GEO DataSets

(Submitter supplied) The aryl hydrocarbon receptor repressor (AHRR) is a bHLH-PAS protein closely related to the aryl hydrocarbon receptor (AHR). AHRR is a transcriptional repressor of AHR and hypoxia-inducible factor (HIF) and is regulated by an AHR-dependent mechanism. Zebrafish possess two AHRR paralogs; AHRRa regulates constitutive AHR signaling during development, while AHRRb regulates polyaromatic hydrocarbon-induced gene expression. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL7302

6 Samples

Download data: TXT

(Submitter supplied) In this study, we compared the genome-wide binding profiles of AHR and AHRR in MCF-7 human breast cancer cells treated for 24 h with TCDD using chromatin immunoprecipitation followed by next generation sequencing (ChIP-Seq). Overall, this study reveals that AHR and AHRR exhibit similar but also distinct genome-wide binding profiles, supporting the notion that AHRR is a context- and gene-specific repressor of AHR activity.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL16791 GPL11154

6 Samples

Download data: TXT, XLSX

(Submitter supplied) This experiment investigates the role of a novel AHR-regulated gene on the global transcriptome in 48 hpf zebrafish exposed to 0.1% DMSO or 1 ng/mL TCDD.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL14875

16 Samples

Download data: TXT, XLSX

(Submitter supplied) Exposure to environmental contaminants can disrupt normal development of the early vertebrate skeleton. 2,3,7,8-Tetrachlorodibenzo-p-dioxin (TCDD) impairs craniofacial skeletal development across many vertebrate species and its effects are especially prominent in early life stages of fish. TCDD activates the aryl hydrocarbon receptor (AHR), a transcription factor that mediates most if not all TCDD responses. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

24 Samples

Download data: CEL

(Submitter supplied) Background: A structurally diverse group of chemicals, including polycyclic aromatic hydrocarbons (PAHs), can inappropriately activate the aryl hydrocarbon receptor (AHR) and lead to adverse health effects. In the zebrafish model, repression of sox9b has a causal role in several AHR-mediated toxic responses, including craniofacial cartilage malformations; however, the mechanism of sox9b repression remains unknown. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23274

16 Samples

Download data: TXT, XLSX

(Submitter supplied) Except complement C1q, the immunological functions of other C1q family members have remained unclear. In vitro studies showed that DrC1q-like could inhibit the apoptosis induced by ActD and CHX in EPC cells, through repressing the activation of caspase 3/9. Moreover, its physiological roles were studied by morpholino-mediated knockdown in zebrafish embryogenesis We used microarrays to compare the global programme of gene expression of DrC1q-like deficient embryos and control embryos. more...

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL1319

2 Samples

Download data: CEL, EXP

(Submitter supplied) 3,3’-Dichlorobiphenyl (PCB-11) is a non-legacy PCB congener widely detected in environmental samples and has been detected in human serum, but its toxicity potential is poorly understood. Zebrafish statically exposed to 4,500 µg/L PCB-11 at 24 hours post fertilization (hpf) were collected at 96 hpf for RNA sequencing.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20828

6 Samples

Download data: BW, FPKM_TRACKING, TXT

(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) We identified a novel paralog of the antioxidant response element transcription factor, Nrf2 in zebrafish. To determine whether the paralogs Nrf2a and Nrf2b regulate different sets of genes, we performed loss-of-function experiments followed by microarray-based gene expression profiling, performed on embryos in which expression of Nrf2a, Nrf2b, or both paralogs was knocked down.

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL14664

12 Samples

Download data: TXT

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

Organism:

Human alphaherpesvirus 1; Human betaherpesvirus 5; human gammaherpesvirus 4; Betapolyomavirus macacae; Rattus norvegicus; JC polyomavirus; Betapolyomavirus hominis; Danio rerio; Homo sapiens; Mus musculus; Human immunodeficiency virus 1; Human gammaherpesvirus 8

Type:

Non-coding RNA profiling by array; Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL15720 GPL10658 GPL7724

36 Samples

Download data: TXT

(Submitter supplied) Although many drugs and environmental chemicals are teratogenic, the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs (miRNAs), single-stranded RNA molecules of ~22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation, are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. more...

Organism:

Danio rerio

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL10658

12 Samples

Download data: TXT

(Submitter supplied) Although many drugs and environmental chemicals are teratogenic, the mechanisms by which most toxicants disrupt embryonic development are not well understood. microRNAs (miRNAs), single-stranded RNA molecules of ~22 nt that regulate protein expression by inhibiting mRNA translation and promoting mRNA sequestration or degradation, are important regulators of a variety of cellular processes including embryonic development and cellular differentiation. more...

Organism:

Human alphaherpesvirus 1; Human betaherpesvirus 5; human gammaherpesvirus 4; Betapolyomavirus macacae; Rattus norvegicus; Betapolyomavirus hominis; Danio rerio; Homo sapiens; Mus musculus; JC polyomavirus; Human immunodeficiency virus 1; Human gammaherpesvirus 8

Type:

Non-coding RNA profiling by array

Platforms:

GPL7724 GPL15720

24 Samples

Download data: TXT

(Submitter supplied) Polycyclic aromatic hydrocarbons (PAHs) can alter gene expression by acting through the aryl hydrocarbon receptor (AHR). In a previous phenotypic screen of over 120 PAHs, we identified four PAHs that induce an ectopic caudal fin (called X-fin) in larval zebrafish: benzo[k]fluoranthene (BkF), dibenzo[b,k]fluoranthene, dibenzo[a,h]anthracene, and benzo[j]fluoranthene. We investigated several plausible mechanisms of X-fin formation using the most potent X-fin inducer, BkF. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18413

8 Samples

Download data: TXT

(Submitter supplied) To fully understand molecular toxicity of TCDD in an in vivo animal model, adult zebrafish were exposed to TCDD at 10 nM for 96 h and the livers were sampled for RNA-sequencing based transcriptomic profiling. A total of 1,058 differently expressed genes were identified based on fold-change>2 and TPM (transcripts per million) >10. Among the top 20 up-regulated genes, 10 novel responsive genes were identified and verified by qRT-PCR analysis on independent samples. more...

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL10658

2 Samples

Download data: TXT

(Submitter supplied) transcriptomic data for 48 hpf Wildtype, slincRosu3 (sg6; slincR +18 bp mutant) and BigD (slincR -131 bp mutant) zebrafish embryos developmentally exposed to TCDD.

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32002

24 Samples

Download data: XLSX

(Submitter supplied) To determine the expression of cytochrome P450 genes during normal development

Organism:

Danio rerio

Type:

Expression profiling by array

Platform:

GPL11077

24 Samples

Download data: TXT

(Submitter supplied) This study combines RNA seq data from a number of different expeirments examining response to chemical treatment to build the first gene co-expression network of zebrafish. We interrogate this network to determine how the transcriptomic map responds to different types of chemicals and what pathways and processes are critical to chemical response

Organism:

Danio rerio

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL14875 GPL23274

170 Samples

Download data: CSV