A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing
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- dc.contributor.author Zhang, Runxuanca
- dc.contributor.author Calixto, Cristiane P. G.ca
- dc.contributor.author Márquez, Yamileca
- dc.contributor.author Venhuizen, Peterca
- dc.contributor.author Tzioutziou, Nikoleta A.ca
- dc.contributor.author Guo, Wenbinca
- dc.contributor.author Spensley, Markca
- dc.contributor.author Entizne, Juan Carlosca
- dc.contributor.author Lewandowska, Dominikaca
- dc.contributor.author Have, Sara Tenca
- dc.contributor.author Frey, Nicolas Freiditca
- dc.contributor.author Hirt, Heribertca
- dc.contributor.author James, Allan B.ca
- dc.contributor.author Nimmo, Hugh G.ca
- dc.contributor.author Barta, Andreaca
- dc.contributor.author Kalyna, Mariaca
- dc.contributor.author Brown, John W. S.ca
- dc.date.accessioned 2018-06-28T07:40:29Z
- dc.date.available 2018-06-28T07:40:29Z
- dc.date.issued 2017
- dc.description.abstract Alternative 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.format.mimetype application/pdf
- dc.identifier.citation Zhang R, Calixto CPG, Marquez Y, Venhuizen P, Tzioutziou NA, Guo W et al. A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Res. 2017 May 19;45(9):5061-5073. DOI: 10.1093/nar/gkx267
- dc.identifier.doi http://dx.doi.org/10.1093/nar/gkx267
- dc.identifier.issn 0305-1048
- dc.identifier.uri http://hdl.handle.net/10230/34992
- dc.language.iso eng
- dc.publisher Oxford University Pressca
- dc.relation.ispartof Nucleic Acids Res. 2017 May 19;45(9):5061-5073
- dc.rights © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. 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.
- dc.rights.accessRights info:eu-repo/semantics/openAccess
- dc.rights.uri http://creativecommons.org/licenses/by/4.0/
- dc.subject.keyword Alternative splicing
- dc.subject.keyword Arabidopsis
- dc.subject.keyword Sequence analysis
- dc.subject.keyword Proteomics
- dc.title A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicingca
- dc.type info:eu-repo/semantics/article
- dc.type.version info:eu-repo/semantics/publishedVersion