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Series GSE32509 Query DataSets for GSE32509
Status Public on Dec 23, 2011
Title Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells
Project ENCODE
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Hundreds of Chromatin Regulators (CRs) control chromatin structure and function by catalyzing and binding histone modifications, yet the rules governing these key processes remain obscure. Here, we present a systematic approach to infer CR function. We developed ChIP-string, a meso-scale assay that combines chromatin immunoprecipitation with a signature readout of 487 representative loci. We applied ChIP-string to screen 145 antibodies, thereby identifying effective reagents, which we used to map the genome-wide binding of 29 CRs in two cell types. We found that specific combinations of CRs co-localize in characteristic patterns at distinct chromatin environments, genes of coherent functions and distal regulatory elements. When comparing between cell types, CRs redistribute to different loci, but maintain their modular and combinatorial associations. Our work provides a multiplex method that substantially enhances the ability to monitor CR binding, presents a large resource of CR maps, and reveals common principles for combinatorial CR function.

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Overall design Study of genom-wide binding of 29 CRs in two cell types.
Contributor(s) Ram O, Goren A, Bernstein BE
Citation(s) 22196736
BioProject PRJNA63443
Submission date Sep 30, 2011
Last update date Nov 19, 2022
Contact name Kevin Dong
Organization name Dana-Farber Cancer Institute
Street address 360 Longwood Ave
City Boston
State/province MASSACHUSETTS
ZIP/Postal code 02215
Country USA
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (59)
GSM830986 K562_CBX2
GSM830987 K562_CBX8
GSM830988 K562_CHD1_1
SRA SRP010385

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE32509_RAW.tar 38.2 Gb (http)(custom) TAR (of BED, BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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