^SERIES = GSE214979
!Series_title = Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer’s disease-specific cis regulatory elements [Multi-omics]
!Series_geo_accession = GSE214979
!Series_status = Public on Jan 09 2023
!Series_submission_date = Oct 06 2022
!Series_last_update_date = Aug 27 2025
!Series_pubmed_id = 36950385
!Series_pubmed_id = 40817596
!Series_summary = Cell type-specific transcriptional differences between brain tissues from donors with Alzheimer’s Disease (AD) and unaffected controls have been well-documented, but few studies have rigorously interrogated the regulatory mechanisms responsible for these alterations. We performed single nucleus multiomics (snRNA-seq + snATAC-seq) on 105,332 nuclei isolated from cortical tissues from 7 AD and 8 unaffected donors to identify candidate cis-regulatory elements (CREs) involved in AD-associated transcriptional changes. We detected 319,861 significant correlations, or links, between gene expression and cell-type specific transposase accessible regions that are enriched for active CREs. Among these, 40,831 were unique to AD tissues. Validation experiments confirmed the activity of many regions, including several candidate regulators of APP expression. We identified ZEB1 and MAFB as transcription factors playing important roles in AD-specific gene regulation in neurons and microglia, respe  ctively. Microglial links were globally enriched for heritability of AD risk and previously identified active regulatory regions.
!Series_overall_design = We performed single nucleus multiomics (snRNA+snATAC) on postmortem DLPFC tissues from 7 AD and 8 unaffected donors.
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = Ashlyn,,Anderson
!Series_contributor = Jacob,,Loupe
!Series_contributor = Lindsay,F,Rizzardi
!Series_sample_id = GSM6619542
!Series_sample_id = GSM6619543
!Series_sample_id = GSM6619544
!Series_sample_id = GSM6619545
!Series_sample_id = GSM6619546
!Series_sample_id = GSM6619547
!Series_sample_id = GSM6619548
!Series_sample_id = GSM6619549
!Series_sample_id = GSM6619550
!Series_sample_id = GSM6619551
!Series_sample_id = GSM6619552
!Series_sample_id = GSM6619553
!Series_sample_id = GSM6619554
!Series_sample_id = GSM6619555
!Series_sample_id = GSM6619556
!Series_sample_id = GSM6619557
!Series_sample_id = GSM6619558
!Series_sample_id = GSM6619559
!Series_sample_id = GSM6619560
!Series_sample_id = GSM6619561
!Series_sample_id = GSM6659217
!Series_sample_id = GSM6659218
!Series_sample_id = GSM6659219
!Series_sample_id = GSM6659220
!Series_sample_id = GSM6659221
!Series_sample_id = GSM6659222
!Series_sample_id = GSM6659223
!Series_sample_id = GSM6659224
!Series_sample_id = GSM6659225
!Series_sample_id = GSM6659226
!Series_sample_id = GSM6659227
!Series_sample_id = GSM6659228
!Series_sample_id = GSM6659229
!Series_sample_id = GSM6659230
!Series_sample_id = GSM6659231
!Series_sample_id = GSM6659232
!Series_sample_id = GSM6659233
!Series_sample_id = GSM6659234
!Series_sample_id = GSM6659235
!Series_sample_id = GSM6659236
!Series_contact_name = Lindsay,,Rizzardi
!Series_contact_email = lrizzardi@hudsonalpha.org
!Series_contact_phone = 2563275220
!Series_contact_laboratory = Richard M. Myers Lab
!Series_contact_institute = HudsonAlpha Institute for Biotechnology
!Series_contact_address = 601 Genome Way
!Series_contact_city = Huntsville
!Series_contact_state = AL
!Series_contact_zip/postal_code = 35806
!Series_contact_country = USA
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE214nnn/GSE214979/suppl/GSE214979_atac_fragments.tsv.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE214nnn/GSE214979/suppl/GSE214979_atac_fragments.tsv.gz.tbi.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE214nnn/GSE214979/suppl/GSE214979_cell_metadata.csv.gz
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE214nnn/GSE214979/suppl/GSE214979_filtered_feature_bc_matrix.h5
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE214nnn/GSE214979/suppl/GSE214979_unfiltered_feature_bc_matrix.h5
!Series_platform_id = GPL24676
!Series_platform_organism = Homo sapiens
!Series_platform_taxid = 9606
!Series_sample_organism = Homo sapiens
!Series_sample_taxid = 9606
!Series_relation = SubSeries of: GSE214637
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA887819

^SAMPLE = GSM6619542
!Sample_title = NT1261, scRNAseq
!Sample_geo_accession = GSM6619542
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = DLPFC
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: DLPFC
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 54
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186894
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823921
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619543
!Sample_title = 1230, scRNAseq
!Sample_geo_accession = GSM6619543
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = DLPFC
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: DLPFC
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 49
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186893
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823922
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619544
!Sample_title = 3329, scRNAseq
!Sample_geo_accession = GSM6619544
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: AD
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 74
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186892
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823923
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619545
!Sample_title = NT1271, scRNAseq
!Sample_geo_accession = GSM6619545
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = DLPFC
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: DLPFC
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 50
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186891
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823924
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619546
!Sample_title = 4482, scRNAseq
!Sample_geo_accession = GSM6619546
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: AD
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 77
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186890
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823925
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619547
!Sample_title = 4313, scRNAseq
!Sample_geo_accession = GSM6619547
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: AD
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 66
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186889
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823926
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619548
!Sample_title = HCT17HEX, scRNAseq
!Sample_geo_accession = GSM6619548
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Apr 23 2024
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA9
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: BA9
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 84
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186888
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823927
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619549
!Sample_title = HCTZZT, scRNAseq
!Sample_geo_accession = GSM6619549
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Apr 23 2024
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA11
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: BA11
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 77
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186887
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823928
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619550
!Sample_title = 4305, scRNAseq
!Sample_geo_accession = GSM6619550
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: AD
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 77
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186886
