GSE110734   Details

GSE Accession GSE110734
Title Open chromatin profiling in adipose tissue marks genomic regions with functional roles in cardiometabolic traits
Submission Date 2/16/18
Last Update Date 1/1/19
Pubmed ID
Experiment Type Genome binding/occupancy profiling by high throughput sequencing
Contributor Maren,E,Cannon; Kevin,W,Currin; Kristin,L,Young; Hannah,J,Perrin; Swarooparani Vadlamudi; Alexias Safi; Lingyun Song; Ying Wu; Martin Wabitsch; Markku Laakso; Gregory,E,Crawford; Karen,L,Mohlke
Contact Name
Contact E-mail
Organization Name
Organism Homo sapiens
Organism ID 9606
Organism Synonym man; human
Summary Open chromatin profiling is a powerful method for characterizing the regulatory landscape of tissues and cells and can guide annotation of loci identified in genome-wide association studies (GWAS). We generated open chromatin profiles of frozen human subcutaneous adipose tissue needle biopsies and the Simpson Golabi-Behmel Syndrome (SGBS) preadipocyte cell strain using an assay for transposase-accessible chromatin (ATAC-seq). After normalizing for peak counts, we observed differences between the location of accessible chromatin between tissue samples, SGBS, and existing adipose and adipocyte datasets. Adipose tissue-specific peaks were located near genes involved in adipocyte, endothelial, and immune processes; SGBS preadipocyte-specific peaks were located near genes involved in extracellular matrix maintenance and other preadipocyte processes. GWAS variants for cardiometabolic traits including waist-hip ratio and adiponectin were enriched in adipose tissue and SGBS peaks. Of 110 recently described cardiometabolic GWAS loci colocalized with adipose tissue expression quantitative trait associations, 52 loci had one or more variants overlapping both tissue and SGBS preadipocyte peaks. Annotated variants at the SNX10 waist-hip ratio locus and the ATP2A1-SH2B1 BMI locus showed allelic differences in regulatory assays. Accessible chromatin in adipose tissue and SGBS preadipocytes is useful to identify regulatory regions and functional non-coding variants at cardiometabolic GWAS loci.
Overall Design ATAC-seq on two replicates of SGBS preadipocyte cells.
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Timepoint Count 0
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