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Series GSE78113 Query DataSets for GSE78113
Status Public on Sep 14, 2016
Title Capture-C reveals preformed chromatin interactions between HIF-binding sites and distant promoters. [ChIP-Seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Hypoxia inducible factor (HIF) directs an extensive transcriptional cascade that transduces numerous adaptive responses to hypoxia. Pan-genomic analyses, using chromatin immunoprecipitation and transcript profiling, have revealed large numbers of HIF-binding sites that are generally associated with hypoxia-inducible transcripts, even over long chromosomal distances. However, these studies do not define the specific targets of HIF-binding sites and do not reveal how induction of HIF affects chromatin conformation over distantly connected functional elements. To address these questions we deployed a recently developed chromosome conformation assay that enables simultaneous high-resolution analyses from multiple viewpoints. These assays defined specific long-range interactions between intergenic HIF-binding regions and one or more promoters of hypoxia-inducible genes, revealing the existence of multiple enhancer-promoter, promoter-enhancer and enhancer-enhancer interactions.
 
Overall design We utilised ChIP-seq to study the histone marks and CTCF binding in MCF7 cells in normoxia and hypoxia
 
Contributor(s) Mole D, Platt J
Citation(s) 27506891
Submission date Feb 19, 2016
Last update date May 15, 2019
Contact name James Platt
Organization name University of Oxford
Street address Roosevelt Drive
City Oxfors
ZIP/Postal code OX3 7BN
Country United Kingdom
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (26)
GSM2067516 MCF7_H3K4me1_N1
GSM2067517 MCF7_H3K4me1_N2
GSM2067518 MCF7_H3K4me1_H1
This SubSeries is part of SuperSeries:
GSE78114 Capture-C reveals preformed chromatin interactions between HIF-binding sites and distant promoters.
Relations
BioProject PRJNA312626
SRA SRP070572

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
GSE78113_RAW.tar 14.0 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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