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Series GSE34871 Query DataSets for GSE34871
Status Public on Feb 01, 2012
Title Genome-wide mapping of HIF-2 binding in 786-O clear cell renal carcinoma cells
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Kidney cancer accounts for more than 100,000 deaths per year world-wide. More than 80% are clear cell tumors (ccRCCs) and the majority are associated with loss of function of the von Hippel Lindau (pVHL) tumor suppressor resulting in upregulation of HIF-{alpha} subunits, and activation of HIF-dependent transcriptional pathways. Recent GWAS studies have discovered RCC-susceptibility loci both within EPAS1 (HIF-2{alpha}) and in an intergenic region of unknown function on 11q13.3. As part of an ongoing study to define the direct transcriptional targets of HIF-2 in renal cancer, we undertook a genome-wide analysis of HIF-2-binding sites in pVHL-defective 786-O cells (that lack functional HIF-1{alpha} due to a truncated transcript) using chromatin immunoprecipitation with antibodies directed against HIF-2{alpha} and its dimerization partner HIF-1{beta}, coupled to high-throughput sequencing (ChIP-seq). Amongst approximately 600 pangenomic HIF-2{beta} ChIP signals, we observed strong binding (ranked 12th by peak height) almost precisely coinciding with the RCC predisposition SNP rs7105934 on 11q13.3.
Overall design We report binding of HIF-2{alpha} and HIF-1{beta} in 786-O clear cell renal carcinoma cells.
3 samples examined, HIF-2{alpha}, HIF-1{beta} and pre-immune control ChIP.
Contributor(s) Mole DR, Schoedel J
Citation(s) 22406644
Submission date Jan 05, 2012
Last update date May 15, 2019
Contact name David Robert Mole
Phone 0044 (0)1865 613956
Organization name University of Oxford
Department Nuffield Department of Medicine
Lab NDM Research Building
Street address Roosevelt Drive, Headington
City Oxford
ZIP/Postal code OX3 7FZ
Country United Kingdom
Platforms (1)
GPL9115 Illumina Genome Analyzer II (Homo sapiens)
Samples (3)
GSM856789 Pre-immune control
GSM856790 HIF-2alpha
GSM856791 HIF-1beta
SRA SRP010128
BioProject PRJNA150099

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Supplementary file Size Download File type/resource
GSE34871_RAW.tar 67.6 Mb (http)(custom) TAR (of BIGWIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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