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A Brassica exon array for whole-transcript gene expression profiling

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Love, Christopher G., Graham, Neil S. , Ó Lochlainn, Seosamh, Bowen, Helen C., May, Sean T., White, Philip J., Broadley, Martin R., Hammond, John P. and King , Graham J. (2010) A Brassica exon array for whole-transcript gene expression profiling. PL o S One, Vol.5 (No.9). doi:10.1371/journal.pone.0012812

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Official URL: http://dx.doi.org/10.1371/journal.pone.0012812

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Abstract

Affymetrix GeneChip® arrays are used widely to study transcriptional changes in response to developmental and environmental stimuli. GeneChip® arrays comprise multiple 25-mer oligonucleotide probes per gene and retain certain advantages over direct sequencing. For plants, there are several public GeneChip® arrays whose probes are localised primarily in 3′ exons. Plant whole-transcript (WT) GeneChip® arrays are not yet publicly available, although WT resolution is needed to study complex crop genomes such as Brassica, which are typified by segmental duplications containing paralogous genes and/or allopolyploidy. Available sequence data were sampled from the Brassica A and C genomes, and 142,997 gene models identified. The assembled gene models were then used to establish a comprehensive public WT exon array for transcriptomics studies. The Affymetrix GeneChip® Brassica Exon 1.0 ST Array is a 5 µM feature size array, containing 2.4 million 25-base oligonucleotide probes representing 135,201 gene models, with 15 probes per gene distributed among exons. Discrimination of the gene models was based on an E-value cut-off of 1E−5, with ≤98% sequence identity. The 135 k Brassica Exon Array was validated by quantifying transcriptome differences between leaf and root tissue from a reference Brassica rapa line (R-o-18), and categorisation by Gene Ontologies (GO) based on gene orthology with Arabidopsis thaliana. Technical validation involved comparison of the exon array with a 60-mer array platform using the same starting RNA samples. The 135 k Brassica Exon Array is a robust platform. All data relating to the array design and probe identities are available in the public domain and are curated within the BrassEnsembl genome viewer at http://www.brassica.info/BrassEnsembl/in​dex.html .

Item Type: Journal Article
Subjects: Q Science > QK Botany
Q Science > QH Natural history > QH426 Genetics
Divisions: Faculty of Science > Life Sciences (2010- ) > Warwick HRI (2004-2010)
Library of Congress Subject Headings (LCSH): Brassica -- Genetics, Brassica -- Genome mapping, Exons (Genetics), Genetic transcription
Journal or Publication Title: PL o S One
Publisher: Public Library of Science
ISSN: 1932-6203
Official Date: 16 September 2010
Dates:
DateEvent
16 September 2010Published
Volume: Vol.5
Number: No.9
DOI: 10.1371/journal.pone.0012812
Status: Peer Reviewed
Access rights to Published version: Open Access
Funder: Biotechnology and Biological Sciences Research Council (Great Britain) (BBSRC), Scotland. Environment and Rural Affairs Dept. (SEERAD)
Grant number: BBG013969 (BBSRC)

Data sourced from Thomson Reuters' Web of Knowledge

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