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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.

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      Most cited references 38

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      Basic local alignment search tool.

      A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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        A new mathematical model for relative quantification in real-time RT-PCR.

         M. Pfaffl (2001)
        Use of the real-time polymerase chain reaction (PCR) to amplify cDNA products reverse transcribed from mRNA is on the way to becoming a routine tool in molecular biology to study low abundance gene expression. Real-time PCR is easy to perform, provides the necessary accuracy and produces reliable as well as rapid quantification results. But accurate quantification of nucleic acids requires a reproducible methodology and an adequate mathematical model for data analysis. This study enters into the particular topics of the relative quantification in real-time RT-PCR of a target gene transcript in comparison to a reference gene transcript. Therefore, a new mathematical model is presented. The relative expression ratio is calculated only from the real-time PCR efficiencies and the crossing point deviation of an unknown sample versus a control. This model needs no calibration curve. Control levels were included in the model to standardise each reaction run with respect to RNA integrity, sample loading and inter-PCR variations. High accuracy and reproducibility (<2.5% variation) were reached in LightCycler PCR using the established mathematical model.
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          Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research.

          We present here Blast2GO (B2G), a research tool designed with the main purpose of enabling Gene Ontology (GO) based data mining on sequence data for which no GO annotation is yet available. B2G joints in one application GO annotation based on similarity searches with statistical analysis and highlighted visualization on directed acyclic graphs. This tool offers a suitable platform for functional genomics research in non-model species. B2G is an intuitive and interactive desktop application that allows monitoring and comprehension of the whole annotation and analysis process. Blast2GO is freely available via Java Web Start at http://www.blast2go.de. http://www.blast2go.de -> Evaluation.
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            Author and article information

            Affiliations
            [*]Institute of Aquaculture, University of StirlingStirling, FK9 4LA, U.K.
            []Scottish Fish Immunology Research Centre, School of Biological Sciences, University of AberdeenTillydrone Avenue, Aberdeen AB24 2TZ, U.K.
            [§]School of Biosciences, Cardiff UniversityMuseum Avenue, Cardiff CF10 3US, U.K.
            []Norwegian School of Veterinary ScienceBasAM-Genetics, P. O. Box 8146 Dep, NO-0033 Oslo, Norway
            [#]ARK-Genomics, Roslin InstituteRoslin, Midlothian EH 25 9PS, U. K.
            Author notes
            †Author to whom correspondence should be addressed. Tel.: +44 1786 467927; fax: + 44 1784 472133; email: j.b.taggart@123456stir.ac.uk
            [‖]

            Present address: British Antarctic Survey, Biological Sciences Division, High Cross, Madingley Road, Cambridge CB3 0ET, U.K.

            Journal
            J Fish Biol
            jfb
            Journal of Fish Biology
            Blackwell Publishing Ltd
            0022-1112
            1095-8649
            June 2008
            : 72
            : 9
            : 2071-2094
            2610384
            19125201
            10.1111/j.1095-8649.2008.01876.x
            © The Authors Journal compilation © 2008 The Fisheries Society of the British Isles

            Re-use of this article is permitted in accordance with the Creative Commons Deed, Attribution 2.5, which does not permit commercial exploitation.

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