^SERIES = GSE183068
!Series_title = AD-linked R47H-TREM2 mutation induces disease-enhancing microglial states via AKT hyperactivation [Hs]
!Series_geo_accession = GSE183068
!Series_status = Public on Jan 07 2022
!Series_submission_date = Aug 30 2021
!Series_last_update_date = Jan 08 2022
!Series_pubmed_id = 34851693
!Series_summary = We identified enrichment of a disease-enhancing, proinflammatory subpopulation of microglia in human AD patient brains with the R47H-TREM2 mutation, and uncovered that enhanced Akt signaling in microglia underlies the proinflammatory cytokine state and synaptic toxicity in our R47H-TREM2 tauopathy mouse model.
!Series_overall_design = Droplet-based single nuclear RNA sequencing of frontal cortical tissues from AD patient with and without the TREM2-R47H mutation and their age, pathology, and sex-matched, controls
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Faten,A,Sayed
!Series_contributor = Lay,,Kodama
!Series_contributor = Li,,Fan
!Series_contributor = Gillian,K,Carling
!Series_contributor = Joe,C,Udeochu
!Series_contributor = David,,Le
!Series_contributor = Qingyun,,Li
!Series_contributor = Lu,,Zhou
!Series_contributor = Man,Y,Wong
!Series_contributor = Rose,,Horowitz
!Series_contributor = Pearly,,Ye
!Series_contributor = Hansruedi,,Mathys
!Series_contributor = Minghui,,Wang
!Series_contributor = Xiang,,Niu
!Series_contributor = Linas,,Mazutis
!Series_contributor = Xueqiao,,Jiang
!Series_contributor = Xueting,,Wang
!Series_contributor = Fuying,,Gao
!Series_contributor = Matthew,,Brendel
!Series_contributor = Maria,,Telpoukhovskaia
!Series_contributor = Tara,E,Tracy
!Series_contributor = Georgia,,Frost
!Series_contributor = Yungui,,Zhou
!Series_contributor = Yaqiao,,Li
!Series_contributor = Zuolin,,Cheng
!Series_contributor = Guoqiang,,Yu
!Series_contributor = John,,Hardy
!Series_contributor = Giovanni,,Coppola
!Series_contributor = Shiaoching,,Gong
!Series_contributor = Fei,,Wang
!Series_contributor = Michael,A,DeTure
!Series_contributor = Bin,,Zhang
!Series_contributor = Lei,,Xie
!Series_contributor = John,Q,Trajnowski
!Series_contributor = Virginia,M,Lee
!Series_contributor = Subhash,,Sinha
!Series_contributor = Dennis,W,Dickson
!Series_contributor = Wenjie,,Luo
!Series_contributor = Li,,Gan
!Series_sample_id = GSM5550450
!Series_sample_id = GSM5550451
!Series_sample_id = GSM5550452
!Series_sample_id = GSM5550453
!Series_sample_id = GSM5550454
!Series_sample_id = GSM5550455
!Series_sample_id = GSM5550456
!Series_sample_id = GSM5550457
!Series_sample_id = GSM5550458
!Series_sample_id = GSM5550459
!Series_sample_id = GSM5550460
!Series_sample_id = GSM5550461
!Series_sample_id = GSM5550462
!Series_sample_id = GSM5550463
!Series_sample_id = GSM5550464
!Series_sample_id = GSM5550465
!Series_sample_id = GSM5550466
!Series_sample_id = GSM5550467
!Series_sample_id = GSM5550468
!Series_sample_id = GSM5550469
!Series_sample_id = GSM5550470
!Series_sample_id = GSM5550471
!Series_sample_id = GSM5550472
!Series_sample_id = GSM5550473
!Series_sample_id = GSM5550474
!Series_sample_id = GSM5550475
!Series_sample_id = GSM5550476
!Series_sample_id = GSM5550477
!Series_sample_id = GSM5550478
!Series_sample_id = GSM5550479
!Series_sample_id = GSM5550480
!Series_sample_id = GSM5550481
!Series_sample_id = GSM5550482
!Series_sample_id = GSM5550483
!Series_sample_id = GSM5550484
!Series_sample_id = GSM5550485
!Series_sample_id = GSM5550486
!Series_sample_id = GSM5550487
!Series_sample_id = GSM5550488
!Series_sample_id = GSM5550489
!Series_sample_id = GSM5550490
!Series_sample_id = GSM5550491
!Series_sample_id = GSM5550492
!Series_sample_id = GSM5550493
!Series_sample_id = GSM5550494
!Series_sample_id = GSM5550495
!Series_sample_id = GSM5550496
!Series_sample_id = GSM5550497
!Series_sample_id = GSM5550498
!Series_sample_id = GSM5550499
!Series_sample_id = GSM5550500
!Series_sample_id = GSM5550501
!Series_sample_id = GSM5550502
!Series_sample_id = GSM5550503
!Series_sample_id = GSM5550504
!Series_contact_name = Li,,Gan
!Series_contact_email = lig2033@med.cornell.edu
!Series_contact_phone = 6087704342
!Series_contact_laboratory = Gan lab
!Series_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Series_contact_institute = Weill Cornell Medicine
!Series_contact_address = 413 East 69th Street, 9th Floor BB904
!Series_contact_city = New York
!Series_contact_state = NY
!Series_contact_zip/postal_code = 10021
!Series_contact_country = USA
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE183nnn/GSE183068/suppl/GSE183068_RAW.tar
!Series_gp_id = PRJNA754520
!Series_platform_id = GPL24676
!Series_platform_organism = Homo sapiens
!Series_platform_taxid = 9606
!Series_sample_organism = Homo sapiens
!Series_sample_taxid = 9606

^SAMPLE = GSM5550450
!Sample_title = Gan_1
!Sample_geo_accession = GSM5550450
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 91
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2019
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793011
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758595
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550450/suppl/GSM5550450_Gan_1.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550450/suppl/GSM5550450_Gan_1.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550450/suppl/GSM5550450_Gan_1.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550451
!Sample_title = Gan_2
!Sample_geo_accession = GSM5550451
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2020
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793012
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758596
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550451/suppl/GSM5550451_Gan_2.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550451/suppl/GSM5550451_Gan_2.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550451/suppl/GSM5550451_Gan_2.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550452
!Sample_title = Gan_3
!Sample_geo_accession = GSM5550452
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 81
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD/DLBD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2021
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793013
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758552
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550452/suppl/GSM5550452_Gan_3.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550452/suppl/GSM5550452_Gan_3.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550452/suppl/GSM5550452_Gan_3.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550453
!Sample_title = Gan_4
!Sample_geo_accession = GSM5550453
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 85
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD/DLBD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2022
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793014
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758563
