Journal article
A Brassica exon array for whole-transcript gene expression profiling
PloS ONE, Vol.5(9), e12812
2010
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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/index.html.
Details
- Title
- A Brassica exon array for whole-transcript gene expression profiling
- Creators
- Christopher G Love - Rothamsted Research, UKNeil S Graham - University of NottinghamSeosamh Ó Lochlainn - University of NottinghamHelen C Bowen - University of Warwick, UKSean T May - University of NottinghamPhilip J White - Scottish Crop Research Institute, UKMartin R Broadley - University of NottinghamJohn P Hammond - University of WarwickGraham J King - Rothamsted Research, UK
- Publication Details
- PloS ONE, Vol.5(9), e12812
- Publisher
- Public Library of Science
- Identifiers
- 1175; 991012821099802368
- Copyright
- © 2010 Love et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License.
- Academic Unit
- Faculty of Science and Engineering; Science; Southern Cross Plant Science
- Language
- English
- Resource Type
- Journal article