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Series GSE178794 Query DataSets for GSE178794
Status Public on Aug 01, 2021
Title Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci [ATAC-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Chromatin accessibility and gene expression in relevant cell contexts can guide identification of regulatory elements and mechanisms at genome-wide association study (GWAS) loci. To identify regulatory elements that display differential activity across adipocyte differentiation, we performed ATAC-seq and RNA-seq in a cell model of preadipocytes and adipocytes at days 4 and 14 of differentiation. For comparison, we created a consensus map of ATAC-seq peaks in 11 subcutaneous adipose tissue samples. A set of 15,919 adipocyte-dependent peaks showed stronger enrichment (60.1%) of adipocyte nuclei enhancers than 51,855 adipose tissue peaks (44.6%) or 18,244 preadipocyte-dependent peaks (11.5%). We linked context-dependent peaks to genes based on adipocyte promoter capture Hi-C data, overlap with adipose eQTL variants, and differential gene expression. Of 16,167 context-dependent peaks that could be linked to a gene, 5,184 were linked by two or more strategies to 1,675 genes. Among GWAS loci for cardiometabolic traits, adipocyte peaks showed the strongest enrichment for waist-to-hip ratio, coronary artery disease, and HDL-cholesterol, while adipose tissue peaks also showed significant enrichment for LDL-cholesterol and triglyceride levels. We identified 666 peaks linked to 507 genes by two or more methods and overlapping a GWAS signal, suggesting a regulatory mechanism at these loci. At one GWAS locus for palmitoleic acid, rs603424 was located in an adipocyte-dependent peak linked to SCD and exhibited allelic differences in transcriptional activity in adipocytes (P=0.003) but not preadipocytes (P=0.09). These results demonstrate that context-dependent peaks and genes can guide discovery of regulatory variants at GWAS loci and aid identification of regulatory mechanisms.
 
Overall design ATAC-seq on SGBS preadipocytes and adipocytes at days 0, 2, 4, and 14 of differentiation and bulk adipose tissue from 17 individuals
**Please note that the 'adiposeTissue' raw data require controlled access and thus are not provided****
 
Contributor(s) Perrin HJ, Currin KW, Vadlamudi S, Pandey GK, Ng KK, Wabitsch M, Laakso M, Love MI, Mohlke KL
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Submission date Jun 23, 2021
Last update date Aug 02, 2021
Contact name Karen L Mohlke
E-mail(s) mohlke@med.unc.edu
Organization name University of North Carolina at Chapel Hill
Department Genetics
Street address 120 Mason Farm Road
City Chapel Hill
State/province NC
ZIP/Postal code 27599-7264
Country USA
 
Platforms (2)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (44)
GSM5397851 SGBS_day0_batch1_rep1
GSM5397852 SGBS_day0_batch1_rep2
GSM5397853 SGBS_day0_batch2_rep1
This SubSeries is part of SuperSeries:
GSE178796 Chromatin accessibility and gene expression during adipocyte differentiation identify context-dependent effects at cardiometabolic GWAS loci
Relations
BioProject PRJNA740464
SRA SRP325411

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Supplementary file Size Download File type/resource
GSE178794_DESeq2Datasets_forGEO_ATAC_SGBS-days0-2-4-14.RData.gz 69.7 Mb (ftp)(http) RDATA
GSE178794_RAW.tar 23.0 Mb (http)(custom) TAR (of NARROWPEAK)
GSE178794_SGBS-day0_consensusPeaks-fromUnionRepPeaks_top100k-byMedianPval.bed.gz 2.3 Mb (ftp)(http) BED
GSE178794_SGBS-day14_consensusPeaks-fromUnionRepPeaks_top100k-byMedianPval.bed.gz 2.2 Mb (ftp)(http) BED
GSE178794_SGBS-day2_consensusPeaks-fromUnionRepPeaks_top100k-byMedianPval.bed.gz 2.2 Mb (ftp)(http) BED
GSE178794_SGBS-day4_consensusPeaks-fromUnionRepPeaks_top100k-byMedianPval.bed.gz 2.3 Mb (ftp)(http) BED
GSE178794_adiposeTissue_consensusPeaks-from11samples_unionPeaksInAtLeast3samples.bed.gz 594.7 Kb (ftp)(http) BED
GSE178794_adiposeTissue_consensusPeaks-from17samples_unionPeaksInAtLeast3samples.bed.gz 913.6 Kb (ftp)(http) BED
GSE178794_mergedConsensusPeaks_forDifferentialTesting_SGBS-days0-2-4-14.bed.gz 2.1 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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