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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
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/index.html .
| Item Type: | Journal Article | ||||
|---|---|---|---|---|---|
| Subjects: | Q Science > QK Botany Q Science > QH Natural history > QH426 Genetics |
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| 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: |
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| 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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