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

doi:10.1016/j.gdata.2014.07.002

ChIP-seq profiling of the active chromatin marker H3K4me3 and PPARγ, CEBPα and LXR target genes in human SGBS adipocytes

Genom Data. 2014 Aug 6:2:230-6. doi: 10.1016/j.gdata.2014.07.002. eCollection 2014 Dec.

Authors

Mafalda Galhardo¹, Lasse Sinkkonen¹, Philipp Berninger², Jake Lin³, Thomas Sauter¹, Merja Heinäniemi⁴

Affiliations

¹ Life Sciences Research Unit, University of Luxembourg, 162a Avenue de la Faïencerie, L-1511 Luxembourg, Luxembourg.
² Biozentrum, Universität Basel and Swiss Institute of Bioinformatics, Klingelbergstrasse 50-70, 4056 Basel, Switzerland.
³ Luxembourg Centre for Systems Biomedicine, University of Luxembourg, House of Biomedicine, 7 Avenue des Hauts-Fourneaux, L-4362 Esch/Alzette, Luxembourg.
⁴ Institute of Biomedicine, School of Medicine, University of Eastern Finland, FI-70120 Kuopio, Finland.

Abstract

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).

Keywords: Adipocyte; ChIP-seq; Transcription factor.