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823929
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619551
!Sample_title = 4443, scRNAseq
!Sample_geo_accession = GSM6619551
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: AD
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 79
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186885
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823930
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619552
!Sample_title = 1238 rep1, scRNAseq
!Sample_geo_accession = GSM6619552
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = DLPFC
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: DLPFC
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 63
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186884
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823931
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619553
!Sample_title = 1238 rep2, scRNAseq
!Sample_geo_accession = GSM6619553
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = DLPFC
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: DLPFC
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 63
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186883
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823932
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619554
!Sample_title = 4627 rep1, scRNAseq
!Sample_geo_accession = GSM6619554
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: AD
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 92
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186882
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823933
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619555
!Sample_title = 4627 rep2, scRNAseq
!Sample_geo_accession = GSM6619555
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: AD
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 92
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186881
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823934
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619556
!Sample_title = 1224, rep1, scRNAseq
!Sample_geo_accession = GSM6619556
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = DLPFC
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: DLPFC
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 55
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186880
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823935
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619557
!Sample_title = 1224 rep2, scRNAseq
!Sample_geo_accession = GSM6619557
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = DLPFC
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: DLPFC
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 55
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186879
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823936
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619558
!Sample_title = 3586 rep1, scRNAseq
!Sample_geo_accession = GSM6619558
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 76
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186878
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823937
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619559
!Sample_title = 3586 rep2, scRNAseq
!Sample_geo_accession = GSM6619559
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 76
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186877
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823938
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619560
!Sample_title = 4481 rep1, scRNAseq
!Sample_geo_accession = GSM6619560
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: AD
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 86
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186876
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823939
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6619561
!Sample_title = 4481 rep2, scRNAseq
!Sample_geo_accession = GSM6619561
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 06 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: AD
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 86
!Sample_molecule_ch1 = polyA RNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic single cell
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31186875
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17823940
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659217
!Sample_title = NT1261, scATACseq
!Sample_geo_accession = GSM6659217
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = DLPFC
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: DLPFC
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 54
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370268
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959421
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659218
!Sample_title = 1230, scATACseq
!Sample_geo_accession = GSM6659218
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = DLPFC
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: DLPFC
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 49
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370267
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959422
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659219
!Sample_title = 3329, scATACseq
!Sample_geo_accession = GSM6659219
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: AD
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 74
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370266
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959423
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659220
!Sample_title = NT1271, scATACseq
!Sample_geo_accession = GSM6659220
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = DLPFC
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: DLPFC
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 50
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370265
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959424
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659221
!Sample_title = 4482, scATACseq
!Sample_geo_accession = GSM6659221
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: AD
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 77
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370264
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959425
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659222
!Sample_title = 4313, scATACseq
!Sample_geo_accession = GSM6659222
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: AD
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 66
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370263
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959426
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659223
!Sample_title = HCT17HEX, scATACseq
!Sample_geo_accession = GSM6659223
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Apr 23 2024
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA10
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: BA10
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 84
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370262
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959427
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659224
!Sample_title = HCTZZT, scATACseq
!Sample_geo_accession = GSM6659224
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Apr 23 2024
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA12
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: BA12
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 77
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370261
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959428
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659225
!Sample_title = 4305, scATACseq
!Sample_geo_accession = GSM6659225
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: AD
