GEO DataSets

(Submitter supplied) Histone acetylation is a pivotal epigenetic modification that controls chromatin structures and regulates gene expression. It plays an essential role in modulating zygotic transcription and cell lineage specification of developing embryos. While the outcomes of many inductive signals have been described to require enzymatic activities of histone acetyltransferases and deacetylases (HDACs), the mechanisms by which HDACs confines the utilization of the zygotic genome are not well-characterized. more...

Organism:

Xenopus tropicalis

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL23182 GPL30018

45 Samples

Download data: NARROWPEAK, RESULTS

(Submitter supplied) We generated a cellular class I HDAC toolbox allowing to discriminate between catalytic and non-catalytic roles of class I HDACs. Our study reveals a comprehensive, functional analysis of class I HDACs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21290

69 Samples

Download data: TSV

(Submitter supplied) Histone deacetylase 1 (HDAC1) is an enzyme that promotes deacetylation of acetylated lysine residues in histones and other proteins. Histone acetylation is often associated with gene activation and expression. Los of HDAC1 leads to severe problems in development and proliferation. Moreover, it seems to be the major histone deacetylase in mouse embryonic stem cells. We used microarrays to identify putative HDAC1 target genes. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS2294

Platform:

GPL81

6 Samples

Download data: CAB, CEL, EXP, XLS

Analysis of embryonic stem cells lacking histone deacetylase 1 (HDAC1). HDACs catalyze the removal of acetyl groups from core histones resulting in chromatin compaction. Results provide insight into the role of HDAC1 in transcriptional regulation.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 genotype/variation sets

Platform:

GPL81

Series:

GSE5583

6 Samples

Download data: CEL, EXP

(Submitter supplied) Epigenetic regulation of gene expression is important in maintaining self-renewal of embryonic stem (ES) cells and trophoblast stem (TS) cells. Histone deacetylases (HDACs) negatively control histone acetylation by removing covalent acetylation marks from histone tails. Because histone acetylation is a known mark for active transcription, HDACs presumably associate with inactive genes. Here, we used genome-wide chromatin immunoprecipitation to investigate targets of HDAC1 in ES cells and TS cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array; Genome binding/occupancy profiling by genome tiling array

Platforms:

GPL1261 GPL5811

18 Samples

Download data: BAR, CEL

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Bos taurus; Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL24247 GPL26012

42 Samples

Download data

(Submitter supplied) Zygotic genome activation (ZGA) is an impressed biological event following fertilization during early embryo development. Precise reprogramming of epigenetic modifications (e.g. histone H3 lysine 27 acetylation, H3K27ac) have been found contribute to safeguard ZGA in zebrafish and Drosophila, but the dynamic of H3K27ac and the underlying regulation mechanism in mammal embryos are still enigmatic yet. more...

Organism:

Bos taurus; Mus musculus

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24247 GPL26012

26 Samples

Download data: TXT

(Submitter supplied) Histone acetyltransferases (HATs) and deacetylases (HDACs) function antagonistically to control histone acetylation. As acetylation is a histone mark for active transcription, HATs have been associated with active and HDACs with inactive genes. We describe here genome-wide mapping of HATs and HDACs binding on chromatin and find that both are found at active genes with acetylated histones. Our data provide evidence that HATs and HDACs are both targeted to transcribed regions of active genes by phosphorylated RNA Pol II. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing; Expression profiling by array

Platforms:

GPL570 GPL9052

41 Samples

Download data: BED, CEL, CHP, TXT, XLS, ZIP

(Submitter supplied) We compare patterns of H3K79me and H2Bub across genes in budding yeast

Organism:

Saccharomyces cerevisiae BY4741

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18330

20 Samples

Download data: BW

(Submitter supplied) Transcriptional profiling of mouse embryonic kidneys (E13.5) comparing UB HDAC1,2-/- kidneys with wild type kidneys. Studies in our lab showed that histone deacetylase 1 (HDAC1) and 2 (HDAC2) perform redundant, yet essential functions in the developing mouse ureteric bud (UB) tissue. Double deletion of HDAC1 and HDAC2 in the UB results in impaired UB branching morphogenesis, followed by severe kidney dysgenesis. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL4134

8 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL7735

21 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of hdac1 ATG morphant zebrafish embryos in comparison to standard control injected embryos. Embryos where injected at the one cell stage with either a translation blocking morpholino (Hdac1 ATG) or Standard control morpholino (StCo). RNA was extracted at 12, 18 and 27hpf from both sets of embryos and compared with a two-colour hybridisation.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL7735

9 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of hdac1 morphant zebrafish embryos in comparison to standard control injected embryos. Embryos where injected at the one cell stage with either a translation blocking morpholino (Hdac1 ATG), splice blocking morpholino (Hdac1 Splice) or Hdac1 mismatch control morpholino (Hdac1 control). RNA was extracted and compared in a two-colour hybridisation to the comman reference Standard control morpholino injected embryos.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL7735

6 Samples

Download data: TXT

(Submitter supplied) Transcriptional profiling of hdac1 mutant zebrafish in comparison to their sibling embryos. Embryos resulting from a cross between heterozygous hdac1 mutant zebrafish (hi1618/+) where cultured together then mutants separated from the siblings one the basis of phenotype and RNA extracted from the two groups at 27hpf was compared in a two-colour hybridisation.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL7735

8 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL21493 GPL24247

34 Samples

Download data: BED, BIGWIG, BW

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

18 Samples

Download data: BIGWIG, TXT

(Submitter supplied) Purpose: We performed RNA-seq differential expression analysis after 72h HDAC1 and HDAC7 knockdown in order to evaluate the transcriptional regulation exerted by HDAC1 and HDAC7 in a stem-like (BPLER) vs. non-stem (HMLER) breast cancer (BrCa) cell model (please search for keywords "BPLER" or "HMLER" in GEO to access over 240 associated data sets). Results: HDAC7 knockdown by a pool of siRNAs resulted in altered expression of nearly three times the genes in BPLER vs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

14 Samples

Download data: TXT

(Submitter supplied) We sought to investigate the effects of HDAC1 and HDAC7 inhibition on genome-wide histone 3 lysine 27 acetylation (H3K27ac) in BPLER cells, a stem-like breast cancer (BrCa) cell model (please search for keyword "BPLER" in GEO to access over 30 associated datasets). Treatment of BPLER cells with MS-275 (Entinostat), a HDAC1 and HDAC3 specific inhibitor, specifically downregulates HDAC7 mRNA and protein. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

4 Samples

Download data: BIGWIG, TXT

(Submitter supplied) We report the chromatin accessibility with knock down of HDAC1 and HDAC2 from the epithelium of the adult mouse kidney

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

4 Samples

Download data: BED, CSV, H5, TBI, TSV

(Submitter supplied) In this study, we report the acetylation changes during cytotrophoblast cells differentiating into syncytiotrophoblast. We identified several genomic regions in which acetylation patterns are altered during cytotrophoblast differentiation that correlate with the robust changes in gene transcription required during differentiation.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

9 Samples

Download data: BED