Spotted cotton oligonucleotide microarrays for gene expression analysis

Persistent Link:
http://hdl.handle.net/10150/610000
Title:
Spotted cotton oligonucleotide microarrays for gene expression analysis
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
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
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

Full metadata record

DC FieldValue Language
dc.contributor.authorUdall, Joshuaen
dc.contributor.authorFlagel, Lexen
dc.contributor.authorCheung, Fooen
dc.contributor.authorWoodward, Andrewen
dc.contributor.authorHovav, Ranen
dc.contributor.authorRapp, Ryanen
dc.contributor.authorSwanson, Jordanen
dc.contributor.authorLee, Jinsuken
dc.contributor.authorGingle, Alanen
dc.contributor.authorNettleton, Danen
dc.contributor.authorTown, Christopheren
dc.contributor.authorChen, Z. J.en
dc.contributor.authorWendel, Jonathanen
dc.date.accessioned2016-05-20T08:56:05Z-
dc.date.available2016-05-20T08:56:05Z-
dc.date.issued2007en
dc.identifier.citationBMC Genomics 2007, 8:81 doi:10.1186/1471-2164-8-81en
dc.identifier.doi10.1186/1471-2164-8-81en
dc.identifier.urihttp://hdl.handle.net/10150/610000-
dc.description.abstractBACKGROUND: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.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/8/81en
dc.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)en
dc.titleSpotted cotton oligonucleotide microarrays for gene expression analysisen
dc.typeArticleen
dc.identifier.eissn1471-2164en
dc.contributor.departmentDepartment of Plant and Animal Sciences, Brigham Young University, Provo, UT, 84062, USAen
dc.contributor.departmentDepartment of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USAen
dc.contributor.departmentThe Institute for Genomic Research, A Division of the J. Craig Venter Institute, 9712 Medical Center Drive, Rockville MD 20850 USAen
dc.contributor.departmentSection of Molecular Cell and Developmental Biology and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, 78712, USAen
dc.contributor.departmentCenter for Applied Genetic Technologies, University of Georgia, Athens, Georgia, 30602, USAen
dc.contributor.departmentDepartment of Statistics, Iowa State University, Ames, IA, 50011, USAen
dc.identifier.journalBMC Genomicsen
dc.description.collectioninformationThis 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.en
dc.eprint.versionFinal published versionen
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