AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana
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- dc.contributor.author Zhang, Runxuanca
- dc.contributor.author Calixto, Cristiane P. G.ca
- dc.contributor.author Tzioutziou, Nikoleta A.ca
- dc.contributor.author James, Allan B.ca
- dc.contributor.author Simpson, Craig G.ca
- dc.contributor.author Guo, Wenbinca
- dc.contributor.author Marquez, Yamileca
- dc.contributor.author Kalyna, Mariaca
- dc.contributor.author Patro, Robca
- dc.contributor.author Eyras Jiménez, Eduardoca
- dc.contributor.author Barta, Andreaca
- dc.contributor.author Nimmo, Hugh G.ca
- dc.contributor.author Brown, John W. S.ca
- dc.date.accessioned 2016-02-15T14:21:01Z
- dc.date.available 2016-02-15T14:21:01Z
- dc.date.issued 2015
- dc.description.abstract RNA-sequencing (RNA-seq) allows global gene expression analysis at the individual transcript level. Accurate quantification of transcript variants generated by alternative splicing (AS) remains a challenge. We have developed a comprehensive, nonredundant Arabidopsis reference transcript dataset (AtRTD) containing over 74 000 transcripts for use with algorithms to quantify AS transcript isoforms in RNA-seq. The AtRTD was formed by merging transcripts from TAIR10 and novel transcripts identified in an AS discovery project. We have estimated transcript abundance in RNA-seq data using the transcriptome-based alignment-free programmes Sailfish and Salmon and have validated quantification of splicing ratios from RNA-seq by high resolution reverse transcription polymerase chain reaction (HR RT-PCR). Good correlations between splicing ratios from RNA-seq and HR RT-PCR were obtained demonstrating the accuracy of abundances calculated for individual transcripts in RNA-seq. The AtRTD is a resource that will have immediate utility in analysing Arabidopsis RNA-seq data to quantify differential transcript abundance and expression.ca
- dc.description.sponsorship This research was supported by funding from the Biotechnology and Biological Sciences Research Council (BBSRC) (BB/K006568/1 to J.W.S.B.; BB/K006835/1 to H.G.N.), the Scottish Government Rural and Environment Science and Analytical Services division (RESAS) and by the Austrian Science Fund (FWF) (P26333) to M.K. and (DK W1207) to A.B. The authors acknowledge the European Alternative Splicing Network of Excellence (EURASNET), LSHG-CT-2005-518238 for catalysing important collaborations.
- dc.format.mimetype application/pdfca
- dc.identifier.citation Zhang R, Calixto CP, Tzioutziou NA, James AB, Simpson CG, Guo W et al. AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana. New Phytologist. 2015;208(1):96-101. DOI: 10.1111/nph.13545ca
- dc.identifier.doi http://dx.doi.org/10.1111/nph.13545
- dc.identifier.issn 0028-646X
- dc.identifier.uri http://hdl.handle.net/10230/25817
- dc.language.iso engca
- dc.publisher Wileyca
- dc.relation.ispartof New Phytologist. 2015;208(1):96-101
- dc.rights © 2015 New Phytologist Trust. This is an open access article under the terms of the Creative Commons Attribution License, which permits use,/ndistribution and reproduction in any medium, provided the original work is properly cited.ca
- dc.rights.accessRights info:eu-repo/semantics/openAccessca
- dc.rights.uri http://creativecommons.org/licenses/by/4.0/ca
- dc.subject.keyword Alternative splicing
- dc.subject.keyword Arabidopsis thaliana
- dc.subject.keyword High resolution reverse transcription (HR RT)-PCR, RNA-sequencing (RNA-seq)
- dc.subject.keyword SAILFISH
- dc.subject.keyword SALMON
- dc.subject.keyword Transcripts per million
- dc.subject.other RNAca
- dc.title AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thalianaca
- dc.type info:eu-repo/semantics/articleca
- dc.type.version info:eu-repo/semantics/publishedVersionca