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Series GSE140493 Query DataSets for GSE140493
Status Public on Dec 12, 2019
Title Multi-omic profiling of single nuclei uncovers regulatory diversity of brain cell types and diseases
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary Most existing single-cell techniques can only make one type of molecular measurements. Although computational approaches have been developed to integrate single-cell datasets, their efficacy still needs to be determined with reference to authentic single-cell multi-omic profiles. To address this challenge, we devised single-nucleus methylCytosine, Chromatin accessibility and Transcriptome sequencing (snmC2T-seq) and applied the approach to post-mortem human frontal cortex tissue. We developed a computational framework to evaluate the quality of finely defined cell types using multi-modal information and validated the efficacy of computational multi-omic integration methods. Correlation analysis in individual cells revealed gene groups showing distinct relations between methylation and expression. Integration of snmC2T-seq with other multi- and single- modal datasets enabled joint analyses of the methylome, chromatin accessibility, transcriptome, and chromatin architecture for 63 human cortical cell types. We reconstructed the regulatory lineage of these cortical cell types and found pronounced cell-type-specific enrichment of disease risks for neuropsychiatric traits, predicting causal cell types that can be targeted for treatment.
 
Overall design snmC2T-seq and snATAC-seq
 
Contributor(s) Luo C, Liu H, Xie F, Doyle W, Armand E, Niu S, Zhou J, Lee D, Wang B, Bartlett A, Castanon R, Rivkin A, Lucero J, Nery JR, Dixon JR, Ren B, Behrens MM, Mukamel EA, Ecker JR
Citation(s) 35419551
Submission date Nov 15, 2019
Last update date Apr 20, 2022
Contact name Joseph R Ecker
E-mail(s) ecker@salk.edu
Phone 8584534100
Organization name HHMI-Salk-Institute
Department Genomic Analysis Laboratory
Lab Ecker lab
Street address 10010 North Torrey Pines Road
City La Jolla
State/province CA
ZIP/Postal code 92037
Country USA
 
Platforms (3)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (8494)
GSM4162955 171009_mCT_hs_h1_h1_mCT_pool_10_AD006_indexed
GSM4162956 171009_mCT_hs_h1_h1_mCT_pool_10_AD010_indexed
GSM4162957 171009_mCT_hs_h1_h1_mCT_pool_11_AD008_indexed
Relations
BioProject PRJNA589980
SRA SRP230258

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE140493_MCDS_data.tar.gz 5.9 Gb (ftp)(http) TAR
GSE140493_RAW.tar 1.1 Tb (http)(custom) TAR (of HDF5, TSV)
GSE140493_snm3C-seq.CGN_cov_chrom100k_da.csv.gz 153.0 Mb (ftp)(http) CSV
GSE140493_snm3C-seq.CGN_cov_gene_da.csv.gz 209.0 Mb (ftp)(http) CSV
GSE140493_snm3C-seq.CGN_mc_chrom100k_da.csv.gz 142.5 Mb (ftp)(http) CSV
GSE140493_snm3C-seq.CGN_mc_gene_da.csv.gz 191.4 Mb (ftp)(http) CSV
GSE140493_snm3C-seq.CHN_cov_chrom100k_da.csv.gz 246.2 Mb (ftp)(http) CSV
GSE140493_snm3C-seq.CHN_cov_gene_da.csv.gz 329.1 Mb (ftp)(http) CSV
GSE140493_snm3C-seq.CHN_mc_chrom100k_da.csv.gz 128.7 Mb (ftp)(http) CSV
GSE140493_snm3C-seq.CHN_mc_gene_da.csv.gz 152.4 Mb (ftp)(http) CSV
GSE140493_snmC-seq_and_snmC-seq2.CGN_cov_chrom100k_da.csv.gz 206.7 Mb (ftp)(http) CSV
GSE140493_snmC-seq_and_snmC-seq2.CGN_cov_gene_da.csv.gz 281.9 Mb (ftp)(http) CSV
GSE140493_snmC-seq_and_snmC-seq2.CGN_mc_chrom100k_da.csv.gz 196.5 Mb (ftp)(http) CSV
GSE140493_snmC-seq_and_snmC-seq2.CGN_mc_gene_da.csv.gz 261.1 Mb (ftp)(http) CSV
GSE140493_snmC-seq_and_snmC-seq2.CHN_cov_chrom100k_da.csv.gz 330.1 Mb (ftp)(http) CSV
GSE140493_snmC-seq_and_snmC-seq2.CHN_cov_gene_da.csv.gz 431.6 Mb (ftp)(http) CSV
GSE140493_snmC-seq_and_snmC-seq2.CHN_mc_chrom100k_da.csv.gz 196.1 Mb (ftp)(http) CSV
GSE140493_snmC-seq_and_snmC-seq2.CHN_mc_gene_da.csv.gz 238.2 Mb (ftp)(http) CSV
GSE140493_snmC2T-seq.GCYN_cov_chrom100k_da.csv.gz 157.4 Mb (ftp)(http) CSV
GSE140493_snmC2T-seq.GCYN_cov_gene_da.csv.gz 206.5 Mb (ftp)(http) CSV
GSE140493_snmC2T-seq.GCYN_mc_chrom100k_da.csv.gz 103.2 Mb (ftp)(http) CSV
GSE140493_snmC2T-seq.GCYN_mc_gene_da.csv.gz 131.4 Mb (ftp)(http) CSV
GSE140493_snmC2T-seq.HCGN_cov_chrom100k_da.csv.gz 123.4 Mb (ftp)(http) CSV
GSE140493_snmC2T-seq.HCGN_cov_gene_da.csv.gz 164.1 Mb (ftp)(http) CSV
GSE140493_snmC2T-seq.HCGN_mc_chrom100k_da.csv.gz 118.0 Mb (ftp)(http) CSV
GSE140493_snmC2T-seq.HCGN_mc_gene_da.csv.gz 153.0 Mb (ftp)(http) CSV
GSE140493_snmC2T-seq.HCHN_cov_chrom100k_da.csv.gz 206.6 Mb (ftp)(http) CSV
GSE140493_snmC2T-seq.HCHN_cov_gene_da.csv.gz 263.0 Mb (ftp)(http) CSV
GSE140493_snmC2T-seq.HCHN_mc_chrom100k_da.csv.gz 120.7 Mb (ftp)(http) CSV
GSE140493_snmC2T-seq.HCHN_mc_gene_da.csv.gz 143.0 Mb (ftp)(http) CSV
GSE140493_snmC2T-seq.gene_rna_counts.4358cell.60606gene.csv.gz 30.2 Mb (ftp)(http) CSV
GSE140493_snmC2T-seq.rna_gene_counts.csv.gz 30.4 Mb (ftp)(http) CSV
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
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