Dataset features

Specifications


Application: ChIP-seq analysis, RNA-seq analysis
Number of samples: 24
Release date: Jul 6 2016
Last update date: Oct 24 2018
Access: Public
Diseases: Coronary Artery Disease, Myocardial Infarction
Computational protocol: seeQTL, STAR, HTSeq, DESeq2, EDASeq, LocusZoom, eQTL Browser, eqtl.uchicago.edu, GBrowse, Blood eQTL browser
Dataset link Integrative fine-mapping of regulatory variants and mechanisms at coronary artery disease loci

Experimental Protocol


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.

Repositories


GEO

GSE72696

ArrayExpress

E-GEOD-72696

ENA

SRP063675

BioProject

PRJNA295524

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Contact


Thomas Quertermous

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