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| 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 (ATAC-Seq) |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| 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.
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| Overall design |
Human coronary artery smooth muscle cells (HCASMC) grown in serum and 71 lines were pooled. Approximately 50k cells per sample were freshly prepared for nuclei extraction.
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| Contributor(s) |
Zhao Q, Dacre M, Nguyen T, Pjanic M, Liu B, Iyer D, Cheng PP, Wirka R, Kim JB, Fraser HB, Quertermous T |
| Citation(s) |
32513244 |
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| Submission date |
Dec 10, 2019 |
| Last update date |
Aug 06, 2020 |
| Contact name |
Thomas Quertermous |
| E-mail(s) |
tomq1@stanford.edu
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| Phone |
650-723-5012
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| Organization name |
Stanford University
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| Department |
Medicine Cardiology
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| Lab |
Quertermous
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| Street address |
300 Pasteur Drive
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| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
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| Platforms (1) |
| GPL20301 |
Illumina HiSeq 4000 (Homo sapiens) |
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| Samples (1) |
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| This SubSeries is part of SuperSeries: |
| GSE141752 |
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 |
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| Relations |
| BioProject |
PRJNA594623 |
| SRA |
SRP235556 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE141748_RAW.tar |
3.4 Mb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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