^SERIES = GSE157827
!Series_title = Single-nucleus transcriptome analysis reveals dysregulation of angiogenic endothelial cells and neuroprotective glia in Alzheimer's disease
!Series_geo_accession = GSE157827
!Series_status = Public on Sep 28 2020
!Series_submission_date = Sep 11 2020
!Series_last_update_date = Aug 02 2023
!Series_pubmed_id = 32989152
!Series_pubmed_id = 37117777
!Series_web_link = https://www.pnas.org/content/early/2020/09/25/2008762117
!Series_summary = Alzheimer’s disease (AD) is the most common form of dementia but has no effective treatment. A comprehensive investigation of cell-type-specific responses and cellular heterogeneity in AD is required to provide precise molecular and cellular targets for therapeutic development. Accordingly, we perform single-nucleus transcriptome analysis of 169,496 nuclei from the prefrontal cortical samples of AD patients and normal control (NC) subjects. Differential analysis shows that the cell-type-specific transcriptomic changes in AD are associated with the disruption of biological processes including angiogenesis, immune activation, synaptic signaling, and myelination. Subcluster analysis reveals that compared to NC brains, AD brains contain fewer neuroprotective astrocytes and oligodendrocytes. Importantly, our findings show that a subpopulation of angiogenic endothelial cells is induced in the brain in patients with AD. These angiogenic endothelial cells exhibit increased expression of angiogenic growth factors and their receptors (i.e., EGFL7, FLT1, and VWF) and antigen-presentation machinery (i.e., B2M and HLA-E). This suggests that these endothelial cells contribute to angiogenesis and immune response in AD pathogenesis. Thus, our comprehensive molecular profiling of brain samples from patients with AD reveals previously unknown molecular changes as well as cellular targets that potentially underlie the functional dysregulation of endothelial cells, astrocytes, and oligodendrocytes in AD, providing important insights for therapeutic development.
!Series_overall_design = Single-nucleus RNA-sequencing of prefrotnal cortex from AD patients and healthy control.
!Series_overall_design = 
!Series_overall_design = NOTE: Endothelial cells cluster, originally described in the publication, contains other vascular cell types including pericytes, smooth muscle cells, and fibroblasts (See Sun et al., Nature Neuroscience, 2023).
!Series_type = Expression profiling by high throughput sequencing
!Series_contributor = N,,Ip N
!Series_contributor = S,F,Lau
!Series_sample_id = GSM4775561
!Series_sample_id = GSM4775562
!Series_sample_id = GSM4775563
!Series_sample_id = GSM4775564
!Series_sample_id = GSM4775565
!Series_sample_id = GSM4775566
!Series_sample_id = GSM4775567
!Series_sample_id = GSM4775568
!Series_sample_id = GSM4775569
!Series_sample_id = GSM4775570
!Series_sample_id = GSM4775571
!Series_sample_id = GSM4775572
!Series_sample_id = GSM4775573
!Series_sample_id = GSM4775574
!Series_sample_id = GSM4775575
!Series_sample_id = GSM4775576
!Series_sample_id = GSM4775577
!Series_sample_id = GSM4775578
!Series_sample_id = GSM4775579
!Series_sample_id = GSM4775580
!Series_sample_id = GSM4775581
!Series_contact_name = Nancy,,Ip
!Series_contact_email = iplabgenetics@gmail.com
!Series_contact_institute = Hong Kong University of Science and Technology
!Series_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Series_contact_city = Hong Kong
!Series_contact_zip/postal_code = 000000
!Series_contact_country = China
!Series_supplementary_file = ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE157nnn/GSE157827/suppl/GSE157827_RAW.tar
!Series_platform_id = GPL24676
!Series_platform_organism = Homo sapiens
!Series_platform_taxid = 9606
!Series_sample_organism = Homo sapiens
!Series_sample_taxid = 9606
!Series_relation = BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA662923
!Series_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP282056

^SAMPLE = GSM4775561
!Sample_title = AD1
!Sample_geo_accession = GSM4775561
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100290
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106584
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775561/suppl/GSM4775561_AD1_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775561/suppl/GSM4775561_AD1_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775561/suppl/GSM4775561_AD1_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775562
!Sample_title = AD2
!Sample_geo_accession = GSM4775562
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100292
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106585
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775562/suppl/GSM4775562_AD2_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775562/suppl/GSM4775562_AD2_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775562/suppl/GSM4775562_AD2_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775563
!Sample_title = AD4
!Sample_geo_accession = GSM4775563
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100291
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106586
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775563/suppl/GSM4775563_AD4_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775563/suppl/GSM4775563_AD4_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775563/suppl/GSM4775563_AD4_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775564
!Sample_title = AD5
!Sample_geo_accession = GSM4775564
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100289
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106587
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775564/suppl/GSM4775564_AD5_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775564/suppl/GSM4775564_AD5_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775564/suppl/GSM4775564_AD5_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775565
