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Series GSE9020 Query DataSets for GSE9020
Status Public on Sep 12, 2007
Title Comparative Genomics Identifies Gene Targets for Retinoic Acid in the Embryonic Zebrafish Hearts
Organism Danio rerio
Experiment type Expression profiling by array
Summary 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. We used hierarchical clustering to compare the transcriptional responses produced in the embryonic heart by RA and TCDD. We could identify no early responses in common between the two agents. However, at 12 h both treatments produced a dramatic downregulation of a common cluster of cell cycle progression genes, which we term the Cell Cycle Gene Cluster (CCGC). This was associated with a halt in heart growth. These results suggest that RA and TCDD ultimately trigger a common transcriptional response associated with heart failure, but not through the direct activation of a common set of genes. Among the genes rapidly induced by RA was Nr2F5, a member of the COUP-TF family of transcription repressors. We found that induction of Nr2F5 was both necessary and sufficient for the cardiotoxic response to RA.
Keywords: Comparative Genomics, Timecourse
 
Overall design For RA study, total of 24 samples were collected and analyzed by microarray. Samples of zebrafish embryonic hearts were collected at four timepoints: 1, 2, 4, 12 hours post RA dosing. For each timepoint, there are three replicates of microarray studies. Each replicate includes microarray studies of one sample of RA treated heats and one sample of vehicle control (DMSO) treated hearts.
 
Contributor(s) Chen J, Carney SA, Peterson RE, Heideman W
Citation(s) 18230668
Submission date Sep 12, 2007
Last update date Jan 25, 2018
Contact name Jing Chen
E-mail(s) chen12@wisc.edu
Phone 6082624525
Organization name University of Wisconsin - Madison
Department pharmaceutical Sciences
Street address 777 Highland Ave
City Madison
State/province WI
ZIP/Postal code 53705
Country USA
 
Platforms (1)
GPL1319 [Zebrafish] Affymetrix Zebrafish Genome Array
Samples (48)
GSM228871 embryonic hearts, RA treatment, T1h, biological replicate1
GSM228872 embryonic hearts, RA treatment, T1h, biological replicate2
GSM228873 embryonic hearts, RA treatment, T1h, biological replicate3
Relations
BioProject PRJNA102513

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE9020_RAW.tar 158.3 Mb (http)(custom) TAR (of CEL, EXP)
Raw data provided as supplementary file
Processed data included within Sample table

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