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Series GSE101063 Query DataSets for GSE101063
Status Public on Jul 11, 2017
Title Open Chromatin and HIF-binding in renal tubular cells [ChIP-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Un-physiological activation of hypoxia inducible factor (HIF) is an early event in most renal cell cancers (RCC) following inactivation of the von Hippel-Lindau tumor suppressor. Despite intense study, how this impinges on cancer development is incompletely understood. To test for the impact of genetic signals on this pathway, we aligned human RCC-susceptibility polymorphisms with genome-wide assays of HIF-binding and observed highly significant overlap. Allele-specific assays of HIF binding, chromatin conformation and gene expression together with eQTL analyses in human tumors were applied to mechanistic analysis of one such overlapping site at chromosome 12p12.1. This defined a novel stage-specific mechanism in which the risk polymorphism, rs12814794, directly creates a new HIF-binding site that mediates HIF-1? isoform specific upregulation of its target BHLHE41. The alignment of multiple sites in the HIF cis-acting apparatus with RCC-susceptibility polymorphisms strongly supports a causal model in which minor variation in this pathway exerts significant effects on RCC development.
 
Overall design This study consists of HIF ChIP-seq samples (HIF-1a and HIF-1b) from one individual and FAIRE-seq samples from three individuals
 
Contributor(s) Schödel J, Kranz F
Citation(s) 28715484
Submission date Jul 10, 2017
Last update date May 15, 2019
Contact name Johannes Schödel
E-mail(s) Johannes.Schoedel@uk-erlangen.de
Organization name FAU Erlangen-Nürnberg
Street address Ulmenweg 18
City Erlangen
ZIP/Postal code 91054
Country Germany
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (2)
GSM2698833 HIF-1a ChIP-seq
GSM2698834 HIF-1b ChIP-seq
This SubSeries is part of SuperSeries:
GSE101064 Open Chromatin and HIF-binding in renal tubular cells
Relations
BioProject PRJNA393660
SRA SRP111449

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
GSE101063_RAW.tar 454.8 Mb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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