title: A description of the origins, design and performance of the TRAITS-SGP Atlantic salmon Salmo salar L. cDNA microarray.
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 1.2x) 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.
authors.forename: J B
authors.initials: JB
authors.lastname: Taggart
authors.forename: J E
authors.initials: JE
authors.lastname: Bron
authors.forename: S A M
authors.initials: SA
authors.lastname: Martin
authors.forename: P J
authors.initials: PJ
authors.lastname: Seear
authors.forename: B
authors.initials: B
authors.lastname: Høyheim
authors.forename: R
authors.initials: R
authors.lastname: Talbot
authors.forename: S N
authors.initials: SN
authors.lastname: Carmichael
authors.forename: L A N
authors.initials: LA
authors.lastname: Villeneuve
authors.forename: G E
authors.initials: GE
authors.lastname: Sweeney
authors.forename: D F
authors.initials: DF
authors.lastname: Houlihan
authors.forename: C J
authors.initials: CJ
authors.lastname: Secombes
authors.forename: D R
authors.initials: DR
authors.lastname: Tocher
authors.forename: A J
authors.initials: AJ
authors.lastname: Teale