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Series GSE79427 Query DataSets for GSE79427
Status Public on Aug 25, 2016
Title Direct GR binding sites potentiate clusters of TF binding across the human genome [4]
Organism Homo sapiens
Experiment type Other
Summary The glucocorticoid receptor (GR) binds the human genome at >10,000 sites, but only regulates the expression of hundreds of genes. To determine the functional effect of each site, we measured the glucocorticoid (GC) responsive activity of nearly all GR binding sites (GBSs) captured using chromatin immunoprecipitation (ChIP) in A549 cells. 13% of GBSs assayed had GC-induced activity. The responsive sites were defined by direct GR binding via a GC response element (GRE) and exclusively increased reporter- gene expression. Meanwhile, most GBSs lacked GC-induced reporter activity. The non-responsive sites had epigenetic features of steady state enhancers and clustered around direct GBSs. Together, our data support a model in which clusters of GBSs observed with ChIP-seq reflect interactions between direct and tethered GBSs over tens of kilobases. We further show that those interactions can synergistically modulate the activity of direct GBSs, and may therefore play a major role in driving gene activation in response to GCs.
 
Overall design Glucoroticoid receptor binding site chip-seq libraries were cloned into STARR-seq for massively parallel functional analysis. The results were confirmed by ChIP-Exo performed on the GR in A549 cells treated with 100 nM dexamethasone for one hour.
This dataset [4] contains the sequences of GR ChIP-seq fragments that have been cloned into the STARR-seq backbone.
[4] *.fragments files contain DNA fragments that were cloned into a massively parallel reporter assay. These fragments were generated via ChIP-seq for the glucororticoid receptor. The ChIP-seq library that was used for this source material was sequenced and the data from that sequencing was deposited in [8]. The [4] *.fragments file contains the abundance of each reporter plasmid produced by cloning the GR ChIP-seq library into the reporter vector.
 
Contributor(s) Vockley CM, D'Ippolito AM, McDowell IC, Majoros WH, Safi A, Song L, Crawford  GE, Reddy TE
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Submission date Mar 21, 2016
Last update date May 15, 2019
Contact name Christopher Vockley
E-mail(s) christopher.vockley@gmail.com
Organization name Duke University
Street address 101 science drive rm 2193
City Durham
State/province NC
ZIP/Postal code 27708
Country USA
 
Platforms (1)
GPL15520 Illumina MiSeq (Homo sapiens)
Samples (4)
GSM2095198 ChIP-reporter_input_pool1
GSM2095199 ChIP-reporter_input_pool2
GSM2095200 ChIP-reporter_input_pool3
This SubSeries is part of SuperSeries:
GSE79432 Direct GR binding sites potentiate clusters of TF binding across the human genome
Relations
BioProject PRJNA315841
SRA SRP072105

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
GSE79427_RAW.tar 25.2 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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