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Series GSE42084 Query DataSets for GSE42084
Status Public on Dec 05, 2012
Title Analysis of Unique and Overlapping Patterns of Gene Expression After Treatment of Zebrafish Embryos with Estradiol and/or Dioxin
Organism Danio rerio
Experiment type Expression profiling by array
Summary To increase the utility of the zebrafish gene expression bioassay for assessing EDC effects on multiple gene targets and tissue types, and to expand our understanding of genetic overlap between estrogen receptor (ER) and arylhydrocarbon receptor (AhR) mediated signaling pathways, we conducted microarray analysis of zebrafish embryos exposed to estradiol and dioxin alone or in combination. Of >16,000 probe sets on the array, 34 were regulated by estradiol (E2), 86 by dioxin (TCDD) and 109 by E2+TCDD (as chosen by >2-fold change and p<0.1). Of 62 genes selected for verification by QPCR, 14 genes, or 22% were reproducibly up- or down-regulated, offering potential additional target genes for screening of estrogen- and dioxin-like EDC. The majority of these successful hits, 11, were TCDD-responsive. In addition, all of the target genes routinely evaluated in this laboratory (AroB, Vtg1, and Esr1: E2-responsive; Cyp1a: TCDD- responsive; Vtg1: E2+TCDD-responsive) were verified with these arrays, testifying to the power of microarray analysis in finding reliable responsive genes. However, over two-thirds of the novel up- or down- regulated probes were not annotated as zebrafish genes, and many of the identified genes were changed only 2- to 3-fold, an effect often not reproduced by QPCR. Additional responsive genes were identified for each treatment condition, and while low levels of expression and low magnitude fold changes make those for E2 responsiveness or interaction between E2 and TCDD response unlikely to serve as robust biomarkers, their response to EDCs may assist in understanding the regulation of existing biomarkers and zebrafish endocrine systems as a whole. In addition to a source for potential EDC screening biomarkers, these studies provide an entry point to further study physiological effects of ER and AHR ligands and cross-talk between these signaling pathways, in a physiologically relevant in vivo model.
 
Overall design Hybridizations of three biological replicates (n=30 zebrafish embryos/larvae pooled per treatment group) were performed, in two independent batches, for each of four treatment groups: 0.1% DMSO (control), 0.1µM E2, 1nM TCDD, and 0.1µM E2 + 1nM TCDD
 
Contributor(s) Griffin LB, Callard GV
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Submission date Nov 06, 2012
Last update date Jun 25, 2019
Contact name Boston University Microarray and Sequencing Resource
E-mail(s) msrdata@bu.edu
Organization name Boston University
Department Microarray and Sequencing Resource
Street address 72 East Concord Street, E631
City Boston
State/province MA
ZIP/Postal code 02118
Country USA
 
Platforms (1)
GPL1319 [Zebrafish] Affymetrix Zebrafish Genome Array
Samples (12)
GSM1032213 DMSO 1
GSM1032214 E2 1
GSM1032215 TCDD 1
Relations
BioProject PRJNA179096

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
GSE42084_RAW.tar 25.1 Mb (http)(custom) TAR (of CEL)
Raw data provided as supplementary file
Processed data included within Sample table

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