title: A Brassica exon array for whole-transcript gene expression profiling.
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.
authors.affiliation: Rothamsted Research, Harpenden, UK.
authors.forename: Christopher G
authors.initials: CG
authors.lastname: Love
authors.forename: Neil S
authors.initials: NS
authors.lastname: Graham
authors.forename: Seosamh
authors.initials: S
authors.lastname: O Lochlainn
authors.forename: Helen C
authors.initials: HC
authors.lastname: Bowen
authors.forename: Sean T
authors.initials: ST
authors.lastname: May
authors.forename: Philip J
authors.initials: PJ
authors.lastname: White
authors.forename: Martin R
authors.initials: MR
authors.lastname: Broadley
authors.forename: John P
authors.initials: JP
authors.lastname: Hammond
authors.forename: Graham J
authors.initials: GJ
authors.lastname: King
mesh_terms: D001937:Brassica / Q000235:genetics*; D005091:Exons; D020869:Gene Expression Profiling / Q000379:methods*; D018745:Genome, Plant; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D014158:Transcription, Genetic