GEO DataSets

(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) miRNA profiling of zebrafish embryos comparing control MO with Lin28A MO or Lin28B MO injected embryos at 5hpf

Organism:

Danio rerio

Type:

Non-coding RNA profiling by array

Platform:

GPL17951

3 Samples

Download data: TXT

(Submitter supplied) Cells respond to changes in environment by shifting their gene expression profile to deal with the new conditions. The cellular response to changes in metal homeostasis is an important example of this. Transition metals such as iron, zinc, and copper are essential micronutrients but other metals such as cadmium are simply toxic. The cell must maintain metal concentrations in a window that supports efficient metabolic function but must also protect against the damaging effects of high concentrations of these metals. more...

Organism:

Drosophila melanogaster

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL6629

3 Samples

Download data: BAR, CEL

(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) We used the Dmrt2a inducible transgenic line Tg(hsp70:HA-dmrt2a) to do a brief dmrt2a overexpression at bud-stage in order to identify Dmrt2a immediate targets and understand its mechanism of action. Both wildtype and transgenic embryos received the same treatment. Zebrafish embryos were collected between 2 hours and 2 hours 30 minutes after heat-shock (Dmrt2a overexpression) and were microdissected in two regions: Region 1 (contains the somites and all associated tissues) and Region 2 (contains the tailbud, Kupffer's Vesicle and all associated tissues)

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL20312

12 Samples

Download data: CEL, CHP

(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) Zebrafish is an important model system for the study of vertebrate embryonic development and adaptive immunese response. Recent years have seen great advancement in the understanding of the regulatory mechanisms during zebrafish embryogenesis and immune processes, yet large gaps still remain in the functional pathways critical for each developmental stage, especially for the late embryonic development. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10658

9 Samples

Download data: TXT

(Submitter supplied) Post-transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte-to-embryo transition, which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions, changes to the RNA content are solely dependent on RNA degradation. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

114 Samples

Download data: TSV, 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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Danio rerio

Type:

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

Platforms:

GPL21741 GPL24776

62 Samples

Download data: BEDGRAPH, BW, NARROWPEAK, TXT

(Submitter supplied) In this study, we compared MTF-1 CUT&RUN of cadmium resistant MDA-MB-231 cells vs untreated controls.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

4 Samples

Download data: BED, BW

(Submitter supplied) In this study, we compared RNA-seq of cadmium resistant MDA-MB-231 cells vs untreated controls.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20301

4 Samples

Download data: TXT

(Submitter supplied) In this study, we compared ATAC-seq of cadmium resistant MDA-MB-231 cells vs untreated controls.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL20301

4 Samples

Download data: BW

(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) A great number of studies have investigated changes induced by morphine exposure in gene expression using several experimental models. In this study, we examined gene expression changes during chronic exposure to morphine during maturation and differentiation of zebrafish CNS. Our study identified different functional classes of genes and individual candidates involved in the mechanisms underlying susceptibility to morphine actions related to CNS development. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

12 Samples

Download data: CEL

(Submitter supplied) Here we performed single-cell RNAseq analysis of whole wildtype zebrafish trunks at 30hpf using 10x Genomics' Chromium platform. 22 distinct cell populations were identified, spanning all three embryonic germ layers.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

1 Sample

Download data: MTX, TSV

(Submitter supplied) In future high-throughput transcriptomic studies, we propose that the use of cell lines nullizygous for important targets of environmental chemicals will greatly facilitate the interpretation of regulated genes. To provide proof of this concept, we generated transcript profiles from wild-type and MTF-1-null cells exposed to zinc (Zn) and six putative activators of MTF-1 generated using TempO-Seq targeted sequencing of ~3000 human genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

48 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