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Series GSE51178 Query DataSets for GSE51178
Status Public on Jun 16, 2014
Title Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program [ChIP-Seq]
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Skeletal muscle tissue shows an extraordinary cellular plasticity, but the underlying molecular mechanisms are still poorly understood. Here we use a combination of experimental and computational approaches to unravel the complex transcriptional network of muscle cell plasticity centered on the peroxisome proliferator-activated receptor γ coactivator 1α (PGC-1α), a regulatory nexus in endurance training adaptation. By integrating data on genome-wide binding of PGC-1α and gene expression upon PGC-1α over-expression with comprehensive computational prediction of transcription factor binding sites (TFBSs), we uncover a hitherto underestimated number of transcription factor partners involved in mediating PGC-1α action. In particular, principal component analysis of TFBSs at PGC-1α binding regions predicts that, besides the well-known role of the estrogen-related receptor α (ERRα), the activator protein-1 complex (AP-1) plays a major role in regulating the PGC-1α-controlled gene program of hypoxia response. Our findings thus reveal the complex transcriptional network of muscle cell plasticity controlled by PGC-1α.
 
Overall design We performed ChIP-Seq experiments to identify all DNA recruitment sites for PGC-1alpha in C2C12 cells on genome-wide scale. The experiment was performed in duplicate and the Whole Cell Extract (WCE; =input DNA) was used as background condition.
 
Contributor(s) Baresic M, Salatino S, van Nimwegen E, Handschin C, Kupr B
Citation(s) 24912679
Submission date Sep 25, 2013
Last update date May 15, 2019
Contact name Christoph Handschin
Organization name Biozentrum, University of Basel
Street address Klingelbergstrasse 50/70
City Basel
ZIP/Postal code 4056
Country Switzerland
 
Platforms (2)
GPL9250 Illumina Genome Analyzer II (Mus musculus)
GPL11002 Illumina Genome Analyzer IIx (Mus musculus)
Samples (4)
GSM1240211 IP flag PGC-1alpha rep.1
GSM1240212 IP flag PGC-1alpha rep.2
GSM1240213 WCE rep.1
This SubSeries is part of SuperSeries:
GSE51191 Transcriptional network analysis in muscle reveals AP-1 as a partner of PGC-1α in the regulation of the hypoxic gene program
Relations
BioProject PRJNA221528
SRA SRP030459

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE51178_PGC1a_peaks.bed.gz 54.4 Kb (ftp)(http) BED
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Raw data are available in SRA
Processed data are available on Series record

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