Expansion of the genomics research on Atlantic salmon Salmo salar L. project (GRASP) microarray tools

Authors

  • K. R. VonSchalburg,

    1. * Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5 Canada, Ocean Sciences Centre, Memorial University of Newfoundland, St John’s, Newfoundland, A1C 5S7 Canada and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada
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  • G. A. Cooper,

    1. * Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5 Canada, Ocean Sciences Centre, Memorial University of Newfoundland, St John’s, Newfoundland, A1C 5S7 Canada and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada
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  • J. Leong,

    1. * Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5 Canada, Ocean Sciences Centre, Memorial University of Newfoundland, St John’s, Newfoundland, A1C 5S7 Canada and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada
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  • A. Robb,

    1. * Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5 Canada, Ocean Sciences Centre, Memorial University of Newfoundland, St John’s, Newfoundland, A1C 5S7 Canada and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada
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  • R. Lieph,

    1. * Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5 Canada, Ocean Sciences Centre, Memorial University of Newfoundland, St John’s, Newfoundland, A1C 5S7 Canada and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada
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  • M. L. Rise,

    1. * Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5 Canada, Ocean Sciences Centre, Memorial University of Newfoundland, St John’s, Newfoundland, A1C 5S7 Canada and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada
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  • W. S. Davidson,

    1. * Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5 Canada, Ocean Sciences Centre, Memorial University of Newfoundland, St John’s, Newfoundland, A1C 5S7 Canada and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada
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  • B. F. Koop

    Corresponding author
    1. * Centre for Biomedical Research, University of Victoria, Victoria, British Columbia, V8W 3N5 Canada, Ocean Sciences Centre, Memorial University of Newfoundland, St John’s, Newfoundland, A1C 5S7 Canada and Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, V5A 1S6 Canada
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§Author to whom correspondence should be addressed at present address: Department of Biology, University of Victoria, P. O. Box 3020, Victoria, British Columbia, V8W 3N5 Canada. Tel.: (250) 472 4071; fax: (250) 472 4075; email: bkoop@uvic.ca

Abstract

Salmonids are the most widely studied group of fish, and in the last few years, genomics technologies have begun to contribute to this rich biology. The first salmonid microarrays appeared in 2004 and since then several dozen studies have demonstrated the utility of genomic approaches. The widespread use of the genomics research on Atlantic salmon project 16 k array and greatly expanded genome resources have led to the development of an experimental 5 k oligo (70-mer) array and a 32 k cDNA microarray in the near future. In this paper, the authors examined some of the procedures used in the development of past arrays and reexamined them in light of new genomic data available. Some preliminary control experiments of the new 5 k array were investigated that examine oligo designs based on distance from the polyA tail, the effects of mismatches and cross-species hybridization specificity. Beneficial approaches are also identified in the development of the new 32 k cDNA array.

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