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550453/suppl/GSM5550453_Gan_4.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550453/suppl/GSM5550453_Gan_4.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550453/suppl/GSM5550453_Gan_4.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550454
!Sample_title = Gan_5
!Sample_geo_accession = GSM5550454
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 65
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD/CAA
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2023
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793015
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758574
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550454/suppl/GSM5550454_Gan_5.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550454/suppl/GSM5550454_Gan_5.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550454/suppl/GSM5550454_Gan_5.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550455
!Sample_title = Gan_6
!Sample_geo_accession = GSM5550455
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 65
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD/CAA
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2024
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793016
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758585
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550455/suppl/GSM5550455_Gan_6.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550455/suppl/GSM5550455_Gan_6.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550455/suppl/GSM5550455_Gan_6.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550456
!Sample_title = Gan_7
!Sample_geo_accession = GSM5550456
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 62
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2025
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793017
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758591
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550456/suppl/GSM5550456_Gan_7.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550456/suppl/GSM5550456_Gan_7.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550456/suppl/GSM5550456_Gan_7.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550457
!Sample_title = Gan_8
!Sample_geo_accession = GSM5550457
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 67
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2026
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793018
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758592
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550457/suppl/GSM5550457_Gan_8.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550457/suppl/GSM5550457_Gan_8.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550457/suppl/GSM5550457_Gan_8.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550458
!Sample_title = Gan_9
!Sample_geo_accession = GSM5550458
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 71
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD/DLBD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2027
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793019
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758593
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550458/suppl/GSM5550458_Gan_9.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550458/suppl/GSM5550458_Gan_9.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550458/suppl/GSM5550458_Gan_9.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550459
!Sample_title = Gan_10
!Sample_geo_accession = GSM5550459
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 72
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD/DLBD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2028
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793020
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758594
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550459/suppl/GSM5550459_Gan_10.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550459/suppl/GSM5550459_Gan_10.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550459/suppl/GSM5550459_Gan_10.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550460
!Sample_title = Gan_11
!Sample_geo_accession = GSM5550460
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 85
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD/ALB
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2029
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793021
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758597
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550460/suppl/GSM5550460_Gan_11.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550460/suppl/GSM5550460_Gan_11.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550460/suppl/GSM5550460_Gan_11.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550461
!Sample_title = Gan_13
!Sample_geo_accession = GSM5550461
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 87
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD/VaD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2030
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793022
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758543
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550461/suppl/GSM5550461_Gan_13.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550461/suppl/GSM5550461_Gan_13.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550461/suppl/GSM5550461_Gan_13.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550462
!Sample_title = Gan_14
!Sample_geo_accession = GSM5550462
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 86
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD/VaD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2031
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793023
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758544
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550462/suppl/GSM5550462_Gan_14.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550462/suppl/GSM5550462_Gan_14.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550462/suppl/GSM5550462_Gan_14.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550463
!Sample_title = Gan_15
!Sample_geo_accession = GSM5550463
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 85
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD/VaD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2032
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793024
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758545
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550463/suppl/GSM5550463_Gan_15.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550463/suppl/GSM5550463_Gan_15.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550463/suppl/GSM5550463_Gan_15.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550464
!Sample_title = Gan_16
!Sample_geo_accession = GSM5550464
