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Series GSE54911 Query DataSets for GSE54911
Status Public on Feb 23, 2014
Title Vascular histone deacetylation by pharmacological HDAC inhibition [TSA, MBD-seq]
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary HDAC inhibitors are thought to regulate gene expression by post-translational modification of histone as well as non-histone proteins. Often studied at single loci, increased histone acetylation is the paradigmatic mechanism of action, however, little is known of the extent of genome-wide changes of the mammalian genome when stimulated by the hydroxamic acids, TSA and SAHA. In primary human vascular endothelial cells we map the chromatin modifications, histone H3 acetylation of lysine 9 and 14 (H3K9/14ac) using chromatin immunoprecipitation (ChIP) coupled with massive parallel sequencing (ChIP-seq). Since acetylation mediated gene expression is often associated with modification of other lysine residues we also examined H3K4me3 and H3K9me3 as well as changes in CpG methylation (CpG-seq). Genome-wide mRNA sequencing indicates the differential expression of about 30% of genes, with almost equal numbers being up- and down- regulated. We observe deacetylation conferred by TSA and SAHA that are associated with decreased gene expression. Histone deacetylation is associated with the loss of p300/CBP binding at gene promoters. This study provides an important framework for HDAC inhibitor function in vascular biology and a comprehensive description of genome-wide deacetylation.
 
Overall design HAEC MethylMiner profiles of TSA treated and control samples were generated by deep sequencing, in triplicate, using Illumina GAIIx.
 
Contributor(s) Rafehi H, Balcerczyk A, Lunke S, Kaspi A, Ziemann M, Kn H, Okabe J, Khurana I, Ooi J, Khan AW, Du X, Chang L, Haviv I, Keating ST, Karagiannis TC, El-Osta A
Citation(s) 24732587, 29657262
Submission date Feb 12, 2014
Last update date Jul 31, 2019
Contact name Assam El-Osta
Organization name Baker Heart and Diabetes Institute
Lab Human Epigenetics
Street address 75 Commercial Road
City Melbourne
ZIP/Postal code 3004
Country Australia
 
Platforms (1)
GPL10999 Illumina Genome Analyzer IIx (Homo sapiens)
Samples (9)
GSM1326460 HAEC CpG control1 [MBD-seq]
GSM1326461 HAEC CpG control2 [MBD-seq]
GSM1326462 HAEC CpG control3 [MBD-seq]
This SubSeries is part of SuperSeries:
GSE37378 Vascular histone deacetylation by pharmacological HDAC inhibition
Relations
BioProject PRJNA238014
SRA SRP037717

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
GSE54911_RAW.tar 4.8 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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