 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 06, 2016 |
| Title |
Integrative fine-mapping of regulatory variants and mechanisms at coronary artery disease loci |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Expression profiling by high throughput sequencing
|
| Summary |
Coronary artery disease (CAD) is the leading cause of mortality and morbidity driven by both genetic and environmental risk factors. Meta-analyses of genome-wide association studies (GWAS) have identified multiple single nucleotide polymorphisms (SNPs) associated with CAD and myocardial infarction (MI) susceptibility in multi-ethnic populations. The majority of these variants reside in non-coding regulatory regions and are co-inherited with hundreds of candidate regulatory SNPs. Herein, we use integrative genomic, epigenomic, and transcriptomic fine-mapping in human coronary artery smooth muscle cells (HCASMC) and tissues to identify causal regulatory variation and mechanisms responsible for CAD associations. Using these genome-wide maps we prioritize 65 candidate variants and perform allele-specific binding and expression analyses on 7 top candidates. We validate our findings in two independent cohorts of diseased human arterial expression quantitative trait loci (eQTL), which together demonstrate fundamental links between CAD associations and regulatory function in the appropriate disease context.
|
| |
|
| Overall design |
We performed ATAC-seq, ChIP-seq, and RNA-seq on human coronary artery smooth muscle cells grown in SmGM-2 Smooth Muscle Growth Medium-2 including hEGF, insulin, hFGF-B and FBS, but without antibiotics (Lonza, #CC-3182). For ATAC-seq and RNA-seq we performed stimulations with growth factors (TGF-B1, PDGF-BB, PDGF-DD) versus serum-free control. We conducted two biological replicates for each condition using independent donors. For ATAC-seq experiments, sequencing was completed on an Illumina Hiseq 2500, paired-end 50bp reads. For ChIP-seq we performed immunoprecipitations using H3K27ac (Abcam ab4729). We conducted two biological replicates using HCASMC from independent donors, and also did an IgG control for these studies. For RNA-seq we also conducted two replicates using HCASMC from independent donors. For both ChIP-seq and RNA-seq experiments, sequencing was completed on an Illumina HiSeq 2500, paired-end 100bp reads. We also performed ex-vivo ATAC-seq on frozen tissues (isolated media) from normal and atherosclerotic human coronary arteries, using three independent donors for each. Sequencing was also completed on an Illumina HiSeq 2500, paired end 50bp reads.
|
| |
|
| Contributor(s) |
Miller C, Pjanic M, Quertermous T |
| Citation(s) |
27386823 |
| |
| Submission date |
Sep 03, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Thomas Quertermous |
| E-mail(s) |
[email protected]
|
| 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 (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
|
| Samples (24)
|
|
| Relations |
| BioProject |
PRJNA295524 |
| SRA |
SRP063675 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE72696_DownReg_Result_Table_SF_vs_PDGF1h.csv.gz |
82.2 Kb |
(ftp)(http) |
CSV |
| GSE72696_DownReg_Result_Table_SF_vs_TGF1h.csv.gz |
80.6 Kb |
(ftp)(http) |
CSV |
| GSE72696_RAW.tar |
80.0 Mb |
(http)(custom) |
TAR (of BED, TXT) |
| GSE72696_Result_Table_SF_vs_PDGF1h.csv.gz |
1.5 Mb |
(ftp)(http) |
CSV |
| GSE72696_Result_Table_SF_vs_TGF1h.csv.gz |
1.5 Mb |
(ftp)(http) |
CSV |
| GSE72696_UpReg_Result_Table_SF_vs_PDGF1h.csv.gz |
82.2 Kb |
(ftp)(http) |
CSV |
| GSE72696_UpReg_Result_Table_SF_vs_TGF1h.csv.gz |
80.6 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...