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 77
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370260
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959429
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659226
!Sample_title = 4443, scATACseq
!Sample_geo_accession = GSM6659226
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: AD
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 79
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370259
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959430
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659227
!Sample_title = 1238 rep1, scATACseq
!Sample_geo_accession = GSM6659227
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = DLPFC
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: DLPFC
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 63
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370258
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959431
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659228
!Sample_title = 1238 rep2, scATACseq
!Sample_geo_accession = GSM6659228
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = DLPFC
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: DLPFC
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 63
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370257
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959432
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659229
!Sample_title = 4627 rep1, scATACseq
!Sample_geo_accession = GSM6659229
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: AD
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 92
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370256
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959433
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659230
!Sample_title = 4627 rep2, scATACseq
!Sample_geo_accession = GSM6659230
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: AD
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 92
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370255
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959436
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659231
!Sample_title = 1224 rep1, scATACseq
!Sample_geo_accession = GSM6659231
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = DLPFC
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: DLPFC
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 55
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370254
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959437
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659232
!Sample_title = 1224 rep2, scATACseq
!Sample_geo_accession = GSM6659232
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = DLPFC
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: DLPFC
!Sample_characteristics_ch1 = Sex: F
!Sample_characteristics_ch1 = age: 55
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370253
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959439
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659233
!Sample_title = 3586 rep1, scATACseq
!Sample_geo_accession = GSM6659233
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 76
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370252
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959440
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659234
!Sample_title = 3586 rep2, scATACseq
!Sample_geo_accession = GSM6659234
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: control
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 76
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370251
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959434
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659235
!Sample_title = 4481 rep1, scATACseq
!Sample_geo_accession = GSM6659235
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: AD
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 86
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370250
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959435
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
^SAMPLE = GSM6659236
!Sample_title = 4481 rep2, scATACseq
!Sample_geo_accession = GSM6659236
!Sample_status = Public on Jan 09 2023
!Sample_submission_date = Oct 19 2022
!Sample_last_update_date = Jan 09 2023
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = BA46
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = disease state: AD
!Sample_characteristics_ch1 = tissue: BA46
!Sample_characteristics_ch1 = Sex: M
!Sample_characteristics_ch1 = age: 86
!Sample_molecule_ch1 = genomic DNA
!Sample_extract_protocol_ch1 = Approximately 50-100 mg of frozen tissue per sample was homogenized in 4 mL of nuclei extraction buffer [0.32 M sucrose, 10 mM Tris pH 7.4, 5 mM CaCl2, 3 mM Mg acetate, 1 mM DTT, 0.1 mM EDTA, 0.1% Triton X-100, 0.2U/uL Protector RNAse inhibitor (Sigma cat. 3335399001)] by douncing 30 times in a 40 mL dounce homogenizer. Filter through 70 um filter and spin at 500xg, 5 min at 4°C in a swinging bucket centrifuge. Resuspend nuclei in 500 uL nuclei extraction buffer and layer over 750 uL sucrose solution (1.8 M sucrose, 10 mM Tris pH 7.4, 3 mM Mg acetate, 1 mM DTT) in a 1.5 mL tube. The samples were then centrifuged at >16,000 x g for 30 min at 4°C. After centrifugation, the supernatant was removed by aspiration and the nuclear pellet was resuspended in 125 uL PBS with 1% BSA and centrifuged 5 min at 500 x g at 4°C in a swinging bucket centrifuge. Permeabilization was performed according to 10X Genomics protocol CG000375 Rev B:  nuclei were resuspended in 100 uL lysis buffer (10 mM Tris-HCl pH 7.4,10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.01% Tween-20, 0.01% NP-40, 0.001% digitonin, 1 mM DTT, 1 U/uL Protector RNase inhibitor) and incubated 2 min on ice. Nuclei were washed once and resuspended in 30 uL of 1X nuclei buffer with 1 mM DTT and 0.5 U/uL of Protector RNAse inhibitor. Nuclei quality and concentrations were determined using the Countess. 
!Sample_extract_protocol_ch1 = Library was performed according to the manufacter’s instructions (single cell multiome protocol CG000338 Rev E, 10x Genomics).
!Sample_description = 10x Genomics
!Sample_data_processing = The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger Arc software v2.0.0 (https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc)
!Sample_data_processing = Sample demultiplexing was done with cellSNP and vireo (https://cellsnp-lite.readthedocs.io/en/latest/ , https://vireosnp.readthedocs.io/en/latest/) to get a list of barcodes assigned to each sample. Cellranger-arc bams were split on list of barcodes for each sample then converted back to fastqs with cellranger bamtofastq.
!Sample_data_processing = Processed files include paired scRNAseq and scATACseq counts from the same cells
!Sample_data_processing = Assembly: hg38
!Sample_data_processing = Supplementary files format and content: 10x HDF5 RNA+ATAC counts matrix; table of cell barcodes by seurat meta data
!Sample_platform_id = GPL24676
!Sample_contact_name = Lindsay,,Rizzardi
!Sample_contact_email = lrizzardi@hudsonalpha.org
!Sample_contact_phone = 2563275220
!Sample_contact_laboratory = Richard M. Myers Lab
!Sample_contact_institute = HudsonAlpha Institute for Biotechnology
!Sample_contact_address = 601 Genome Way
!Sample_contact_city = Huntsville
!Sample_contact_state = AL
!Sample_contact_zip/postal_code = 35806
!Sample_contact_country = USA
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = other
!Sample_library_source = genomic single cell
!Sample_library_strategy = ATAC-seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN31370249
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX17959438
!Sample_supplementary_file_1 = NONE
!Sample_series_id = GSE214637
!Sample_series_id = GSE214979
!Sample_data_row_count = 0
