GEO DataSets

(Submitter supplied) Ethanol is a well-known teratogen. While this teratogenic potential is well-characterized clinically, the mechanisms through which ethanol exposure results in developmental defects remain unclear. Here we use the zebrafish model to elucidate eye-specific mechanisms that may underlie ethanol-mediated microphthalmia (reduced eye size), using time-series microarray analysis of gene expression of eye tissues of embryos exposed to 1.5% ethanol vs. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Dataset:

GDS5357

Platform:

GPL1319

9 Samples

Download data: CEL, CHP

Analysis of eyes from 24-48 hour post-fertilization embryos exposed to 1.5% ethanol. Ethanol exposure during retinal neurogenesis associated with microphthalmic defects. Results provide insight into molecular mechanisms underlying ethanol exposure-mediated developmental retinal defects.

Organism:

Danio rerio

Type:

Expression profiling by array, count, 2 agent, 5 time sets

Platform:

GPL1319

Series:

GSE51427

9 Samples

Download data: CEL, CHP

(Submitter supplied) We have characterised the zebrafish ortholog, setb, and investigated its role in embryogenesis. Phylogenetic analysis showed that zebrafish Setb has an amino acid sequence identity of approximately 96% with the mammalian orthologs. Whole mount immunofluorescence analysis revealed that Setb is expressed mainly in the eye, the lateral line neuromasts and the olfactory pit. Knockdown of setb using antisense morpholino oligonucleotides resulted in increased apoptosis, reduced cell proliferation and severe morphological defects. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL16933

6 Samples

Download data: CEL

(Submitter supplied) The MTF-1 transcription factor is considered to be a master regulator of zinc homoestasis. We previously characterized a constitutively nuclear, dominant-negative zebrafish MTF-1/eGFP fusion protein (dnMTF-1). In this study, in vitro transcribed dnMTF-1 mRNA was microinjected into zebrafish embryos (2-cell stage), with controls consisting of zebrafish embryos (2-cell stage) microinjected with in vitro transcribed enhanced green fluorescent protein (eGFP) mRNA. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL11077

16 Samples

Download data: TXT

(Submitter supplied) Eye development and photoreceptor maintenance requires the retinal pigment epithelium (RPE), a thin layer of cells that underlies the neural retina. Despite its importance, RPE development has not been studied by a genomic approach. A microarray expression profiling methodology was established in this study for studying RPE development. The intact retina with RPE attached was dissected from developing embryos, and differentially expressed genes in RPE were inferred by comparing the dissected tissues with retinas without RPE using microarray and statistical analyses. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Dataset:

GDS2556

Platform:

GPL1319

6 Samples

Download data: CEL, DAT

Analysis of microdissected embryonic retinas with or without the retinal pigment epithelium (RPE). The RPE is a thin layer of cells that underlies the neural retina and supports the function and development of photoreceptors. Results provide insight into the development of the RPE.

Organism:

Danio rerio

Type:

Expression profiling by array, count, 2 tissue sets

Platform:

GPL1319

Series:

GSE5048

6 Samples

Download data: CEL, DAT

(Submitter supplied) Acetylcholinesterase (AChE) inhibitors are widely used as pesticides and drugs. Their primary effect is the overstimulation of muscular activity. Whether AChE inhibitors and related neurotoxic compound also provoke specific changes in gene transcription patterns that allow to establish a mechanistic link useful for diagnostic purposes has, however, yet not been investigated. Therefore, as a proof of principle, we examined the transcriptomic response of a known AChE inhibitor, the organophosphate azinphos-methyl (APM), in zebrafish embryos and compared the response with two non-AChE inhibiting control compounds, 1,4-dimethoxybenzene (DMB) and 2,4-dinitrophenol (DNP). more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL6563

32 Samples

Download data: TXT

(Submitter supplied) Ethanol exposure during prenatal development causes fetal alcohol spectrum disorder (FASD), the most frequent preventable birth defect and neurodevelopmental disability syndrome. The molecular targets of ethanol toxicity during development are poorly understood. Developmental stages surrounding gastrulation are very sensitive to ethanol exposure. To understand the effects of ethanol on early transcripts during embryogenesis, we treated zebrafish embryos with ethanol during pre-gastrulation period and examined the transcripts by Affymetrix GeneChip microarray before gastrulation. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

12 Samples

Download data: CEL

(Submitter supplied) Gene expression was measured using microarrays in 8 hour postfertilization embryos, comparing control versus ethanol-treated (2 to 8 hours postfertilization) embryos. This experiment was performed to determine the gene expression changes that occur in response to ethanol treatment as a model of fetal alcohol spectrum disorder. Fetal alcohol spectrum disorder (FASD) occurs when pregnant mothers consume alcohol, causing embryonic ethanol exposure and characteristic birth defects that include craniofacial, neural and cardiac defects. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Dataset:

GDS5082

Platform:

GPL1319

14 Samples

Download data: CEL, CHP

Analysis of embryos treated with ethanol in embryo medium from 2 hours post fertilization (hpf) to 8hpf. FASD occurs when pregnant mothers consume alcohol, causing embryonic ethanol exposure and characteristic developmental defects. Results provide insight into molecular basis of FASD pathogenesis.

