Please note that we have stopped the regular imports of Gene Expression Omnibus (GEO) data into ArrayExpress. This may not be the latest version of this experiment.

E-GEOD-38042 - The zebrafish embryo as an alternative model for the evaluation of liver toxicity using histopathology and expression profiling

Status
Released on 15 May 2015, last updated on 19 August 2015
Organism
Danio rerio
Samples (2)
Protocols (3)
Description
The zebrafish is as a powerful vertebrate model system for modeling human disease including liver pathology. In ZFE, hepatic responses can be expected after exposure to hepatotoxicants, because hepatocytes are present from 36-hpf and at 72-hpf the liver is fully functioning. These characteristics make the whole ZFE an attractive alternative model for compound-induced hepatotoxicity screening. Therefore, the main objective of this study is to further strengthen the applicability of whole ZFE as an alternative model for hepatotoxicity testing, with a special focus on the ability to identify gene expression responses in whole ZFE that are suggestive of hepatotoxicity. Deep sequence technology is applied to assess whether hepatotoxicity-specific transcripts that are identified in livers of hepatotoxicant treated adult zebrafish can be detected in whole ZFE as well. Whole zebrafish embryo and adult zebrafish are exposed for 48 hours to human hepatotoxicants. Afterwards, the adult liver is dissected and snap frozen untill processed for RNA isolation. The whole zebrafish embryos are pooled, one sample consists of 15 embryos, and are also snap frozen untill processed for RNA isolation. For every sample RNA is isolated according to the protocol of de Jong et al (2009). and then equal amounts of every sample is pooled. The two pools (one for the adult zebrafish liver, the other for the whole zebrafish embryo) are sequenced.
Experiment type
RNA-seq of coding RNA 
Contacts
Anne S Kienhuis, Bob van de Water, Evert-Jan van den Brandhof, Herman P Spaink, Jeroen A Pennings, Leo M van der Ven, Marianne Roodbergen, Marja Driessen, Tessa E Pronk
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-38042.idf.txt
Sample and data relationshipE-GEOD-38042.sdrf.txt
Processed data (1)E-GEOD-38042.processed.1.zip
Links