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Series GSE54909 Query DataSets for GSE54909
Status Public on Feb 23, 2014
Title Vascular histone deacetylation by pharmacological HDAC inhibition [SAHA, ChIP-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy 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 ChIP-seq profiles for 3 histone marks of SAHA 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, 28886276, 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 (21)
GSM1326437 HAEC H3K4Me3 control1 [ChIP-seq]
GSM1326438 HAEC H3K4Me3 control2 [ChIP-seq]
GSM1326439 HAEC H3K4Me3 control3 [ChIP-seq]
This SubSeries is part of SuperSeries:
GSE37378 Vascular histone deacetylation by pharmacological HDAC inhibition
BioProject PRJNA238015
SRA SRP037715

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Supplementary file Size Download File type/resource
GSE54909_HAEC_hg19_H3Ac_MockvsSAHA_peaks.bed.gz 292.4 Kb (ftp)(http) BED
GSE54909_HAEC_hg19_H3Ac_SAHAvsMock_peaks.bed.gz 297.0 Kb (ftp)(http) BED
GSE54909_HAEC_hg19_H3K4me3_MockvsSAHA_peaks.bed.gz 63.6 Kb (ftp)(http) BED
GSE54909_HAEC_hg19_H3K4me3_SAHAvsMock_peaks.bed.gz 156.6 Kb (ftp)(http) BED
GSE54909_HAEC_hg19_H3K9me3_MockvsSAHA_peaks.bed.gz 42.1 Kb (ftp)(http) BED
GSE54909_HAEC_hg19_H3K9me3_SAHAvsMock_peaks.bed.gz 74.5 Kb (ftp)(http) BED
GSE54909_HAEC_hg19_Methylminer_MockvsSAHA_peaks.bed.gz 260.2 Kb (ftp)(http) BED
GSE54909_HAEC_hg19_Methylminer_SAHAvsMock_peaks.bed.gz 197.1 Kb (ftp)(http) BED
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