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A description of the origins, design and performance of the TRAITS–SGP Atlantic salmon Salmo salar L. cDNA microarray

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Abstract:

The origins, design, fabrication and performance of an Atlantic salmon microarray are described. The microarray comprises 16 950 Atlantic salmon-derived cDNA features, printed in duplicate and mostly sourced from pre-existing expressed sequence tag (EST) collections [SALGENE and salmon genome project (SGP)] but also supplemented with cDNAs from suppression subtractive hybridization libraries and candidate genes involved in immune response, protein catabolism, lipid metabolism and the parr–smolt transformation. A preliminary analysis of a dietary lipid experiment identified a number of genes known to be involved in lipid metabolism. Significant fold change differences (as low as 1·2×) were apparent from the microarray analysis and were confirmed by quantitative real-time polymerase chain reaction analysis. The study also highlighted the potential for obtaining artefactual expression patterns as a result of cross-hybridization of similar transcripts. Examination of the robustness and sensitivity of the experimental design employed demonstrated the greater importance of biological replication over technical (dye flip) replication for identification of a limited number of key genes in the studied system. The TRAITS (TRanscriptome Analysis of Important Traits of Salmon)–salmon genome project microarray has been proven, in a number of studies, to be a powerful tool for the study of key traits of Atlantic salmon biology. It is now available for use by researchers in the wider scientific community.

Keywords: Atlantic salmon; DNA microarray; gene expression; immune response; lipid metabolism; smoltification

Document Type: Regular Paper

DOI: https://doi.org/10.1111/j.1095-8649.2008.01876.x

Affiliations: 1: Institute of Aquaculture, University of Stirling, Stirling, FK9 4LA, U.K. 2: Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Tillydrone Avenue, Aberdeen AB24 2TZ, U.K. 3: Norwegian School of Veterinary Science, BasAM-Genetics, P. O. Box 8146 Dep, NO-0033 Oslo, Norway 4: ARK-Genomics, Roslin Institute, Roslin, Midlothian EH 25 9PS, U. K. 5: School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3US, U.K.

Publication date: 2008-06-01

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