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Series GSE141752 Query DataSets for GSE141752
Status Public on May 07, 2020
Title Quantitative trait loci mapped for TCF21 binding, chromatin accessibility and chromosomal looping in coronary artery smooth muscle cells reveal molecular mechanisms of coronary disease loci
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Other
SNP genotyping by SNP array
Genome variation profiling by SNP array
Summary To better understand the fundamental molecular mechanisms that contribute to complex human diseases such as coronary artery disease (CAD), we have created a catalog of genetic variants associated with three stages of transcriptional cis-regulation in primary human coronary artery vascular smooth muscle cells. To this end, we used a pooling approach to map quantitative trait locus associations (QTLs) for TCF21 binding (ChIPseq), chromatin accessibility (ATACseq), and chromosomal looping (HiC). We find significant overlap of these QTLs, and several analyses indicate their relationship to smooth muscle specific genes, the binding of smooth muscle transcription factors, and enrichment in CAD-associated loci. These QTLs are extensively validated and allele-specific chromatin looping at the FN1 disease locus is shown to be mediated by activation of the CAD-associated TGFb1 pathway. In sum, these results uncover thousands of loci affecting cis-regulation in a key cell type for CAD, including many that may contribute to CAD risk.
 
Overall design 72 Human coronary artery smooth muscle cells (HCASMC) grown in serum. Approximately 1M cells per sample were freshly prepared for nuclei extraction.
 
Citation(s) 32513244
Submission date Dec 10, 2019
Last update date Aug 06, 2020
Contact name Thomas Quertermous
E-mail(s) tomq1@stanford.edu
Phone 650-723-5012
Organization name Stanford University
Department Medicine Cardiology
Lab Quertermous
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platforms (3)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
GPL20795 HiSeq X Ten (Homo sapiens)
GPL24127 Illumina Infinium Multi-Ethnic Global-8 v1.0 Array
Samples (18)
GSM4212720 pooled ATACseq
GSM4212721 pooled HiC
GSM4212728 pooled TCF21 ChIPseq
This SuperSeries is composed of the following SubSeries:
GSE141748 Quantitative trait loci mapped for TCF21 binding, chromatin accessibility and chromosomal looping in coronary artery smooth muscle cells reveal molecular mechanisms of coronary disease loci (ATAC-Seq)
GSE141749 Quantitative trait loci mapped for TCF21 binding, chromatin accessibility and chromosomal looping in coronary artery smooth muscle cells reveal molecular mechanisms of coronary disease loci (Hi-C)
GSE141751 Quantitative trait loci mapped for TCF21 binding, chromatin accessibility and chromosomal looping in coronary artery smooth muscle cells reveal molecular mechanisms of coronary disease loci (ChIP-Seq)
Relations
BioProject PRJNA594615

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
GSE141752_RAW.tar 1.7 Gb (http)(custom) TAR (of BED, BEDPE, HIC, TXT)
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