Organism:

Danio rerio

Type:

Expression profiling by array, count, 2 protocol sets

Platform:

GPL1319

Series:

GSE48380

14 Samples

Download data: CEL, CHP

(Submitter supplied) Oxidative stress is an important mechanism of chemical toxicity, contributing to teratogenesis as well as to cardiovascular and neurodegenerative diseases. Developing animals may be especially sensitive to chemicals causing oxidative stress. To assess the response to chemicals at different stages of development, zebrafish (Danio rerio) embryos at 1, 2, 3, 4, 5, and 6 days post-fertilization (dpf) were exposed to 0.1% dimethyl sulfoxide (DMSO), 2 nM 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), or 10 uM tert-butylhydroquinone (tBHQ) for 6 hr. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL2878

12 Samples

Download data: TXT

(Submitter supplied) Estrogen signaling is important for vertebrate embryonic development. Here we have used zebrafish (Danio rerio) as a vertebrate model to identify estrogen regulated genes during the first 4 days of development. Zebrafish embryos were exposed to 1 µM 17β-estradiol from 3 hours post fertilization to 4 days post fertilization, harvested daily and subjected to RNA extraction for transcriptome analysis using microarrays. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL6457

28 Samples

Download data: TXT

(Submitter supplied) During an ENU (N-ethyl-N-nitrosourea) mutagenesis screen, we observed a dominant small-eye mutant mouse with viable homozygotes. A corresponding mutant line was established and referred to as Aey69 (abnormality of the eye #69). Comprehensive phenotyping of the homozygous Aey69 mutants in the German Mouse Clinic revealed only a subset of statistically significant alterations between wild types and homozygous mutants. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL6885

40 Samples

Download data: TXT

(Submitter supplied) It provides an opportunity to make the first comparative study of molecular programs used by embryonic and post-embryonic neurogenic programs in the vertebrate retina.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24995

8 Samples

Download data: MTX, TSV

(Submitter supplied) In zebrafish, vitellogenic oocytes can incorporate significant amounts of 17β-estradiol released from nearby granulosa cells according to a first-order kinetics, since the steroid low polarity ensures high permeability and affinity for yolk lipids. Estrogen bioactivity is likely, because the maternal mRNA for the estrogen receptor-β2 (ers2a) is highly expressed in ovulated oocytes. This transcript is available for translation in the embryo until its sharp decline from 4 to 8 hours post-fertilization (hpf), being replaced by low levels of zygotic ers2a mRNA from 24 hpf to hatching at 48 hpf, as determined by qRT-PCR. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL6457

2 Samples

Download data: TXT

(Submitter supplied) Retinoic acid (RA) and 2,3,7,8-tetrachlorodibenzo-p-dioxin activate distinct ligand-dependent transcription factors, and both cause cardiac malformation and heart failure in zebrafish embryos. We hypothesized that they cause this response by hyperactivating a common set of genes critical for heart development. To test this, we used microarrays to measure transcripts changes in hearts isolated from zebrafish embryos 1,2,4 and 12 h after exposure to 1μM RA. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Dataset:

GDS2965

Platform:

GPL1319

48 Samples

Download data: CEL, EXP

Analysis of hearts from embryos treated for up to 12 hours with retinoic acid (RA) or 2,3,7,8 tetrachlorodibenzo-p-dioxin (TCDD). Zebrafish embryos treated with RA or TCDD develop cardiac malformation and heart failure.

Organism:

Danio rerio

Type:

Expression profiling by array, transformed count, 4 agent, 4 time sets

Platform:

GPL1319

Series:

GSE9020

48 Samples

Download data: CEL, EXP

(Submitter supplied) Investigation of whole genome expression pattern of 60 and 72 hours post fertilization Danio Rerio embryos exposed to TMT and vehicle control

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL13318

12 Samples

Download data: CALLS, PAIR

(Submitter supplied) Identification of genes that are differentially-expressed in dusp2um287/um287;dusp6um286/um286 mutant embryos compared to wildtype

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

6 Samples

Download data: TSV

(Submitter supplied) Prenatal exposure to ethanol leads to a myriad of developmental disorders known as fetal alcohol spectrum disorder, often characterized by growth and mental retardation, central nervous system damage and specific craniofacial dysmorphic features. Although the exact mechanisms of ethanol toxicity are not well understood it is known that ethanol exposure during development affects the expression of several genes involved in cell cycle control, apoptosis and transcription. more...

Organism:

Drosophila melanogaster; Rattus norvegicus; Takifugu rubripes; Caenorhabditis elegans; Homo sapiens; Mus musculus; Danio rerio; Gallus gallus

Type:

Non-coding RNA profiling by array

Platform:

GPL14672

6 Samples

Download data: TXT