292976
!Sample_title = Sample-194 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292976
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 7.25
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129709
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859774
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292977
!Sample_title = Sample-195 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292977
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 70
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 7.75
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129708
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859775
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292978
!Sample_title = Sample-196 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292978
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 66
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 10.38
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129707
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859776
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292979
!Sample_title = Sample-197 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292979
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 7
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129706
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859777
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292980
!Sample_title = Sample-198 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292980
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 67
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 2.72
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129705
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859778
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292981
!Sample_title = Sample-199 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292981
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 74
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 2.75
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129704
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859779
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292982
!Sample_title = Sample-2 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292982
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 84
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 1.82
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129703
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859780
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292983
!Sample_title = Sample-20 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292983
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 7.8
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129702
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859781
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292984
!Sample_title = Sample-200 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292984
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 70
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 5.2
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129701
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859782
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292985
!Sample_title = Sample-201 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292985
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: NA
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129700
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859783
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292986
!Sample_title = Sample-202 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292986
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 74
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 7.75
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: CB
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129699
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859784
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292987
!Sample_title = Sample-21 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292987
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 89
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.67
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129698
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859785
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292988
!Sample_title = Sample-22 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292988
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 86
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.47
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129697
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859786
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292989
!Sample_title = Sample-23 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292989
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 84
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 6.67
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129696
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859787
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292990
!Sample_title = Sample-24 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292990
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 86
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.2
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129695
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859788
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292991
!Sample_title = Sample-25 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292991
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 87
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 6.17
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129775
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859789
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292992
!Sample_title = Sample-26 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292992
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.58
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129774
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859790
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292993
!Sample_title = Sample-27 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292993
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 81
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 2.87
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129773
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859791
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292994
!Sample_title = Sample-28 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292994
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 5.92
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129772
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859792
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292995
!Sample_title = Sample-3 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292995
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.8
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129771
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859793
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292996
!Sample_title = Sample-30 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292996
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.75
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129770
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859794
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292997
!Sample_title = Sample-31 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292997
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 78
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 11.78
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129769
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859795
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292998
!Sample_title = Sample-32 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292998
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 89
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 8.3
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129768
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859796
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5292999
!Sample_title = Sample-33 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5292999
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 80
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.75
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129767
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859797
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293000
!Sample_title = Sample-34 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293000
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 66
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.25
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129766
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859798
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293001
!Sample_title = Sample-35 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293001
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 58
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.83
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129765
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859799
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293002
!Sample_title = Sample-36 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293002
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.43
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129764
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859800
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293003
!Sample_title = Sample-37 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293003
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 87
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.25
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129763
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859801
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293004
!Sample_title = Sample-38 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293004
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 5.63
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129762
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859802
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293005
!Sample_title = Sample-4 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293005
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129761
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859803
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293006
!Sample_title = Sample-40 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293006
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.75
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129760
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859804
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293007
!Sample_title = Sample-41 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293007
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 86
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.17
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129759
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859805
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293008
!Sample_title = Sample-42 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293008
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 76
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.82
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129758
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859806
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293009
!Sample_title = Sample-43 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293009
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.17
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129757
