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Series GSE13277 Query DataSets for GSE13277
Status Public on Jun 01, 2009
Title ChIP-on-chip examination of inducible genes in T cells
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by genome tiling array
Summary Specific chromatin characteristics, especially the modification status of the core histone proteins, are associated with different gene expression states. For example, active genes are marked by histone acetylation and methylation on specific lysine residues while inactive genes are marked by histones that are methylated on a different set of lysine residues and are not acetylated. There is growing interest in the chromatin characteristics of genes that respond to environmental or developmental signals with evidence that developmentally regulated genes may possess distinct chromatin marks. Using a T cell model, we examined the chromatin characteristics of inducible genes that respond to activation using ChIP-on-chip. We find that inducible genes, especially rapidly induced primary response genes, are more likely to display the chromatin characteristics of active genes, ie high levels of H3K9 acetylation. Consequently, only a small percentage of inducible genes display an increase in chromatin acetylation following activation. Our results provide evidence that inducible genes, especially rapidly induced genes, can be defined by their chromatin signature.

Keywords: ChIP-chip
Overall design Cells were stimulated for 0h, 0.5h or 4h. Extracts were immunoprecipitated with either, H3K9ac, H3 or no antibody and total genomic input DNA was also collected. H3K9acetylated ChIP samples were compared to either total input genomic DNA or pan histone 3 (H3) ChIP samples. Mock ChIP samples were compared to total input DNA. 2 biological replicates were used for all treatments except for non-stimulated EL4 cells where 3 replicates were used.
Contributor(s) Hardy K, Lim C, Shannon F, Ma L, Peng K
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Submission date Oct 20, 2008
Last update date Oct 14, 2014
Contact name Kristine Hardy
Organization name University of Canberra
Lab Cytokine Gene Expression
Street address University of Canberra
City Bruce
State/province ACT
ZIP/Postal code 0200
Country Australia
Platforms (1)
GPL5811 [Mm_PromPR] Affymetrix Mouse Promoter 1.0R Array
Samples (9)
GSM335206 H3K9ac_against_TotalInput
GSM335207 NoAb_against_TotalInput
GSM335208 H3K9ac_against_TotalH3
This SubSeries is part of SuperSeries:
GSE13279 Defining the chromatin signature of inducible genes in T cells
BioProject PRJNA114011

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
GSE13277_RAW.tar 2.2 Gb (http)(custom) TAR (of BAR, BED, CEL)
Processed data provided as supplementary file

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