GEO DataSets

(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) 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 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:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

36 Samples

Download data

(Submitter supplied) The wild type and rb1 mutant transcriptomes were used to identify molecular pathways and epigenetic regulators altered in rb1 mutant brain cells. The data was also used for comparative analysis with zebrafish rb1-embryonal brain tumor transcriptome, to identify molecular pathways that distinguish transformed rb1- tumor cells from non-transformed rb1-/- mutant cells.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

12 Samples

Download data: TXT

(Submitter supplied) Zebrafish wildtype adult brain and rb1-embryonal brain tumor transcriptomes were used to identify candidate rb1-interacting chromatin remodelers and epigenetic regulators altered in rb1- transformed brain tumor cells. The data was also used for comparative analysis with zebrafish rb1-/- mutant transcriptome, to identify molecular pathways that distinguish transformed rb1- tumor cells from non-transformed rb1-/- mutant cells.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

24 Samples

Download data: TXT

(Submitter supplied) Coordinated transcriptional and epigenetic mechanisms that direct development of the later differentiating second heart field (SHF) progenitors remain largely unknown. Here, we show that a novel zebrafish histone deacetylase 1 (hdac1) mutant allele cardiac really gone (crg) has a deficit of ventricular CMs and smooth muscle within the outflow tract (OFT) due to both cell and non-cell autonomous loss in SHF progenitor proliferation. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

8 Samples

Download data: TXT

(Submitter supplied) Very little is known on the nature of epigenetic states in developing zebrafish despite its growing importance as a model organism in developmental biology. We report histone modifications on promoters of pluripotency genes in zebrafish embryos at the mid-late blastula transition (MBT+) stage. We identify three classes of expressed genes based on these profiles: (1) those with a promoter occupied by marks of active genes without any repressive marks; (2) those co-occupied by both activating and repressive modifications; of these genes, klf4 was notably found to be mosaically expressed in the embryo, possibly accounting for this epigenetic pattern; (3) those occupied by repressive marks with, surprisingly, little not acetylated H3K9 or H4. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL9998

7 Samples

Download data: TXT

(Submitter supplied) Multicellular organism requires concise gene regulation during ontogeny and epigenetic modifications, such as DNA methylation and histone modification, facilitate the concise regulation. The conservative reprogramming patterns of DNA methylation in vertebrates have been well described but knowledge of how histone modifications are passed on to zygote from gametes are limited and conservations of histone modifications are not clear.We profiled H3K4me3/H3K27me3 modifications in gametes and early embryos in zebrafish and find out that patterns in gene promoter regions have been largely set to either bivalent or active states in gametes and then passed on to zygote. more...

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23085

29 Samples

Download data

(Submitter supplied) In this study, we have applied ChIP-Seq to identify putative regulatory elements throughout the zebrafish genome. For this purpose we identified sequences within the zebrafish genome that associate with H3K4me1 and H3K4me3, which are epigenetic modifications known to be associated with active cis-regulatory elements in other species.

Organism:

Danio rerio

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10164

6 Samples

Download data: BED, WIG

(Submitter supplied) The B1 SOX transcription factors SOX1/2/3/19 have been implicated in various processes of early embryogenesis. However, their regulatory functions in stages from the blastula to early neurula remain largely unknown, primarily because loss-of-function studies have not been informative to date. In our present study, we systematically knocked down the B1 sox genes in zebrafish. Only the quadruple knockdown of the four B1 sox genes sox2/3/19a/19b, which are active in the early embryo, resulted in very severe developmental abnormalities, confirming that the B1 sox genes are functionally redundant. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

12 Samples

Download data: CEL

(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) The production of functional mRNA involves multiple steps including transcription initiation, elongation, and termination. spt5 encodes a conserved essential transcription elongation factor that controls RNAPII processivity in vitro and co-localizes with RNAPII in vivo. We used microarrays to detail the global expression of gene expression at 24 hours post fertilization in wild-type and Spt5 mutant (fog-sk8) to identify Spt5 transcriptionally dependent genes and affected pathways. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Dataset:

GDS3464

Platform:

GPL1319

6 Samples

Download data: CEL

Analysis of fog-sk8 mutant embryos containing a severe truncation of Spt5. Spt5 regulates transcription elongation. Results identify Spt5 target genes during development.

Organism:

Danio rerio

Type:

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

Platform:

GPL1319

Series:

GSE12826

6 Samples

Download data: CEL

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

Organism:

Mus musculus

Type:

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

Platforms:

GPL7202 GPL13112 GPL11002

14 Samples

Download data: TXT, WIG

(Submitter supplied) Based on the cDNA microarrays performed with the RNAs prepared from the differentiated cells at day 3 with or without 24 hrs TSA treatment initiated at day 2, we reveal that the upregulated gene sets were highly enriched for biological functions related to mesoderm development, mesoderm morphogenesis and others.

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL7202

6 Samples

Download data: TXT

(Submitter supplied) Using acetylated histone H3 ChIP-seq, we reveal that the histone H3 acetylation level is gradually increased on the neural gene loci while decreased on the neural-inhibitory gene loci during mouse ESC neural differentiation. By overlapping with the targets of HDAC1 ChIP-seq, we identify Nodal as a target gene repressed by histone deacetylation. Thus, our study reveals an intrinsic mechanism that epigenetic histone deacetylation ensures neural fate commitment by restricting Nodal signaling.

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL13112 GPL11002

8 Samples

Download data: BED, WIG