ChIP-seq profiling of the active chromatin marker H3K4me3 and PPARγ, CEBPα and LXR target genes in human SGBS adipocytes
Mafalda Galhardo,
Lasse Sinkkonen,
Philipp Berninger,
Jake Lin,
Thomas Sauter,
Merja Heinäniemi
Affiliations
Mafalda Galhardo
Life Sciences Research Unit, University of Luxembourg, 162a Avenue de la Faïencerie, L-1511 Luxembourg, Luxembourg
Lasse Sinkkonen
Life Sciences Research Unit, University of Luxembourg, 162a Avenue de la Faïencerie, L-1511 Luxembourg, Luxembourg
Philipp Berninger
Biozentrum, Universität Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland
Jake Lin
Luxembourg Centre for Systems Biomedicine, University of Luxembourg, House of Biomedicine, 7 Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg
Thomas Sauter
Life Sciences Research Unit, University of Luxembourg, 162a Avenue de la Faïencerie, L-1511 Luxembourg, Luxembourg
Merja Heinäniemi
Institute of Biomedicine, School of Medicine, University of Eastern Finland, FI-70120 Kuopio, Finland
Transcription factors (TFs) represent key factors to establish a cellular phenotype. It is known that several TFs could play a role in disease, yet less is known so far how their targets overlap. We focused here on identifying the most highly induced TFs and their putative targets during human adipogenesis. Applying chromatin immunoprecipitation coupled with deep sequencing (ChIP-Seq) in the human SGBS pre-adipocyte cell line, we identified genes with binding sites in their vicinity for the three TFs studied, PPARγ, CEBPα and LXR. Here we describe the experimental design and quality controls in detail for the deep sequencing data and related results published by Galhardo et al. in Nucleic Acids Research 2014 [1] associated with the data uploaded to NCBI Gene Expression Omnibus (GSE41578).