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 85
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD/VaD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2033
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793025
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758546
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550464/suppl/GSM5550464_Gan_16.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550464/suppl/GSM5550464_Gan_16.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550464/suppl/GSM5550464_Gan_16.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550465
!Sample_title = Gan_18
!Sample_geo_accession = GSM5550465
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 81
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD/VaD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2034
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793026
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758547
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550465/suppl/GSM5550465_Gan_18.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550465/suppl/GSM5550465_Gan_18.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550465/suppl/GSM5550465_Gan_18.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550466
!Sample_title = Gan_19
!Sample_geo_accession = GSM5550466
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 81
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2035
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793027
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758548
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550466/suppl/GSM5550466_Gan_19.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550466/suppl/GSM5550466_Gan_19.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550466/suppl/GSM5550466_Gan_19.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550467
!Sample_title = Gan_20
!Sample_geo_accession = GSM5550467
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 80
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2036
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793028
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758549
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550467/suppl/GSM5550467_Gan_20.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550467/suppl/GSM5550467_Gan_20.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550467/suppl/GSM5550467_Gan_20.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550468
!Sample_title = Gan_21
!Sample_geo_accession = GSM5550468
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 66
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2037
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793029
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758550
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550468/suppl/GSM5550468_Gan_21.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550468/suppl/GSM5550468_Gan_21.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550468/suppl/GSM5550468_Gan_21.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550469
!Sample_title = Gan_22
!Sample_geo_accession = GSM5550469
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 67
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2038
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793030
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758551
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550469/suppl/GSM5550469_Gan_22.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550469/suppl/GSM5550469_Gan_22.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550469/suppl/GSM5550469_Gan_22.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550470
!Sample_title = Gan_23
!Sample_geo_accession = GSM5550470
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 78
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2039
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793031
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758553
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550470/suppl/GSM5550470_Gan_23.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550470/suppl/GSM5550470_Gan_23.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550470/suppl/GSM5550470_Gan_23.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550471
!Sample_title = Gan_24
!Sample_geo_accession = GSM5550471
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 81
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2040
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793032
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758554
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550471/suppl/GSM5550471_Gan_24.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550471/suppl/GSM5550471_Gan_24.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550471/suppl/GSM5550471_Gan_24.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550472
!Sample_title = Gan_25
!Sample_geo_accession = GSM5550472
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 88
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2041
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793033
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758555
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550472/suppl/GSM5550472_Gan_25.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550472/suppl/GSM5550472_Gan_25.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550472/suppl/GSM5550472_Gan_25.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550473
!Sample_title = Gan_26
!Sample_geo_accession = GSM5550473
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 89
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2042
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793034
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758556
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550473/suppl/GSM5550473_Gan_26.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550473/suppl/GSM5550473_Gan_26.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550473/suppl/GSM5550473_Gan_26.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550474
!Sample_title = Gan_27
!Sample_geo_accession = GSM5550474
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 74
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2043
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793035
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758557
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550474/suppl/GSM5550474_Gan_27.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550474/suppl/GSM5550474_Gan_27.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550474/suppl/GSM5550474_Gan_27.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550475
!Sample_title = Gan_29
!Sample_geo_accession = GSM5550475
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 76
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD/TLBD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2044