!Sample_title = AD6
!Sample_geo_accession = GSM4775565
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100286
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106588
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775565/suppl/GSM4775565_AD6_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775565/suppl/GSM4775565_AD6_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775565/suppl/GSM4775565_AD6_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775566
!Sample_title = AD8
!Sample_geo_accession = GSM4775566
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100284
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106589
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775566/suppl/GSM4775566_AD8_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775566/suppl/GSM4775566_AD8_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775566/suppl/GSM4775566_AD8_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775567
!Sample_title = AD9
!Sample_geo_accession = GSM4775567
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100282
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106590
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775567/suppl/GSM4775567_AD9_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775567/suppl/GSM4775567_AD9_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775567/suppl/GSM4775567_AD9_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775568
!Sample_title = AD10
!Sample_geo_accession = GSM4775568
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100280
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106591
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775568/suppl/GSM4775568_AD10_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775568/suppl/GSM4775568_AD10_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775568/suppl/GSM4775568_AD10_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775569
!Sample_title = AD13
!Sample_geo_accession = GSM4775569
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100278
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106592
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775569/suppl/GSM4775569_AD13_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775569/suppl/GSM4775569_AD13_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775569/suppl/GSM4775569_AD13_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775570
!Sample_title = AD19
!Sample_geo_accession = GSM4775570
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100276
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106593
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775570/suppl/GSM4775570_AD19_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775570/suppl/GSM4775570_AD19_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775570/suppl/GSM4775570_AD19_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775571
!Sample_title = AD20
!Sample_geo_accession = GSM4775571
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100304
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106594
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775571/suppl/GSM4775571_AD20_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775571/suppl/GSM4775571_AD20_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775571/suppl/GSM4775571_AD20_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775572
!Sample_title = AD21
!Sample_geo_accession = GSM4775572
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: AD
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100302
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106595
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775572/suppl/GSM4775572_AD21_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775572/suppl/GSM4775572_AD21_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775572/suppl/GSM4775572_AD21_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775573
!Sample_title = NC3
!Sample_geo_accession = GSM4775573
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: healthy control
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100299
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106596
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775573/suppl/GSM4775573_NC3_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775573/suppl/GSM4775573_NC3_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775573/suppl/GSM4775573_NC3_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775574
!Sample_title = NC7
!Sample_geo_accession = GSM4775574
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: healthy control
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100297
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106597
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775574/suppl/GSM4775574_NC7_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775574/suppl/GSM4775574_NC7_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775574/suppl/GSM4775574_NC7_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775575
!Sample_title = NC11
!Sample_geo_accession = GSM4775575
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: healthy control
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100296
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106598
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775575/suppl/GSM4775575_NC11_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775575/suppl/GSM4775575_NC11_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775575/suppl/GSM4775575_NC11_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775576
!Sample_title = NC12
!Sample_geo_accession = GSM4775576
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: healthy control
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100295
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106599
