Genomics

Dataset Information

295

Formaldehyde-assisted isolation of regulatory elements with next generation sequencing (FAIRE-seq) in primary human macrophages and foam cells


ABSTRACT: We report the open chromatin landscape in primary human macrophages and foam cells using FAIRE-seq CD14+ monocytes were isolated from the blood of 3 healthy volunteers. Monocytes were differentiated into macrophages by culture for 7 days with 50ng/ml macrophage colony stimulating factor and then treated for 48 hours with either oxidized low density lipoprotein (oxLDL) to induce foam cell formation or with a control buffer that lacked oxLDL. The resulting six samples were then subjected to FAIRE-seq using an established protocol (Simon JM, Giresi PG, Davis IJ, Lieb JD. Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA. Nature protocols 2012;7:256-67).

ORGANISM(S): Homo sapiens  

SUBMITTER: Michael E Reschen   Christopher O'Callaghan 

PROVIDER: E-GEOD-54971 | ArrayExpress | 2015-04-08

SECONDARY ACCESSION(S): GSE54971SRP037758PRJNA238178

REPOSITORIES: GEO, ArrayExpress, ENA

altmetric image

Publications

Lipid-induced epigenomic changes in human macrophages identify a coronary artery disease-associated variant that regulates PPAP2B Expression through Altered C/EBP-beta binding.

Reschen Michael E ME   Gaulton Kyle J KJ   Lin Da D   Soilleux Elizabeth J EJ   Morris Andrew J AJ   Smyth Susan S SS   O'Callaghan Christopher A CA  

PLoS genetics 20150402 4


Genome-wide association studies (GWAS) have identified over 40 loci that affect risk of coronary artery disease (CAD) and the causal mechanisms at the majority of loci are unknown. Recent studies have suggested that many causal GWAS variants influence disease through altered transcriptional regulation in disease-relevant cell types. We explored changes in transcriptional regulation during a key pathophysiological event in CAD, the environmental lipid-induced transformation of macrophages to lipi  ...[more]

Similar Datasets

2015-04-08 | E-GEOD-54972 | ArrayExpress
2015-04-08 | E-GEOD-66192 | ArrayExpress
2011-06-10 | E-GEOD-29881 | ArrayExpress
2015-02-23 | E-GEOD-63747 | ArrayExpress
2015-04-08 | E-GEOD-54666 | ArrayExpress
2015-01-02 | E-GEOD-64062 | ArrayExpress
2014-03-02 | E-MTAB-2298 | ArrayExpress
2012-03-23 | E-GEOD-32358 | ArrayExpress
2016-07-14 | E-GEOD-75770 | ArrayExpress
2011-06-29 | E-GEOD-30224 | ArrayExpress