AtRTD – a comprehensive reference transcript dataset resource for accurate quantification of transcript‐specific expression in Arabidopsis thaliana. Issue 1 (25th June 2015)

• Record Type: Journal Article
• Authors: Zhang, Runxuan; Calixto, Cristiane P. G.; Tzioutziou, Nikoleta A.; James, Allan B.; Simpson, Craig G.; Guo, Wenbin; Marquez, Yamile; Kalyna, Maria; Patro, Rob; Eyras, Eduardo; Barta, Andrea; Nimmo, Hugh G.; Brown, John W. S.
• Is Part Of: New phytologist. Volume 208:Issue 1(2015:Oct. 01)
• Page Start: 96
• Page End: 101
• Publication Date: 2015-06-25
• Subjects: Botany -- Periodicals; 580
• DOI: 10.1111/nph.13545
• Languages: English
• ISSNs: 0028-646X

Abstract

<abstract abstract-type="main" id="nph13545-abs-0001"> <title>Summary</title> <p> <list id="nph13545-list-0001" list-type="bullet"> <list-item> <p>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.</p> </list-item> <list-item> <p>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 S<sc>ailfish</sc> and S<sc>almon</sc> and have validated quantification of splicing ratios from RNA‐seq by high resolution reverse transcription polymerase chain reaction (HR RT‐PCR).</p> </list-item> <list-item> <p>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.</p> </list-item> <list-item> <p>The AtRTD is a resource that will have immediate utility in analysing Arabidopsis RNA‐seq data to quantify differential transcript abundance and expression.</p> </list-item> </list> </p> </abstract>