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Spotted Cotton Oligonucleotide Microarrays for Gene Expression Analysis
BMC Genomics
  • Joshua A. Udall, Brigham Young University - Provo
  • Lex E. Flagel, Iowa State University
  • Foo Cheung, J. Craig Venter Institute
  • Andrew W. Woodard, University of Texas at Austin
  • Ran Hovav, Iowa State University
  • Ryan Adam Rapp, Iowa State University
  • Jordan M. Swanson, Iowa State University
  • Jinsuk J. Lee, University of Texas at Austin
  • Alan R. Gingle, University of Georgia
  • Dan Nettleton, Iowa State University
  • Christopher D. Town, J. Craig Venter Institute
  • Z. Jeffrey Chen, University of Texas at Austin
  • Jonathan F. Wendel, Iowa State University
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Published Version
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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. 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. The cotton oligonucleotide microarray provides a reproducible platform for transcription profiling in cotton, and is made publicly available through

This article is from BMC Genomics 8 (2007): 81, doi:10.1186/1471-2164-8-81. Posted with permission.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
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Joshua A. Udall, et al.
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Citation Information
Joshua A. Udall, Lex E. Flagel, Foo Cheung, Andrew W. Woodard, et al.. "Spotted Cotton Oligonucleotide Microarrays for Gene Expression Analysis" BMC Genomics Vol. 8 (2007) p. 1 - 8
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