A Brassica exon array for whole-transcript gene expression profiling.
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 Ge...
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Public Library of Science (PLoS)
2010-09-01
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| Series: | PLoS ONE |
| Online Access: | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0012812&type=printable |
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| author | Christopher G Love Neil S Graham Seosamh O Lochlainn Helen C Bowen Sean T May Philip J White Martin R Broadley John P Hammond Graham J King |
| author_facet | Christopher G Love Neil S Graham Seosamh O Lochlainn Helen C Bowen Sean T May Philip J White Martin R Broadley John P Hammond Graham J King |
| author_sort | Christopher G Love |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-4980ff1eb9bf4e609acd98352f295a7c |
| institution | OA Journals |
| issn | 1932-6203 |
| language | English |
| publishDate | 2010-09-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj-art-4980ff1eb9bf4e609acd98352f295a7c2025-08-20T02:01:58ZengPublic Library of Science (PLoS)PLoS ONE1932-62032010-09-0159e1281210.1371/journal.pone.0012812A Brassica exon array for whole-transcript gene expression profiling.Christopher G LoveNeil S GrahamSeosamh O LochlainnHelen C BowenSean T MayPhilip J WhiteMartin R BroadleyJohn P HammondGraham J KingAffymetrix 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.https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0012812&type=printable |
| spellingShingle | Christopher G Love Neil S Graham Seosamh O Lochlainn Helen C Bowen Sean T May Philip J White Martin R Broadley John P Hammond Graham J King A Brassica exon array for whole-transcript gene expression profiling. PLoS ONE |
| title | A Brassica exon array for whole-transcript gene expression profiling. |
| title_full | A Brassica exon array for whole-transcript gene expression profiling. |
| title_fullStr | A Brassica exon array for whole-transcript gene expression profiling. |
| title_full_unstemmed | A Brassica exon array for whole-transcript gene expression profiling. |
| title_short | A Brassica exon array for whole-transcript gene expression profiling. |
| title_sort | brassica exon array for whole transcript gene expression profiling |
| url | https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0012812&type=printable |
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