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Series GSE24685 Query DataSets for GSE24685
Status Public on Nov 15, 2010
Title Genome-wide binding of the orphan nuclear receptor TR4 suggests its general role in fundamental biological processes
Project ENCODE
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The orphan nuclear receptor TR4 (human testicular receptor 4 or NR2C2) plays a pivotal role in a variety of biological and metabolic processes. With no known ligand and few known target genes, the mode of TR4 function was unclear. We report the first genome-wide identification and characterization of TR4 in vivo binding. Using chromatin immunoprecipitation followed by high throughput sequencing (ChIP-seq), we identified TR4 binding sites in 4 different human cell types and found that the majority of target genes were shared among different cells. TR4 target genes are involved in fundamental biological processes such as RNA metabolism and protein translation. In addition, we found that a subset of TR4 target genes exerts cell-type specific functions. Analysis of the TR4 binding sites revealed that less than 30% of the peaks from any of the cell types contained the DR1 motif previously derived from in vitro studies, suggesting that TR4 may be recruited to the genome via interaction with other proteins. A bioinformatics analysis of the TR4 binding sites predicted a cis regulatory module involving TR4 and ETS transcription factors. To test this prediction, we performed ChIP-seq for the ETS factor ELK4 and found that 30% of TR4 binding sites were also bound by ELK4. Motif analysis of the sites bound by both factors revealed a lack of the DR1 element, suggesting that TR4 binding at a subset of sites is facilitated through the ETS transcription factor ELK4. Further studies will be required to investigate the functional interdependence of these two factors.

For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
 
Overall design 8 total ChIP-seq datasets; four TR4 and datasets done in duplicate from 4 different cell lines; ELK4 (Sap1a) duplicate dataset done from HeLa cells; 1 ELK1 replicate in HeLa cells, 2 individual replicates for histone mod datasets from K562 cells
Web link http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
 
Contributor(s) O'Geen H, Farnham PJ
Citation(s) 21126370
BioProject PRJNA63447
Submission date Oct 13, 2010
Last update date May 15, 2019
Contact name Philip Cayting
E-mail(s) pcayting@stanford.edu
Organization name Stanford University
Department Genetics
Lab Snyder
Street address 1501 S California Ave
City Palo Alto
State/province CA
ZIP/Postal code 94304
Country USA
 
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (15)
GSM608153 TR4_K562_ChIP-seq_rep1
GSM608154 TR4_K562_ChIP-seq_rep2
GSM608155 TR4_HepG2_ChIP-seq_rep1a
Relations
SRA SRP003812

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
GSE24685_RAW.tar 5.9 Gb (http)(custom) TAR (of BAM, BED, BIGWIG, TAGALIGN)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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