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Series GSE14083 Query DataSets for GSE14083
Status Public on Mar 01, 2009
Title Global Chromatin Modifications at Enhancers Correlate with Cell Type-Specific Gene Expression in the Human Genome
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by genome tiling array
Expression profiling by array
Summary The human body is composed of diverse cell types with distinct functions. While it is known that lineage specification depends on cell specific gene expression, which in turn is driven by promoters, enhancers, insulators and other cis-regulatory DNA sequences for each gene1-3, the relative roles of these regulatory elements in this process is not clear. We have previously developed a chromatin immunoprecipitation-based microarray method (ChIP-chip) to identify promoters, enhancers and insulator elements in the human genome4-6. Here, we use the same approach to identify these active elements in multiple cell types and investigated their roles in cell type-specific gene expression. We observed that chromatin state at promoters and CTCF-binding at insulators are largely invariant across diverse cell types. By contrast, enhancers are marked with highly cell type-specific histone modification patterns, strongly correlate to cell type-specific gene expression programs on a global scale, and are functionally active in a cell type-specific manner. Our results defined over 55, 000 potential transcriptional enhancers in the human genome, significantly expanding the current catalog of human enhancers and highlighting the role of these elements in cell type-specific gene expression.

Keywords: ChIP-chip
 
Overall design In HeLa cells, we mapped histone modifications H3K4me1 and H3K4me3, as well as binding of the transcription factor STAT1, genome-wide using ChIP-chip. We predicted almost 40,000 transcriptional enhancers using chromatin signatures, designed condensed microarrays to span these enhancers, and then verified them by examining the following marks in replicate experiments: H3K4me1, H3K4me3, H3K27ac, p300, and MED1. We also performed DNase-chip to map regions of DNase I hypersensitivity. Finally, we repeated these experiments in K562 cells, mapping H3K4me1, H3K4me3, H3K27ac, and STAT1 binding genome-wide using ChIP-chip.
 
Citation(s) 19295514
Submission date Dec 21, 2008
Last update date Mar 25, 2019
Contact name Gary Chung Hon
Organization name UT Southwestern
Department OB/GYN
Street address 5323 Harry Hines Blvd.
City Dallas
State/province TX
ZIP/Postal code 75390
Country USA
 
Platforms (97)
GPL570 [HG-U133_Plus_2] Affymetrix Human Genome U133 Plus 2.0 Array
GPL4132 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 01 of 38
GPL4137 Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0 set 02 of 38
Samples (235)
GSM352429 H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 01 of 38
GSM352430 H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 02 of 38
GSM352431 H3K4me1 HeLa Nimblegen 14.6M Human tiling array of hg17 at 100bp resolution v1.0, set 03 of 38
Relations
BioProject PRJNA112507

Download family Format
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Supplementary file Size Download File type/resource
GSE14083_RAW.tar 18.3 Mb (http)(custom) TAR (of CEL)
Processed data included within Sample table
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