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Series GSE105028 Query DataSets for GSE105028
Status Public on Aug 03, 2018
Title Architectural proteins and pluripotency factors cooperate to orchestrate the transcriptional response of hESCs to temperature stress
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Other
Summary Cells respond to temperature stress via up- and down-regulation of hundreds of genes. This process is regulated by the heat shock factor HSF1, which controls the release of RNAPII from promoter-proximal pausing. Here we analyze the events taking place upstream of transcription elongation in hESCs. We find that temperature stress results in the activation or decommissioning of thousands of enhancers. This process involves alterations in the occupancy of transcription factors HSF1, AP-1, NANOG, KLF4, and OCT4, which is accompanied by changes in H3K27ac and H3K27me3, as well as nucleosome remodeling by BRG1. In addition, redistribution of RAD21 and CTCF results in the formation and disassembly of interactions mediated by these two proteins, either individually or in combination. These alterations either tether/untether enhancers to their cognate promoters or remodel insulated neighborhoods with the ultimate goal of transforming the landscape of enhancer-promoter interactions. This loop remodeling process supports unidirectional loop extrusion as a mechanism for the establishment of CTCF/cohesin loops.
 
Overall design Hi-C, HiChIP, ChIP-seq, ATAC-seq, eU-Seq
 
Contributor(s) Lyu X, Rowley J, Corces VG
Citation(s) 30122536
Submission date Oct 16, 2017
Last update date May 15, 2019
Contact name Victor Corces
E-mail(s) xlyu@emory.edu
Phone 4042687305
Organization name Emory University
Street address Rollins Research Center Room 1071B, 1510 Clifton Rd NE
City Atlanta
State/province GA
ZIP/Postal code 30322
Country USA
 
Platforms (1)
GPL11154 Illumina HiSeq 2000 (Homo sapiens)
Samples (93)
GSM2816607 HiC _Rep1
GSM2816608 HiC _Rep2
GSM2816609 HS HiC _Rep1
Relations
BioProject PRJNA414442
SRA SRP120027

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
GSE105028_ATAC-Seq.bw 300.0 Mb (ftp)(http) BW
GSE105028_CTCF_HiChIP.hic 929.0 Mb (ftp)(http) HIC
GSE105028_H3K27ac_HS.bw 170.2 Mb (ftp)(http) BW
GSE105028_H3K27ac_NT.bw 173.4 Mb (ftp)(http) BW
GSE105028_H3K4me1_HiChIP.hic 1.1 Gb (ftp)(http) HIC
GSE105028_H9_Hi-C.1kb.intra.hic 1.7 Gb (ftp)(http) HIC
GSE105028_HS_ATAC-Seq.bw 296.3 Mb (ftp)(http) BW
GSE105028_HS_CTCF_HiChIP.hic 965.5 Mb (ftp)(http) HIC
GSE105028_HS_H3K4me1_HiChIP.hic 1.2 Gb (ftp)(http) HIC
GSE105028_HS_H9_Hi-C.1kb.intra.hic 1.8 Gb (ftp)(http) HIC
GSE105028_HS_NANOG_HiChIP.hic 1.5 Gb (ftp)(http) HIC
GSE105028_HS_OCT4_HiChIP.hic 1.2 Gb (ftp)(http) HIC
GSE105028_HS_Rad21_Hi-ChIP.hic 2.7 Gb (ftp)(http) HIC
GSE105028_KLF4_HiChIP.hic 1.7 Gb (ftp)(http) HIC
GSE105028_NANOG_HiChIP.hic 1.4 Gb (ftp)(http) HIC
GSE105028_OCT4_HiChIP.hic 1007.0 Mb (ftp)(http) HIC
GSE105028_RAW.tar 15.2 Gb (http)(custom) TAR (of BED, BW, HIC)
GSE105028_Rad21_HS.bw 164.3 Mb (ftp)(http) BW
GSE105028_Rad21_Hi-ChIP.hic 1.8 Gb (ftp)(http) HIC
GSE105028_Rad21_NT.bw 153.3 Mb (ftp)(http) BW
GSE105028_siNIPBL_HS_CTCF_HiChIP.hic 808.4 Mb (ftp)(http) HIC
GSE105028_siNIPBL_HS_H3K4me1_HiChIP.hic 1.1 Gb (ftp)(http) HIC
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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