Zhang, RunxuanCalixto, Cristiane P. G.Tzioutziou, Nikoleta A.James, Allan B.Simpson, Craig G.Guo, WenbinMarquez, YamileKalyna, MariaPatro, RobEyras Jiménez, EduardoBarta, AndreaNimmo, Hugh G.Brown, John W. S.2016-02-152016-02-152015Zhang 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.135450028-646Xhttp://hdl.handle.net/10230/25817RNA-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.application/pdfeng© 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.RNAinfo:eu-repo/semantics/articlehttp://dx.doi.org/10.1111/nph.13545Alternative splicingArabidopsis thalianaHigh resolution reverse transcription (HR RT)-PCR, RNA-sequencing (RNA-seq)SAILFISHSALMONTranscripts per millioninfo:eu-repo/semantics/openAccess