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Series GSE107726 Query DataSets for GSE107726
Status Public on Jan 27, 2018
Title ChIP-seq analysis of H3K27ac, GATA1 and TAL1 in MYO1D hub vs non-hub enhancer knockout K562 cells
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Recent studies have highlighted super-enhancers (SEs) as important regulatory elements for gene expression, but their intrinsic properties remain incompletely characterized. Through an integrative analysis of Hi-C and ChIP-seq data, we find that a significant fraction of SEs are hierarchically organized, containing both hub and non-hub enhancers. Hub enhancers share similar histone marks with non-hub enhancers, but are distinctly associated with cohesin and CTCF binding sites and disease-associated genetic variants. Genetic ablation of hub enhancers results in profound defects in gene activation and local chromatin landscape. As such, hub enhancers are the major constituents responsible for SE functional and structural organization.
 
Overall design ChIP-seq was performed to determine the chromatin occupancy of H3K27ac, GATA1 and TAL1 in MYO1D hub or non-hub enhancer knockout K562 cells.

MYO1D Non-hub enhancer deletion: chr17:31220757+31222033 (1277 bp)
MYO1D Hub enhancer deletion: chr17:31236528+31240709 (4182 bp)
 
Contributor(s) Li K, Zhang Y, Xu J
Citation(s) 29507293
Submission date Dec 05, 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 (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (24)
GSM2877103 ChIP-seq_K562_H3K27ac_rep1
GSM2877104 ChIP-seq_K562_H3K27ac_rep2
GSM2877105 ChIP-seq_K562_GATA1_rep1
Relations
BioProject PRJNA421193
SRA SRP126185

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Supplementary file Size Download File type/resource
GSE107726_RAW.tar 4.8 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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