GSE110756
Chromatin Capture Identifies SCARB1-LAG3 Proinflammatory Cardiovascular Disease Gene Networks [ChIP-Seq]
Purpose: Using a selected carrier (C) allele of rs10846744 SNP associated with cardiovascular disease (CVD) and a selected non-carrier (G) allele, chromatin immunoprecipitation of a protein of interest, NR2F2, overexpressed and bound to the rs10846744 region in the risk (CC) cells was performed in triplicate. Methods: Using NR2F2 as the target protein, chromatin was immunoprecipitated from each cell type and subjected to Next-gen sequencing. Input controls for each cell type were also sequenced. Results: MACS (Zhang et al., 2008) was utilized for analysis. The narrow peak results were visualized using the Washington University EpiGenome Browser (Zhou and Wang, 2013) and bedgraph files were visualized in the Integrative Genomics Viewer (Thorvaldsdóttir et al., 2013) as bigwig files. Conclusions: Our study represents the first detailed analysis of significant changes in gene expression by an altered chromatin interaction network from SCARB1 to NR2F2 and LAG3, contributing to CAD proinflammatory gene networks. Overall design: Reference (GG) cells and risk (CC) cells were examined for differences in NR2F2 binding, in triplicate.