Unknown,Transcriptomics,Genomics,Proteomics

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Zebrafish presenillin1 mutant transcriptome

ABSTRACT: Gene expression profile comparing 17-month old wild-type with psen1hu2547 zebrafish. Total RNA from 3-4 brains of 17-month old adult psen1hu2547 or WT fish was extracted using RNeasy mini columns (Qiagen) and quality-checked using NanoDrop 1000 (Thermo Scientific) and formaldehyde gel electrophoresis. cDNA was generated and labeled with Cy3 or Cy5-CTP using the low RNA input linear amplification kit (Perkin-Elmer). Upon purification and fragmentation, labeled cRNA was hybridized to the zebrafish 22K 60-mer oligonucleotide microarray (G2518A-001, Agilent Technologies, Santa Clara, CA, USA) at 65ÂºC for 17 hours. Three independent biological repeats were performed.

ORGANISM(S): Danio rerio

SUBMITTER: Judith Paridaen

PROVIDER: E-GEOD-62083 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description: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. 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

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Zebrafish presenillin1 mutant transcriptome

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