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Series GSE21680 Query DataSets for GSE21680
Status Public on May 06, 2010
Title Zebrafish embryos: exposure to 3,4-dichloraniline, 2,4-dichlorophenol, pentachlorophenol, and cadmium chloride
Organism Danio rerio
Experiment type Expression profiling by array
Summary Large-scale toxicogenomic screening approaches offer great promise for generating a bias-free, system-wide view of toxicological effects and modes-of-action of chemicals and ecotoxicants. Early applications of microarray technology have identified relatively small groups of responding genes with which to define new targets for analysis by conventional means. We have trialled a more intensive approach to the design and interpretation of array experiments incorporating a balanced interwoven ANOVA design with higher levels of biological replication, a more thorough analysis of errors and false discovery rates, and an analysis of response patterns using gene networks. Zebrafish embryos were exposed to ecotoxicants representing different classes - 2,4-dichlorophenol (DCP), 3,4-dichloroaniline (DCA), pentachlorophenol (PCP), and cadmium chloride - at low concentrations producing a developmental disturbance to 10% of embryos, and half of this dose. Extracted RNA was then analysed on microarrays. Analysis revealed responses of 3000–5000 genes, which is 10–1000 times greater than previously reported, with significance at lower levels of fold-change. Some gene responses were common to multiple toxicants and others that were restricted to just one or two toxicants. The gene expression profiles for the different toxicants were distinctive, and analysis using network-based packages provides a high level of detail of affected processes, some of which were novel. This approach provides a more highly refined view of toxic effects, from which meaningful patterns of response can be discerned and related to functional deficits, and from which more reliable indicators of toxicological effect can be predicted.
 
Overall design Interwoven loop design consisting of 12 separate conditions - two exposure concentrations plus control for each of the four toxicants - using six replicates for each conditions, each array was hybridised with independent replicates from each of two conditions resulting in 72 samples on 36 arrays
 
Contributor(s) Sawle AD, Cossins AR, Whale G, Wit E
Citation(s) 20702589
Submission date May 05, 2010
Last update date Apr 15, 2014
Contact name Ashley Sawle
Organization name University of Liverpool
Department Biosciences
Lab Laboratory for Environmental Gene Regulation
Street address Crown Street
City Liverpool
ZIP/Postal code L69 7ZB
Country United Kingdom
 
Platforms (1)
GPL10387 UoL-LMF Zebrafish 17K v1.0
Samples (36)
GSM540804 Zebrafish embryo: DCA Low dose Replicate 1 versus DCA Control Replicate 2
GSM540805 Zebrafish embryo: DCP Low dose Replicate 2 versus DCP Control Replicate 1
GSM540806 Zebrafish embryo: DCP Control Replicate 2 versus DCP Low dose Replicate 3
Relations
BioProject PRJNA125837

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
GSE21680_RAW.tar 43.3 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table
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