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793036
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758558
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550475/suppl/GSM5550475_Gan_29.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550475/suppl/GSM5550475_Gan_29.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550475/suppl/GSM5550475_Gan_29.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550476
!Sample_title = Gan_30
!Sample_geo_accession = GSM5550476
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD/TLBD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2045
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793037
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758559
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550476/suppl/GSM5550476_Gan_30.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550476/suppl/GSM5550476_Gan_30.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550476/suppl/GSM5550476_Gan_30.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550477
!Sample_title = Gan_31
!Sample_geo_accession = GSM5550477
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 77
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD/TLBD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2046
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793038
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758560
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550477/suppl/GSM5550477_Gan_31.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550477/suppl/GSM5550477_Gan_31.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550477/suppl/GSM5550477_Gan_31.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550478
!Sample_title = Gan_33
!Sample_geo_accession = GSM5550478
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD/DLBD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2047
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793039
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758561
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550478/suppl/GSM5550478_Gan_33.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550478/suppl/GSM5550478_Gan_33.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550478/suppl/GSM5550478_Gan_33.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550479
!Sample_title = Gan_35
!Sample_geo_accession = GSM5550479
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 71
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2048
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793040
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758562
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550479/suppl/GSM5550479_Gan_35.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550479/suppl/GSM5550479_Gan_35.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550479/suppl/GSM5550479_Gan_35.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550480
!Sample_title = Gan_37
!Sample_geo_accession = GSM5550480
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 79
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD/CAA
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2049
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793041
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758564
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550480/suppl/GSM5550480_Gan_37.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550480/suppl/GSM5550480_Gan_37.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550480/suppl/GSM5550480_Gan_37.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550481
!Sample_title = Gan_38
!Sample_geo_accession = GSM5550481
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 80
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2050
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793042
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758565
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550481/suppl/GSM5550481_Gan_38.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550481/suppl/GSM5550481_Gan_38.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550481/suppl/GSM5550481_Gan_38.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550482
!Sample_title = Gan_39
!Sample_geo_accession = GSM5550482
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD/CAA/BLBD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2051
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793043
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758566
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550482/suppl/GSM5550482_Gan_39.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550482/suppl/GSM5550482_Gan_39.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550482/suppl/GSM5550482_Gan_39.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550483
!Sample_title = Gan_40
!Sample_geo_accession = GSM5550483
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 74
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD/CAA/BLBD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2052
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793044
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758567
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550483/suppl/GSM5550483_Gan_40.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550483/suppl/GSM5550483_Gan_40.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550483/suppl/GSM5550483_Gan_40.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550484
!Sample_title = Gan_43
!Sample_geo_accession = GSM5550484
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2053
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793045
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758568
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550484/suppl/GSM5550484_Gan_43.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550484/suppl/GSM5550484_Gan_43.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550484/suppl/GSM5550484_Gan_43.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550485
!Sample_title = Gan_44
!Sample_geo_accession = GSM5550485
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 87
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2054
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793046
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758569
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550485/suppl/GSM5550485_Gan_44.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550485/suppl/GSM5550485_Gan_44.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550485/suppl/GSM5550485_Gan_44.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550486
!Sample_title = Gan_45
!Sample_geo_accession = GSM5550486
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 72
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2055
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793047
