title: Spotted cotton oligonucleotide microarrays for gene expression analysis.
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.
  
  
  CONCLUSIONS
  The cotton oligonucleotide microarray provides a reproducible platform for transcription profiling in cotton, and is made publicly available through http://cottonevolution.info.
authors: Department of Plant and Animal Sciences, Brigham Young University, Provo, UT 84062, USA. jaudall@byu.edu
authors: Joshua A
authors: JA
authors: Udall
authors: Lex E
authors: LE
authors: Flagel
authors: Foo
authors: F
authors: Cheung
authors: Andrew W
authors: AW
authors: Woodward
authors: Ran
authors: R
authors: Hovav
authors: Ryan A
authors: RA
authors: Rapp
authors: Jordan M
authors: JM
authors: Swanson
authors: Jinsuk J
authors: JJ
authors: Lee
authors: Alan R
authors: AR
authors: Gingle
authors: Dan
authors: D
authors: Nettleton
authors: Christopher D
authors: CD
authors: Town
authors: Z Jeffrey
authors: ZJ
authors: Chen
authors: Jonathan F
authors: JF
authors: Wendel
mesh_terms: D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D017343:Genes, Plant; D003368:Gossypium / Q000235:genetics*; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis