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    Spotted cotton oligonucleotide microarrays for gene expression analysis

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    Author
    Udall, Joshua
    Flagel, Lex
    Cheung, Foo
    Woodward, Andrew
    Hovav, Ran
    Rapp, Ryan
    Swanson, Jordan
    Lee, Jinsuk
    Gingle, Alan
    Nettleton, Dan
    Town, Christopher
    Chen, Z. J.
    Wendel, Jonathan
    Show allShow less
    Affiliation
    Department of Plant and Animal Sciences, Brigham Young University, Provo, UT, 84062, USA
    Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
    The Institute for Genomic Research, A Division of the J. Craig Venter Institute, 9712 Medical Center Drive, Rockville MD 20850 USA
    Section of Molecular Cell and Developmental Biology and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, 78712, USA
    Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, 30602, USA
    Department of Statistics, Iowa State University, Ames, IA, 50011, USA
    Issue Date
    2007
    
    Metadata
    Show full item record
    Publisher
    BioMed Central
    Citation
    BMC Genomics 2007, 8:81 doi:10.1186/1471-2164-8-81
    Journal
    BMC Genomics
    Rights
    © 2007 Udall et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
    Collection Information
    This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
    Abstract
    BACKGROUND:Microarrays offer a powerful tool for diverse applications plant biology and crop improvement. Recently, two comprehensive assemblies of cotton ESTs were constructed based on three Gossypium species. Using these assemblies as templates, we describe the design and creation and of a publicly available oligonucleotide array for cotton, useful for all four of the cultivated species.RESULTS:Synthetic oligonucleotide probes were generated from exemplar sequences of a global assembly of 211,397 cotton ESTs derived from >50 different cDNA libraries representing many different tissue types and tissue treatments. A total of 22,787 oligonucleotide probes are included on the arrays, optimized to target the diversity of the transcriptome and previously studied cotton genes, transcription factors, and genes with homology to Arabidopsis. A small portion of the oligonucleotides target unidentified protein coding sequences, thereby providing an element of gene discovery. Because many oligonucleotides were based on ESTs from fiber-specific cDNA libraries, the microarray has direct application for analysis of the fiber transcriptome. To illustrate the utility of the microarray, we hybridized labeled bud and leaf cDNAs from G. hirsutum and demonstrate technical consistency of results.CONCLUSION:The cotton oligonucleotide microarray provides a reproducible platform for transcription profiling in cotton, and is made publicly available through http://cottonevolution.info webcite.
    EISSN
    1471-2164
    DOI
    10.1186/1471-2164-8-81
    Version
    Final published version
    Additional Links
    http://www.biomedcentral.com/1471-2164/8/81
    ae974a485f413a2113503eed53cd6c53
    10.1186/1471-2164-8-81
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