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Links from GEO DataSets

Items: 20

1.

Comparative Genomics Identifies Gene Targets for Retinoic Acid in the Embryonic Zebrafish Hearts

(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
Series
Accession:
GSE9020
ID:
200009020
2.
Full record GDS2965

Embryonic heart response to retinoic acid and dioxin: time course

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
DataSet
Accession:
GDS2965
ID:
2965
3.

Transcriptional profiling of embryonic zebrafish expressing a mutant TNNT2

(Submitter supplied) Transcriptional profiling of embryonic zebrafish injected with a control morpholino or a morpholino that causes exclusion of TNNT2 exon 13.
Organism:
Danio rerio
Type:
Expression profiling by array
Platform:
GPL6457
4 Samples
Download data: TXT
Series
Accession:
GSE20179
ID:
200020179
4.

MicroRNA expression profiling after short-term exposure to TCDD in zebrafish embryos

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Mus musculus; Human gammaherpesvirus 4; Human immunodeficiency virus 1; Human gammaherpesvirus 8; Rattus norvegicus; JC polyomavirus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Macaca mulatta polyomavirus 1; Danio rerio; Homo sapiens; Human polyomavirus 1
Type:
Non-coding RNA profiling by array; Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL15720 GPL10658 GPL7724
36 Samples
Download data: TXT
Series
Accession:
GSE39809
ID:
200039809
5.

MicroRNA expression profiling after short-term exposure to TCDD in zebrafish embryos [miRNA-Seq data]

(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
Series
Accession:
GSE39808
ID:
200039808
6.

MicroRNA expression profiling after short-term exposure to TCDD in zebrafish embryos [agilent and exiqon array data]

(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:
Mus musculus; Human gammaherpesvirus 4; JC polyomavirus; Human immunodeficiency virus 1; Human gammaherpesvirus 8; Rattus norvegicus; Human alphaherpesvirus 1; Human betaherpesvirus 5; Macaca mulatta polyomavirus 1; Danio rerio; Homo sapiens; Human polyomavirus 1
Type:
Non-coding RNA profiling by array
Platforms:
GPL7724 GPL15720
24 Samples
Download data: TXT
Series
Accession:
GSE38839
ID:
200038839
7.

AHR Activation by TCDD Downregulates Sox9b Expression Producing Jaw Malformation in Zebrafish Embryos

(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
Series
Accession:
GSE11893
ID:
200011893
8.

Altered gene expression in zebrafish embryos exposed to tert-butylhydroquinone and 2,3,7,8-tetrachlorodibenzo-p-dioxin

(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
Series
Accession:
GSE10157
ID:
200010157
9.

Microarray analysis of 2,3,7,8-Tetrachlorodibenzo-p-dioxin Exposed Amputated Adult Zebrafish Heart Ventricles

(Submitter supplied) The purpose of this experiment is to understand which transcripts are differentially expressed following exposure to TCDD. We used microarrays to understand global changes in gene signal intensity
Organism:
Danio rerio
Type:
Expression profiling by array
Platform:
GPL1319
12 Samples
Download data: CEL, XLS
Series
Accession:
GSE33981
ID:
200033981
10.

Role of AHR in cardiac developmental toxicity of PAHs

(Submitter supplied) Transcriptmic profiling of cardiac tissues in AHR2 knockdown and control zebrafish (Danio rerio) embryos exposed to BaP, FL amd BaP+FL at 2,6,12, and 18 hours post dosing
Organism:
Danio rerio
Type:
Expression profiling by array
Platform:
GPL18725
109 Samples
Download data: TXT
Series
Accession:
GSE57946
ID:
200057946
11.

Fetal mouse heart, TCDD dose-response series

(Submitter supplied) Pregnant C57Bl6N mice were treated with 0 (corn oil), 1.5, 3.0, or 6.0 ug/kg TCDD on gd14.5. Fetal hearts were collected on gd17.5. Hearts from each litter were pooled onto one chip. 4 replicates of each condition were run on affymetrix MG_U74Av2 chips, using standard affymetrix protocols and controls. Keywords: dose-response, 3 doses plus corn oil control, 4 replicates
Organism:
Mus musculus
Type:
Expression profiling by array
Dataset:
GDS1302
Platform:
GPL81
20 Samples
Download data: CEL
Series
Accession:
GSE2812
ID:
200002812
12.
Full record GDS1302

2,3,7,8-tetrachlorodibenzo-p-dioxin effect on cardiovascular development

Analysis of gestational day (GD) 17.5 fetal hearts isolated from pregnant C57BL/6Ns treated at GD 14.5 with up to 6.0 ug/kg 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). TCDD, a cardiovascular teratogen, inhibits cardiomyocyte proliferation, a process that peaks between GD 14.5 to 17.5.
Organism:
Mus musculus
Type:
Expression profiling by array, count, 2 agent, 4 dose sets
Platform:
GPL81
Series:
GSE2812
20 Samples
Download data: CEL
DataSet
Accession:
GDS1302
ID:
1302
13.

