Methodology article
Spotted cotton oligonucleotide microarrays for gene expression analysis
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* Corresponding author: Joshua A Udall jaudall@byu.edu
1 Department of Plant and Animal Sciences, Brigham Young University, Provo, UT, 84062, USA
2 Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, 50011, USA
3 The Institute for Genomic Research, A Division of the J. Craig Venter Institute, 9712 Medical Center Drive, Rockville MD 20850 USA
4 Section of Molecular Cell and Developmental Biology and Institute for Cellular and Molecular Biology, University of Texas, Austin, TX, 78712, USA
5 Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, 30602, USA
6 Department of Statistics, Iowa State University, Ames, IA, 50011, USA
BMC Genomics 2007, 8:81 doi:10.1186/1471-2164-8-81
Published: 27 March 2007Additional files
Additional file 1:
Composition of the cotton oligonucleotide microarray. 22,789 oligonucleotides were designed from three separate sets of genic sequences from cotton (See Table 1). The grey boxes represent the total number of probes in each set. The hatched boxes indicate the number of probes with a putative Arabidopsis hit. The black boxes indicate the number of probes designed from singletons from their respective assemblies. The remaining boxes with dotted squares indicate the number of probes targeting transcription factors.
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Additional file 2:
Distribution of the number of matches of oligonucleotide probes to the Cotton Gene Index 8 (CGI8) assembly. All three sets were queried within the sequences of the CGI8 assembly and only a small number (1,773) of probes target (>93% percent identity) more than one CGI8 unigene indicating a potential cross-hybridization or an 'over-split' assembly for the targeted gene.
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Additional file 3:
Many of the oligonucleotides from the 2nd set were derived from contigs or singletons representing individual libraries (n = 7,319). Library totals reflect the contigs (respective library's ESTs > 90%) and singletons used to design the oligonucleotides. The two large G. raimondii libraries created from heterogeneous seedling and whole flower tissue are not illustrated.
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