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758570
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550486/suppl/GSM5550486_Gan_45.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550486/suppl/GSM5550486_Gan_45.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550486/suppl/GSM5550486_Gan_45.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550487
!Sample_title = Gan_46
!Sample_geo_accession = GSM5550487
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2056
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793048
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758571
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550487/suppl/GSM5550487_Gan_46.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550487/suppl/GSM5550487_Gan_46.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550487/suppl/GSM5550487_Gan_46.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550488
!Sample_title = Gan_47
!Sample_geo_accession = GSM5550488
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 64
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2057
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793049
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758572
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550488/suppl/GSM5550488_Gan_47.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550488/suppl/GSM5550488_Gan_47.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550488/suppl/GSM5550488_Gan_47.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550489
!Sample_title = Gan_48
!Sample_geo_accession = GSM5550489
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 71
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2058
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793050
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758573
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550489/suppl/GSM5550489_Gan_48.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550489/suppl/GSM5550489_Gan_48.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550489/suppl/GSM5550489_Gan_48.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550490
!Sample_title = Gan_49
!Sample_geo_accession = GSM5550490
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 78
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2059
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793051
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758575
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550490/suppl/GSM5550490_Gan_49.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550490/suppl/GSM5550490_Gan_49.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550490/suppl/GSM5550490_Gan_49.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550491
!Sample_title = Gan_50
!Sample_geo_accession = GSM5550491
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 78
!Sample_characteristics_ch1 = r47h genotype: WT
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2060
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793052
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758576
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550491/suppl/GSM5550491_Gan_50.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550491/suppl/GSM5550491_Gan_50.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550491/suppl/GSM5550491_Gan_50.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550492
!Sample_title = Gan_51
!Sample_geo_accession = GSM5550492
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 71
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2061
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793053
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758577
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550492/suppl/GSM5550492_Gan_51.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550492/suppl/GSM5550492_Gan_51.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550492/suppl/GSM5550492_Gan_51.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550493
!Sample_title = Gan_52
!Sample_geo_accession = GSM5550493
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 87
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: AD/ALS
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2062
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793054
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758578
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550493/suppl/GSM5550493_Gan_52.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550493/suppl/GSM5550493_Gan_52.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550493/suppl/GSM5550493_Gan_52.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550494
!Sample_title = Gan_54
!Sample_geo_accession = GSM5550494
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 82
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2063
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793055
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758579
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550494/suppl/GSM5550494_Gan_54.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550494/suppl/GSM5550494_Gan_54.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550494/suppl/GSM5550494_Gan_54.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550495
!Sample_title = Gan_55
!Sample_geo_accession = GSM5550495
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 77
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2064
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793056
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758580
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550495/suppl/GSM5550495_Gan_55.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550495/suppl/GSM5550495_Gan_55.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550495/suppl/GSM5550495_Gan_55.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550496
!Sample_title = Gan_56
!Sample_geo_accession = GSM5550496
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 60
!Sample_characteristics_ch1 = r47h genotype: R47H
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2065
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793057
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758581
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550496/suppl/GSM5550496_Gan_56.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550496/suppl/GSM5550496_Gan_56.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550496/suppl/GSM5550496_Gan_56.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550497
!Sample_title = Gan_59
!Sample_geo_accession = GSM5550497
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 72
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: Normal
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2066
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793058
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758582
