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

• Main Authors: J. B. Taggart, J. E. Bron, S. A. Martin, Paul J. Seear, B. Høyheim, R. Talbot, S. N. Carmichael, L. A. Villeneuve, G. E. Sweeney, D. F. Houlihan, C. J. Secombes, D. R. Tocher, A. J. Teale
• Format: Other Non-Article Part of Journal/Newspaper
• Language: unknown
• Published: 2008
• Subjects: Uncategorized; IR content; Atlantic salmon; Salmo salar
• Online Access: https://figshare.com/articles/journal_contribution/A_description_of_the_origins_design_and_performance_of_the_TRAITS-SGP_Atlantic_salmon_Salmo_salar_L_cDNA_microarray/10160393

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 1.2x) 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.