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775576/suppl/GSM4775576_NC12_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775576/suppl/GSM4775576_NC12_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775576/suppl/GSM4775576_NC12_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775577
!Sample_title = NC14
!Sample_geo_accession = GSM4775577
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: healthy control
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100294
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106600
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775577/suppl/GSM4775577_NC14_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775577/suppl/GSM4775577_NC14_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775577/suppl/GSM4775577_NC14_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775578
!Sample_title = NC15
!Sample_geo_accession = GSM4775578
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: healthy control
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100293
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106601
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775578/suppl/GSM4775578_NC15_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775578/suppl/GSM4775578_NC15_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775578/suppl/GSM4775578_NC15_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775579
!Sample_title = NC16
!Sample_geo_accession = GSM4775579
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: healthy control
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100308
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106602
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775579/suppl/GSM4775579_NC16_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775579/suppl/GSM4775579_NC16_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775579/suppl/GSM4775579_NC16_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775580
!Sample_title = NC17
!Sample_geo_accession = GSM4775580
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: healthy control
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100307
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106603
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775580/suppl/GSM4775580_NC17_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775580/suppl/GSM4775580_NC17_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775580/suppl/GSM4775580_NC17_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
^SAMPLE = GSM4775581
!Sample_title = NC18
!Sample_geo_accession = GSM4775581
!Sample_status = Public on Sep 28 2020
!Sample_submission_date = Sep 11 2020
!Sample_last_update_date = Sep 28 2020
!Sample_type = SRA
!Sample_channel_count = 1
!Sample_source_name_ch1 = prefrontal cortex snRNAseq
!Sample_organism_ch1 = Homo sapiens
!Sample_taxid_ch1 = 9606
!Sample_characteristics_ch1 = tissue: prefrontal cortex
!Sample_characteristics_ch1 = diagnosis: healthy control
!Sample_molecule_ch1 = nuclear RNA
!Sample_extract_protocol_ch1 = we placed frozen cortical tissues directly into a prechilled Dounce homogenizer with ice-cold homogenization buffer (0.25 M sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM tricine-KOH [pH 7.8], 1 mM DTT, 0.15 mM spermine, 0.5 mM spermidine, protease inhibitors, 5 μg/mL actinomycin, 0.32% NP40, and 0.04% BSA). After 25 strokes with a loose pestle, we mixed the homogenate 1:1 in OptiPrep and centrifuged the solution at 10,000 × g for 20 min at 4 °C. We subsequently collected the separated nuclei, which were pelleted at the bottom of the centrifuge tube, washed them once to remove the OptiPrep, and resuspended them in DMEM/F12 supplemented with 10% FBS. We diluted the nuclei to 40,000 nuclei per mL−1, ensuring this dilution by counting with a hemocytometer. We also assessed the purity of the single-nucleus suspensions by flow cytometry; this protocol routinely yielded high-purity, single-nucleus suspensions (i.e., >95% DAPI+ nuclei in all samples). All buffers and gradient solutions for nuclei extraction contained 60 U/mL RNAsin (Promega).
!Sample_extract_protocol_ch1 = We generated snRNA-seq libraries using the Chromium Single Cell 3′ Library Kit v3 (1000078; 10x Genomics) according to the manufacturer’s instructions.
!Sample_data_processing = Alignment is done by cellranger to hg38 pre-mRNA reference
!Sample_data_processing = Downstream differential analysis and subcluster analysis is done by Seurat
!Sample_data_processing = Genome_build: hg38
!Sample_data_processing = Supplementary_files_format_and_content: Filtered mtx files from cellranger outputs
!Sample_platform_id = GPL24676
!Sample_contact_name = Nancy,,Ip
!Sample_contact_email = iplabgenetics@gmail.com
!Sample_contact_institute = Hong Kong University of Science and Technology
!Sample_contact_address = Room 6313, Academic Building The Hong Kong University of Science and Technology Clear Water Bay, Kowloon
!Sample_contact_city = Hong Kong
!Sample_contact_zip/postal_code = 000000
!Sample_contact_country = China
!Sample_instrument_model = Illumina NovaSeq 6000
!Sample_library_selection = cDNA
!Sample_library_source = transcriptomic
!Sample_library_strategy = RNA-Seq
!Sample_relation = BioSample: https://www.ncbi.nlm.nih.gov/biosample/SAMN16100306
!Sample_relation = SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRX9106604
!Sample_supplementary_file_1 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775581/suppl/GSM4775581_NC18_barcodes.tsv.gz
!Sample_supplementary_file_2 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775581/suppl/GSM4775581_NC18_features.tsv.gz
!Sample_supplementary_file_3 = ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM4775nnn/GSM4775581/suppl/GSM4775581_NC18_matrix.mtx.gz
!Sample_series_id = GSE157827
!Sample_data_row_count = 0
