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dc.contributor.authorZhang, Runxuan
dc.contributor.authorCalixto, Cristiane P. G.
dc.contributor.authorMarquez, Yamile
dc.contributor.authorVenhuizen, Peter
dc.contributor.authorTzioutziou, Nikoleta A.
dc.contributor.authorGuo, Wenbin
dc.contributor.authorSpensley, Mark
dc.contributor.authorEntizne, Juan Carlos
dc.contributor.authorLewandowska, Dominika
dc.contributor.authorten Have, Sara
dc.contributor.authorFrei dit Frey, Nicolas
dc.contributor.authorHirt, Heribert
dc.contributor.authorJames, Allan B.
dc.contributor.authorNimmo, Hugh G.
dc.contributor.authorBarta, Andrea
dc.contributor.authorKalyna, Maria
dc.contributor.authorBrown, John W. S.
dc.date.accessioned2017-05-04T06:39:20Z
dc.date.available2017-05-04T06:39:20Z
dc.date.issued2017-04-11
dc.identifier.citationZhang R, Calixto CPG, Marquez Y, Venhuizen P, Tzioutziou NA, et al. (2017) A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Research. Available: http://dx.doi.org/10.1093/nar/gkx267.
dc.identifier.issn0305-1048
dc.identifier.issn1362-4962
dc.identifier.doi10.1093/nar/gkx267
dc.identifier.doi10.1101/051938
dc.identifier.urihttp://hdl.handle.net/10754/623319
dc.description.abstractAlternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34 212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.
dc.description.sponsorshipBiotechnology and Biological Sciences Research Council (BBSRC) [BB/K013661/1 and BB/K006568/1 to J.B.; BB/K006835/1 to H.N.]; Scottish Government Rural and Environment Science and Analytical Services division (RESAS) [to J.B. and R.Z.]; Austrian Science Fund (FWF) [P26333 to M.K., DK W1207 to A.B.]; LABEX Saclay Plant Sciences [to H.H.]; BBSRC EASTBIO PhD studentships (to N.T. and J.C.); European Alternative Splicing Network of Excellence (EURASNET) [LSHG-CT-2005-518238] for catalyzing important collaborations. Funding for open access charge: University of Dundee.
dc.publisherOxford University Press (OUP)
dc.relation.urlhttps://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx267
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.titleA high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing
dc.typeArticle
dc.contributor.departmentBiological and Environmental Science and Engineering (BESE) Division
dc.contributor.departmentCenter for Desert Agriculture
dc.contributor.departmentHirt Lab
dc.contributor.departmentPlant Science
dc.contributor.departmentPlant Science Program
dc.identifier.journalNucleic Acids Research
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionInformatics and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
dc.contributor.institutionPlant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee DD2 5DA, UK
dc.contributor.institutionMax F. Perutz Laboratories, Medical University of Vienna, Dr. Bohrgasse 9/3, 1030 Vienna, Austria
dc.contributor.institutionEMBL/CRG Research Unit in Systems Biology, Centre for Genomic Regulation (CRG), 88 Dr. Aiguader, Barcelona 08003, Spain
dc.contributor.institutionThe Donnelly Centre, University of Toronto, 160 College Street, Toronto, Ontario, Canada
dc.contributor.institutionCell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK
dc.contributor.institutionCentre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
dc.contributor.institutionInstitute of Plant Sciences Paris Saclay, INRA-CNRS-UEVE, Orsay 91405, France
dc.contributor.institutionLaboratoire de Recherche en Sciences V´eg´etales, UMR5546, Universit´e Toulouse 3, CNRS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326, Castanet Tolosan, France
dc.contributor.institutionInstitute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
dc.contributor.institutionDepartment of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences - BOKU, Muthgasse 18, 1190 Vienna, Austria
kaust.personHirt, Heribert
refterms.dateFOA2018-06-14T04:30:52Z
dc.date.published-online2017-04-11
dc.date.published-print2017-05-19


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This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Except where otherwise noted, this item's license is described as This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.