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Series GSE99178 Query DataSets for GSE99178
Status Public on Aug 24, 2017
Title ChIP-seq analysis of BRD4 and RNAPII in K562 cells treated with DMSO or JQ1, NUP98 and NUP153 in K562 cells, and H3K27ac in mouse KH2 undifferentiated embryonic stem cells (ESCs) or differentiated embryonic bodies (EBs)
Organisms Homo sapiens; Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Cis-regulatory elements (CREs) are commonly recognized by correlative chromatin features, yet the molecular composition of the vast majority of CREs in chromatin remains unknown. Here we describe a CRISPR affinity purification in situ of regulatory elements (CAPTURE) approach to unbiasedly identify locus-specific chromatin-regulating protein complexes and long-range DNA interactions. Using an in vivo biotinylated endonuclease-deficient Cas9 protein and sequence-specific guide RNAs, we show high-resolution and selective isolation of chromatin interactions at a single copy genomic locus. Purification of human telomeres using CAPTURE identifies known and new telomeric factors. In situ capture of individual constituents of the enhancer cluster controlling human β-globin genes establishes evidence for composition-based hierarchical organization of enhancer structure. Furthermore, unbiased analysis of chromatin interactions at disease-associated cis-elements and developmentally controlled super-enhancers reveals spatial features causally regulate gene transcription. Thus, comprehensive analysis of locus-specific regulatory composition provides mechanistic insight into genome structure and function in development and disease.
 
Overall design ChIP-seq was performed to determine the BRD4 and RNAPII chromatin occupancy in K562 cells treated with BRD4 inhibitor (JQ1) or vehicle control (DMSO) for 2 or 6 hours, the NUP98 and NUP153 chromatin occupancy in K562 cells, and the H3K27ac mark in mouse KH2 ESCs or differentiated EBs
 
Contributor(s) Liu X, Zhang Y, Xu J
Citation(s) 28841410
Submission date May 22, 2017
Last update date May 15, 2019
Contact name Jian Xu
E-mail(s) Jian.Xu@UTSouthwestern.edu
Phone 214-648-6125
Organization name UT Southwestern Medical Center
Department Children's Research Institute
Street address 6000 Harry Hines Blvd. NL12.108B
City Dallas
State/province TX
ZIP/Postal code 75235
Country USA
 
Platforms (2)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (11)
GSM2635249 ChIP-seq_K562_DMSO_BRD4
GSM2635250 ChIP-seq_K562_DMSO_RNAPII
GSM2635251 ChIP-seq_K562_JQ1-2h_BRD4
This SubSeries is part of SuperSeries:
GSE88817 In situ CAPTURE of chromatin interactions by biotinylated dCas9
Relations
BioProject PRJNA387471
SRA SRP107796

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
GSE99178_RAW.tar 3.6 Gb (http)(custom) TAR (of BED, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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