Inhibition of endogenous MTF-1 signaling in zebrafish embryos identifies novel roles for MTF-1 in development

(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
Series
Accession:
GSE51298
ID:
200051298
14.

Comparison of cardiomyocyte transcripts after knockdown of Gata4 in zebrafish embryos

(Submitter supplied) The Gata4 transcription factor is essential for normal heart development, but the molecular basis for its function remain poorly understood. We profiled at the whole genome level transcript changes in cardiomyocytes when Gata4 is depleted from zebrafish embryos. Our objective was to elucidate the cardiomyocyte-specific molecular program functioning downstream of Gata4 in order to better understand the role of Gata4 in cardiac morphogenesis.
Organism:
Danio rerio
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL14875 GPL9319
6 Samples
Download data: TXT, WIG
Series
Accession:
GSE44233
ID:
200044233
15.

Expression data from zebrafish depleted of Esco2

(Submitter supplied) Our study in zebrafish is the first to use an animal model to understand the biology of the developmental disorder Roberts Syndrome (RBS). RBS is caused by mutations in the ESCO2 gene. We have used morpholinos (MO) to knock down esco2 in zebrafish to better understand the pathology of this rare human syndrome. Our zebrafish model nicely phenocopies the developmental defects observed in RBS.
Organism:
Danio rerio
Type:
Expression profiling by array
Platform:
GPL1319
15 Samples
Download data: CEL
Series
Accession:
GSE27569
ID:
200027569
16.

Expression Analysis of Trimethyltin Chlorides (TMT) Impact on Embryonic Development

(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
Series
Accession:
GSE28131
ID:
200028131
17.

Zebrafish embryos treated with Retinoic Acid or Retinoic acid antagonist during gastrulation and early somitogenesis.

(Submitter supplied) Retinoic acid (RA) is an important developmental signaling molecule responsible for the patterning of multiple vertebrate tissues. RA is also a potent teratogen, causing multi-organ birth defects in humans. Endogenous RA levels must therefore be tightly controlled in the developing embryo. In order to understand the RA function and regulation at the genomic level, we used a microarray approach to identify genes that function as negative feedback regulators of retinoic acid signaling. more...
Organism:
Danio rerio
Type:
Expression profiling by array
Platform:
GPL1319
16 Samples
Download data: CEL
Series
Accession:
GSE16264
ID:
200016264
18.

Zebrafish promoter microarrays identify actively transcribed embryonic genes

(Submitter supplied) We have designed a zebrafish genomic microarray to identify DNA-protein interactions in the proximal promoter regions of over 11,000 zebrafish genes. Using these microarrays, together with chromatin immunoprecipitation with an antibody directed against tri-methylated lysine 4 of Histone H3, we demonstrate the feasibility of this method in zebrafish. This approach will allow investigators to determine the genomic binding locations of DNA interacting proteins during development and expedite the assembly of the genetic networks that regulate embryogenesis. more...
Organism:
Danio rerio
Type:
Genome binding/occupancy profiling by genome tiling array
Platforms:
GPL3766 GPL3767
6 Samples
Download data
Series
Accession:
GSE4863
ID:
200004863
19.

Toxic effects of dietary TCDD on juvenile zebrafish

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Danio rerio
Type:
Expression profiling by array
Platform:
GPL17210
81 Samples
Download data: CALLS, PAIR
Series
Accession:
GSE47549
ID:
200047549
20.

Time-dependent toxic effects of dietary TCDD on juvenile zebrafish

(Submitter supplied) Juvenile zebrafish were fed Biodiet starter (4% body weight per day) for 42 d with TCDD added at 0 ppb, 0.1 ppb, 1 ppb, 10 ppb or 100 ppb. Fish were collected, sexed, weighed and length measured at 0, 7, 14, 28 or 42 d for TCDD assessment, histopathologic and microarray analysis. Microarray experiments were conducted using 0 and 100 ppb-TCDD treated male and female sexed zebrafish at 7, 14, 28 and 42 d. more...
Organism:
Danio rerio
Type:
Expression profiling by array
Platform:
GPL17210
63 Samples
Download data: CALLS, PAIR
Series
Accession:
GSE47547
ID:
200047547
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