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859807
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293010
!Sample_title = Sample-44 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293010
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.25
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129756
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859808
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293011
!Sample_title = Sample-45 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293011
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 89
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.88
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129755
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859809
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293012
!Sample_title = Sample-46 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293012
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.23
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129754
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859810
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293013
!Sample_title = Sample-47 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293013
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 5
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129753
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859811
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293014
!Sample_title = Sample-48 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293014
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.58
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129752
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859812
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293015
!Sample_title = Sample-49 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293015
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 77
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.8
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129751
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859813
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293016
!Sample_title = Sample-5 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293016
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: NA
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129750
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859814
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293017
!Sample_title = Sample-50 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293017
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 89
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.08
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129747
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859815
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293018
!Sample_title = Sample-51 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293018
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 87
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.5
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129746
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859816
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293019
!Sample_title = Sample-52 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293019
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 1.8
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129805
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859817
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293020
!Sample_title = Sample-53 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293020
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 88
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 5.17
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129804
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859818
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293021
!Sample_title = Sample-54 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293021
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 81
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 7
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129803
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859819
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293022
!Sample_title = Sample-56 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293022
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 86
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.38
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129802
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859820
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293023
!Sample_title = Sample-57 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293023
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 5.8
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129801
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859821
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293024
!Sample_title = Sample-58 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293024
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129749
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859822
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293025
!Sample_title = Sample-59 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293025
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.87
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129748
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859823
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293026
!Sample_title = Sample-6 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293026
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 2.4
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129800
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859824
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293027
!Sample_title = Sample-60 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293027
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.82
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129799
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859825
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293028
!Sample_title = Sample-61 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293028
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 13.5
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129798
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859826
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293029
!Sample_title = Sample-62 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293029
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.42
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129797
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859827
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293030
!Sample_title = Sample-63 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293030
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 86
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 6.17
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129796
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859828
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293031
!Sample_title = Sample-64 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293031
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 86
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 2.92
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129795
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859829
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293032
!Sample_title = Sample-65 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293032
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 3.33
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129794
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859830
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293033
!Sample_title = Sample-66 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293033
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 2.92
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129793
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859831
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293034
!Sample_title = Sample-67 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293034
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 86
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.42
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129792
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859832
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293035
!Sample_title = Sample-69 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293035
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 5.5
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129791
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859833
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293036
!Sample_title = Sample-7 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293036
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 2.9
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129790
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859834
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293037
!Sample_title = Sample-70 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293037
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.17
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129789
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859835
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293038
!Sample_title = Sample-71 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293038
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 52
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.88
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129788
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859836
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293039
!Sample_title = Sample-72 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293039
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 2.2
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129787
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859837
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293040
!Sample_title = Sample-73 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293040
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.92
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129786
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859838
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293041
!Sample_title = Sample-74 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293041
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 8.75
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129785
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859839
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293042
!Sample_title = Sample-75 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293042
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 87
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.57
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129784
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859840
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293043
!Sample_title = Sample-76 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293043
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 90
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 6.32
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129783
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859841
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293044
!Sample_title = Sample-77 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293044
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3.18
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129782
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859842