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550497/suppl/GSM5550497_Gan_59.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550497/suppl/GSM5550497_Gan_59.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550497/suppl/GSM5550497_Gan_59.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550498
!Sample_title = Gan_60
!Sample_geo_accession = GSM5550498
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: Normal
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2067
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793059
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758583
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550498/suppl/GSM5550498_Gan_60.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550498/suppl/GSM5550498_Gan_60.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550498/suppl/GSM5550498_Gan_60.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550499
!Sample_title = Gan_61
!Sample_geo_accession = GSM5550499
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 75
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = diagnosis: Normal
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2068
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793060
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758584
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550499/suppl/GSM5550499_Gan_61.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550499/suppl/GSM5550499_Gan_61.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550499/suppl/GSM5550499_Gan_61.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550500
!Sample_title = Gan_62
!Sample_geo_accession = GSM5550500
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 68
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: Normal
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2069
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793061
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758586
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550500/suppl/GSM5550500_Gan_62.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550500/suppl/GSM5550500_Gan_62.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550500/suppl/GSM5550500_Gan_62.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550501
!Sample_title = Gan_63
!Sample_geo_accession = GSM5550501
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 72
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: Normal
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2070
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793062
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758587
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550501/suppl/GSM5550501_Gan_63.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550501/suppl/GSM5550501_Gan_63.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550501/suppl/GSM5550501_Gan_63.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550502
!Sample_title = Gan_64
!Sample_geo_accession = GSM5550502
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 61
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: Normal
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2071
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793063
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758588
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550502/suppl/GSM5550502_Gan_64.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550502/suppl/GSM5550502_Gan_64.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550502/suppl/GSM5550502_Gan_64.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550503
!Sample_title = Gan_65
!Sample_geo_accession = GSM5550503
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 75
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: Normal
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2072
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793064
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758589
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550503/suppl/GSM5550503_Gan_65.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550503/suppl/GSM5550503_Gan_65.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550503/suppl/GSM5550503_Gan_65.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
^SAMPLE = GSM5550504
!Sample_title = Gan_66
!Sample_geo_accession = GSM5550504
!Sample_status = Public on Jan 07 2022
!Sample_submission_date = Aug 30 2021
!Sample_last_update_date = Jan 07 2022
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = single nuclei from frozen postmortem human tissue
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = age: 83
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = diagnosis: Normal
!Sample_characteristics_ch1 = cell type: frontal cortical brain cells
!Sample_treatment_protocol_ch1 = NA
!Sample_growth_protocol_ch1 = NA
!Sample_molecule_ch1 = total RNA
!Sample_extract_protocol_ch1 = Nuclei isolation adapted from Grubman et al. 2073
!Sample_extract_protocol_ch1 = Chromium Single Cell 3' Reagent Kits v3 (10x Genomics)
!Sample_description = mRNA expression in human frontal cortical brain cells
!Sample_data_processing = Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.0.0)Gene counts were obtained by aligning reads to the hg38 genome with Cell Ranger software (v.3.1.0) (10x Genomics)
!Sample_data_processing = To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 3.1.0 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 2 cells, cells with unique gene counts over 4,000 or less than 200, and cells with high fraction of mitochondrial reads (> 5%).
!Sample_data_processing = Predicted multiplets were removed using DoubletFinder (McGinnis et al. 2019)
!Sample_data_processing = Seurat v3.0 (Butler et al., 2018) R package used for analysis.
!Sample_data_processing = Genome_build: hg38 genome
!Sample_data_processing = Supplementary_files_format_and_content: Cell Ranger output files (barcodes, features, matrix)
!Sample_platform_id = GPL24676
!Sample_contact_name = Li,,Gan
!Sample_contact_email = lig2033@med.cornell.edu
!Sample_contact_phone = 6087704342
!Sample_contact_laboratory = Gan lab
!Sample_contact_department = Helen and Robert Appel Alzheimer’s Disease Research Institute
!Sample_contact_institute = Weill Cornell Medicine
!Sample_contact_address = 413 East 69th Street, 9th Floor BB904
!Sample_contact_city = New York
!Sample_contact_state = NY
!Sample_contact_zip/postal_code = 10021
!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/SAMN20793065
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX11758590
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550504/suppl/GSM5550504_Gan_66.barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550504/suppl/GSM5550504_Gan_66.features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM5550nnn/GSM5550504/suppl/GSM5550504_Gan_66.matrix.mtx.gz
!Sample_series_id = GSE183068
!Sample_data_row_count = 0
