A Brassica Exon Array for Whole-Transcript Gene Expression Profiling
Publication Date
September 16, 2010
Journal
PLOS ONE
Authors
Christopher G. Love, Neil S. Graham, Seosamh Ó Lochlainn, Helen C. Bowen, et al
Volume
5
Issue
9
Pages
e12812
DOI
https://dx.plos.org/10.1371/journal.pone.0012812
Publisher URL
http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0012812
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/20862292
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2940909
Europe PMC
http://europepmc.org/abstract/MED/20862292
Web of Science
000281864100026
Scopus
77958561137
Mendeley
http://www.mendeley.com/research/brassica-exon-array-wholetranscript-gene-expression-profiling
Events
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Mendeley | Further Information

{"title"=>"A Brassica exon array for whole-transcript gene expression profiling", "type"=>"journal", "authors"=>[{"first_name"=>"Christopher G.", "last_name"=>"Love", "scopus_author_id"=>"7102181353"}, {"first_name"=>"Neil S.", "last_name"=>"Graham", "scopus_author_id"=>"7201454141"}, {"first_name"=>"Seosamh Ó", "last_name"=>"Lochlainn", "scopus_author_id"=>"36601078900"}, {"first_name"=>"Helen C.", "last_name"=>"Bowen", "scopus_author_id"=>"7004285199"}, {"first_name"=>"Sean T.", "last_name"=>"May", "scopus_author_id"=>"7202919184"}, {"first_name"=>"Philip J.", "last_name"=>"White", "scopus_author_id"=>"7404090046"}, {"first_name"=>"Martin R.", "last_name"=>"Broadley", "scopus_author_id"=>"7003414033"}, {"first_name"=>"John P.", "last_name"=>"Hammond", "scopus_author_id"=>"25421867400"}, {"first_name"=>"Graham J.", "last_name"=>"King", "scopus_author_id"=>"35253705300"}], "year"=>2010, "source"=>"PLoS ONE", "identifiers"=>{"issn"=>"19326203", "scopus"=>"2-s2.0-77958561137", "pui"=>"359839108", "doi"=>"10.1371/journal.pone.0012812", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "sgr"=>"77958561137", "pmid"=>"20862292"}, "id"=>"2e2f548b-e6aa-3cad-a6ca-d006aa4e8f31", "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.", "link"=>"http://www.mendeley.com/research/brassica-exon-array-wholetranscript-gene-expression-profiling", "reader_count"=>22, "reader_count_by_academic_status"=>{"Researcher"=>9, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>1, "Student > Master"=>1, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_user_role"=>{"Researcher"=>9, "Student > Ph. D. Student"=>7, "Student > Postgraduate"=>1, "Student > Master"=>1, "Student > Bachelor"=>3, "Professor"=>1}, "reader_count_by_subject_area"=>{"Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>1, "Agricultural and Biological Sciences"=>19, "Psychology"=>1}, "reader_count_by_subdiscipline"=>{"Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>19}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>1}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"United States"=>1}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/830703"], "description"=>"<p>Density plots of (a, b, e, f) mean probe-set signals from the 135 k exon array, and (c, d, g, h) mean probe signal values from the 95 k 60-mer array, for (a, b, c, d) leaf and (e, f, g, h) root tissue of <i>Brassica rapa</i> R-o-18 (n = 3).</p>", "links"=>[], "tags"=>["probe"], "article_id"=>501064, "categories"=>["Infectious Diseases", "Genetics"], "users"=>["Christopher G. Love", "Neil S. Graham", "Seosamh Ó Lochlainn", "Helen C. Bowen", "Sean T. May", "Philip J. White", "Martin R. Broadley", "John P. Hammond", "Graham J. King"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012812.g002", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dynamic_range_of_probe_set_signals_/501064", "title"=>"Dynamic range of probe set signals.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-16 00:17:44"}
  • {"files"=>["https://ndownloader.figshare.com/files/830931"], "description"=>"<p>Gene Ontology (GO) categories of overrepresented (p<0.05) genes whose transcript abundance was greater (a) or less (b) in leaves compared with roots of <i>Brassica rapa</i> R-o-18. GO categories are based on putative gene orthology between <i>Brassica</i> and <i>Arabidopsis thaliana</i> (TAIR v9). The three portions of each Venn figure represent the Affymetrix GeneChip® Brassica Exon 1.0 ST Array (135 k Brassica Exon array, n = 3), the Agilent 95 k Brassica 60-mer array (n = 3), and <i>A. thaliana</i> data from the AtGen Express data set for leaves (leaf, 7 days old, ATGE_5 A–C, GEO accession GSE5630) and roots (root, 7 days old, ATGE_3A–C, GEO accession GSE5631; Schmid et al., 2005).</p>", "links"=>[], "tags"=>["ontology", "categories", "tissue-specific"], "article_id"=>501289, "categories"=>["Infectious Diseases", "Genetics"], "users"=>["Christopher G. Love", "Neil S. Graham", "Seosamh Ó Lochlainn", "Helen C. Bowen", "Sean T. May", "Philip J. White", "Martin R. Broadley", "John P. Hammond", "Graham J. King"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012812.g004", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Gene_Ontology_categories_of_tissue_specific_transcripts_/501289", "title"=>"Gene Ontology categories of tissue-specific transcripts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-16 00:21:29"}
  • {"files"=>["https://ndownloader.figshare.com/files/831091"], "description"=>"<p>Mean gene-normalised probe-set signals for leaf (open circle) and root tissue (closed circle) of four transcripts (a-rres037505, b-rres046838, c-rres107548, d-rres004182).</p>", "links"=>[], "tags"=>["alternatively", "spliced"], "article_id"=>501454, "categories"=>["Infectious Diseases", "Genetics"], "users"=>["Christopher G. Love", "Neil S. Graham", "Seosamh Ó Lochlainn", "Helen C. Bowen", "Sean T. May", "Philip J. White", "Martin R. Broadley", "John P. Hammond", "Graham J. King"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012812.g005", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Potential_alternatively_spliced_transcripts_/501454", "title"=>"Potential alternatively spliced transcripts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-16 00:24:14"}