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293045
!Sample_title = Sample-78 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293045
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 80
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.05
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129781
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859843
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293046
!Sample_title = Sample-79 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293046
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 87
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 6.28
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129780
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859844
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293047
!Sample_title = Sample-8 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293047
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 6.3
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129779
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859845
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293048
!Sample_title = Sample-80 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293048
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 89
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 5.95
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129778
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859846
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293049
!Sample_title = Sample-81 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293049
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 78
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 5.17
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129777
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859847
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293050
!Sample_title = Sample-82 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293050
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 5
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129776
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859848
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293051
!Sample_title = Sample-83 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293051
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 73
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129745
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859849
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293052
!Sample_title = Sample-85 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293052
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 7.5
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129744
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859850
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293053
!Sample_title = Sample-86 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293053
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 64
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 8
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129743
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859851
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293054
!Sample_title = Sample-87 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293054
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 73
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 10.5
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129742
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859852
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293055
!Sample_title = Sample-88 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293055
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 81
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 6
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129741
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859853
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293056
!Sample_title = Sample-89 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293056
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 71
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 4.5
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129740
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859854
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293057
!Sample_title = Sample-9 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293057
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = AD brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 88
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 3
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129739
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859855
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293058
!Sample_title = Sample-90 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293058
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 4.25
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129738
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859856
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293059
!Sample_title = Sample-91 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293059
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 77
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 7.25
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129737
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859857
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293060
!Sample_title = Sample-92 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293060
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 77
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 2.5
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129736
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859858
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293061
!Sample_title = Sample-93 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293061
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 7.25
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129735
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859859
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293062
!Sample_title = Sample-94 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293062
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 70
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 7.75
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129734
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859860
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293063
!Sample_title = Sample-95 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293063
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 66
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 10.38
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129733
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859861
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293064
!Sample_title = Sample-96 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293064
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 7
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129732
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859862
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293065
!Sample_title = Sample-97 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293065
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 67
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 2.72
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129731
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859863
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293066
!Sample_title = Sample-98 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293066
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 74
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = pmi: 2.75
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129730
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859864
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
^SAMPLE = GSM5293067
!Sample_title = Sample-99 (Total Bulk RNA-seq)
!Sample_geo_accession = GSM5293067
!Sample_status = Public on May 12 2021
!Sample_submission_date = May 12 2021
!Sample_last_update_date = May 14 2021
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = Control brain
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 70
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = pmi: 5.2
!Sample_characteristics_ch1 = diagnosis: Control
!Sample_characteristics_ch1 = brain region: FC
!Sample_characteristics_ch1 = isolation: total RNA isolation
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Total RNA was isolation from frozen brain samples using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = About 500ng total RNA was used to prepare the cDNA library using SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian
!Sample_extract_protocol_ch1 = For snRNA-seq and snATAC-seq, single nucleus suspensions were isolated from about 50mg frozen human prefrontal cortex following 10x genomics recommendation. For bulk RNA-seq, total RNA was isolated using Mini Nucleospin RNA kit, Takarabio
!Sample_extract_protocol_ch1 = Libraries were prepared using 10x genomics Chromium Single Cell ATAC platform (V1), 10x genomics chromium V3 for snRNA-seq and SMARTer Stranded Total RNA Sample Prep kit-HI Mammalian  for bulk RNA-seq
!Sample_description = bulkRNA_processed.rda
!Sample_data_processing = Chromatin accessibility was quantified in single nuclei by mapping snATAC-seq reads to the hg38 reference genome and calling peaks using cellranger-atac count (v1.1.0, 10X Genomics) We constructed a merged peak by barcodes matrix for all snATAC-seq libraries using the cellranger-atac aggr function, which normalizes accessibility signals by sampling fragments from GEM wells to ensure uniform distributions of enriched Tn5 cut sites across libraries. Gene expression was quantified by mapping reads from snRNA-seq libraries to a pre-mRNA build of the same reference genome, ensuring that we account for unprocessed nuclear transcripts, using cellranger count (v3.0.2 10X Genomics). We constructed a merged gene by barcodes matrix for all snRNA-seq libraries using the cellranger aggr function, normalizing for read depth across libraries.
!Sample_data_processing = For bulk RNA-seq, we performed QC on raw fastq reads, sequenced at median read-depth of 50-million paired-end reads/sample, using FastQC. Reads were aligned to the reference genome (GRCh38.p13) using STAR aligner (v2.6.1) and aligned BAM file QC metrics were obtained using PicardTools (v2.21.3)
!Sample_data_processing = Bulk RNA-seq gene expression was quantified as transcripts per million (TPM) using Salmon (v1.3.0). We used linear regression model, similar to our previous work,  to remove the effects of biological covariates
!Sample_data_processing = ‘Pseudo-bulk’ chromatin accessibility coverage profiles of gene body and upstream promoter regions were visualized using the Signac (v0.2.0) function CoveragePlot, while gene expression signals were visualized using Seurat (v3.1.2) snRNA-seq cell type assignments
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Bulk tissue TPM data is save as R data file (rda). Filtered bc matrix file from aggregated cellRanger analysis is available for snATAC and snRNA-seq as .h5 files with corresponding cell metadata as csv file.
!Sample_platform_id = GPL24676
!Sample_contact_name = Vivek,,Swarup
!Sample_contact_email = vswarup@uci.edu
!Sample_contact_department = Neurobiology and Behavior
!Sample_contact_institute = University of California Irvine
!Sample_contact_address = 3400 Bio Sci 3
!Sample_contact_city = Irvine
!Sample_contact_state = CALIFORNIA
!Sample_contact_zip/postal_code = 92697
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN19129729
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX10859865
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE174367
!Sample_data_row_count = 0
