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Series GSE30226 Query DataSets for GSE30226
Status Public on Jun 29, 2011
Title Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity [ChIP_seq].
Project ENCODE
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary The human body contains thousands of unique cell types, each with specialized functions. Cell identity is governed in large part by gene transcription programs, which are determined by regulatory elements encoded in DNA. To identify regulatory elements active in seven cell lines representative of diverse human cell types, we used DNase-seq and FAIRE-seq to map “open chromatin”. Over 870,000 DNaseI or FAIRE sites, which correspond largely to nucleosome depleted regions (NDRs), were identified across the seven cell lines, covering nearly 9% of the genome. The combination of DNaseI and FAIRE is more effective than either assay alone in identifying likely regulatory elements, as judged by coincidence with transcription factor binding locations determined in the same cells. Open chromatin common to all seven cell types tended to be at or near transcription start sites and encompassed more CTCF binding sites, while open chromatin sites found in only one cell type were typically located away from transcription start sites, and contained DNA motifs recognized by regulators of cell-type identity. As one example of its ability to identify functional DNA, we show that open chromatin regions bound by CTCF are potent insulators. We identified clusters of open regulatory elements (COREs) that were physically near each other and whose appearance was coordinated among one or more cell types. Gene expression and RNA Pol II binding data support the hypothesis that COREs control gene activity required for the maintenance of cell-type identity. This publicly available atlas of regulatory elements may prove valuable in identifying non-coding DNA sequence variants that are causally linked to human disease.

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Overall design DNase-seq, FAIRE-seq, and ChIP-seq were performed on seven human cell lines: GM12878 (lymphoblastoid), K562 (leukemia), HepG2 (hepatocellular carcinoma), HelaS3 (cervical carcinoma), HUVEC (human umbilical vein endothelial cells), NHEK (keratinocytes), and H1-ES (embryonic stem cells). For each cell line, two or three replicates were independently grown and split into three, one for each of the three experimental methods. Control ChIP experiments were performed on five of the cell lines with NHEK and H1-ES being excluded due to lack of material.
Web link
Contributor(s) Furey TS, Iyer VR, Crawford GE
Citation(s) 21750106
BioProject PRJNA63447
Submission date Jun 27, 2011
Last update date May 15, 2019
Contact name Terry Furey
Organization name UNC-Chapel Hill
Department Genetics
Lab Furey
Street address 5022 Genetic Medicine Building, CB#7264
City Chapel Hill
State/province NC
ZIP/Postal code 27599
Country USA
Platforms (1)
GPL9052 Illumina Genome Analyzer (Homo sapiens)
Samples (33)
GSM748526 GM12878_cMYC_REP1
GSM748527 GM12878_cMYC_REP2
GSM748528 GM12878_PolII_REP1
This SubSeries is part of SuperSeries:
GSE30227 Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
GSE32883 Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells
SRA SRP007350

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
GSE30226_GM12878_UTAChIPSeqPolII.narrowPeak.gz 2.0 Mb (ftp)(http) NARROWPEAK
GSE30226_GM12878_UTAChIPSeqcMYC.narrowPeak.gz 368.9 Kb (ftp)(http) NARROWPEAK
GSE30226_H1_ES_UTAChIPSeqPolII.narrowPeak.gz 2.7 Mb (ftp)(http) NARROWPEAK
GSE30226_H1_ES_UTAChIPSeqcMYC.narrowPeak.gz 269.4 Kb (ftp)(http) NARROWPEAK
GSE30226_HUVEC_UTAChIPSeqPolII.narrowPeak.gz 2.3 Mb (ftp)(http) NARROWPEAK
GSE30226_HUVEC_UTAChIPSeqcMYC.narrowPeak.gz 926.5 Kb (ftp)(http) NARROWPEAK
GSE30226_HelaS3_UTAChIPSeqPolII.narrowPeak.gz 1.8 Mb (ftp)(http) NARROWPEAK
GSE30226_HelaS3_UTAChIPSeqcMYC.narrowPeak.gz 258.4 Kb (ftp)(http) NARROWPEAK
GSE30226_HepG2_UTAChIPSeqCTCF.narrowPeak.gz 1.3 Mb (ftp)(http) NARROWPEAK
GSE30226_HepG2_UTAChIPSeqPolII.narrowPeak.gz 3.6 Mb (ftp)(http) NARROWPEAK
GSE30226_HepG2_UTAChIPSeqcMYC.narrowPeak.gz 815.5 Kb (ftp)(http) NARROWPEAK
GSE30226_K562_UTAChIPSeqPolII.narrowPeak.gz 2.8 Mb (ftp)(http) NARROWPEAK
GSE30226_K562_UTAChIPSeqcMYC.narrowPeak.gz 667.0 Kb (ftp)(http) NARROWPEAK
GSE30226_NHEK_UTAChIPSeqPolII.narrowPeak.gz 2.4 Mb (ftp)(http) NARROWPEAK
GSE30226_NHEK_UTAChIPSeqcMYC.narrowPeak.gz 335.5 Kb (ftp)(http) NARROWPEAK
GSE30226_RAW.tar 4.3 Gb (http)(custom) TAR (of BED)
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Raw data are available in SRA
Processed data provided as supplementary file
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