  • {"files"=>["https://ndownloader.figshare.com/files/831226"], "description"=>"<p>Components of the Brassica 135 k unigene set.</p>", "links"=>[], "tags"=>["brassica", "135", "unigene"], "article_id"=>501585, "categories"=>["Infectious Diseases", "Genetics"], "users"=>["Christopher G. Love", "Neil S. Graham", "Seosamh Ó Lochlainn", "Helen C. Bowen", "Sean T. May", "Philip J. White", "Martin R. Broadley", "John P. Hammond", "Graham J. King"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012812.t001", "stats"=>{"downloads"=>3, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Components_of_the_Brassica_135_k_unigene_set_/501585", "title"=>"Components of the Brassica 135 k unigene set.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-16 00:26:25"}
  • {"files"=>["https://ndownloader.figshare.com/files/830812"], "description"=>"<p>Relationship between mean normalised probe-set signals from the 135 k Brassica Exon array and mean normalised probe signal values from the 95 k Brassica 60-mer array, for a) leaf and b) root tissue of <i>Brassica rapa</i> R-o-18 (n = 3). Relationships between probe-sets from the 135 k Brassica Exon array and probes from the 95 k Brassica 60-mer array are based on shared <i>Arabidopsis thaliana</i> gene models.</p>", "links"=>[], "tags"=>["transcript", "abundance"], "article_id"=>501172, "categories"=>["Infectious Diseases", "Genetics"], "users"=>["Christopher G. Love", "Neil S. Graham", "Seosamh Ó Lochlainn", "Helen C. Bowen", "Sean T. May", "Philip J. White", "Martin R. Broadley", "John P. Hammond", "Graham J. King"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012812.g003", "stats"=>{"downloads"=>4, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_of_transcript_abundance_on_different_array_platforms_/501172", "title"=>"Comparison of transcript abundance on different array platforms.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-16 00:19:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/830600"], "description"=>"<p>Data were collated from several sources. Collated dataset were filtered to remove redundancy and orientated where possible. Unigenes passing the Affymetrix quality thresholds were tiled onto the array.</p>", "links"=>[], "tags"=>["affymetrix", "brassica", "exon", "st"], "article_id"=>500949, "categories"=>["Infectious Diseases", "Genetics"], "users"=>["Christopher G. Love", "Neil S. Graham", "Seosamh Ó Lochlainn", "Helen C. Bowen", "Sean T. May", "Philip J. White", "Martin R. Broadley", "John P. Hammond", "Graham J. King"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012812.g001", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Work_flow_of_the_Affymetrix_GeneChip_174_Brassica_Exon_1_0_ST_Array_data_selection_pipeline_/500949", "title"=>"Work flow of the Affymetrix GeneChip® Brassica Exon 1.0 ST Array, data selection pipeline.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2010-09-16 00:15:49"}
  • {"files"=>["https://ndownloader.figshare.com/files/413155", "https://ndownloader.figshare.com/files/413198"], "description"=>"<div><p>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 <em>Brassica</em>, which are typified by segmental duplications containing paralogous genes and/or allopolyploidy. Available sequence data were sampled from the <em>Brassica</em> 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<sup>−5</sup>, with ≤98% sequence identity. The 135 k Brassica Exon Array was validated by quantifying transcriptome differences between leaf and root tissue from a reference <em>Brassica rapa</em> line (R-o-18), and categorisation by Gene Ontologies (GO) based on gene orthology with <em>Arabidopsis thaliana</em>. 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 <a href=\"http://www.brassica.info/BrassEnsembl/index.html\">http://www.brassica.info/BrassEnsembl/index.html</a>.</p></div>", "links"=>[], "tags"=>["exon", "whole-transcript", "profiling"], "article_id"=>141622, "categories"=>["Cancer", "Genetics"], "users"=>["Christopher G. Love", "Neil S. Graham", "Seosamh Ó Lochlainn", "Helen C. Bowen", "Sean T. May", "Philip J. White", "Martin R. Broadley", "John P. Hammond", "Graham J. King"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0012812.s001", "https://dx.doi.org/10.1371/journal.pone.0012812.s002"], "stats"=>{"downloads"=>11, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/A_Brassica_Exon_Array_for_Whole_Transcript_Gene_Expression_Profiling/141622", "title"=>"A <em>Brassica</em> Exon Array for Whole-Transcript Gene Expression Profiling", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2010-09-16 00:27:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/831176"], "description"=>"<p>Summary statistics for the probe set withing the Affymetrix GeneChip® Brassica Exon 1.0 ST Array.</p>", "links"=>[], "tags"=>["probe", "withing", "affymetrix", "brassica", "exon", "st"], "article_id"=>501525, "categories"=>["Infectious Diseases", "Genetics"], "users"=>["Christopher G. Love", "Neil S. Graham", "Seosamh Ó Lochlainn", "Helen C. Bowen", "Sean T. May", "Philip J. White", "Martin R. Broadley", "John P. Hammond", "Graham J. King"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0012812.t002", "stats"=>{"downloads"=>1, "page_views"=>3, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_statistics_for_the_probe_set_withing_the_Affymetrix_GeneChip_174_Brassica_Exon_1_0_ST_Array_/501525", "title"=>"Summary statistics for the probe set withing the Affymetrix GeneChip® Brassica Exon 1.0 ST Array.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2010-09-16 00:25:25"}

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