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At RTD – a comprehensive reference transcript dataset resource for accurate quantification of transcript‐specific expression in Arabidopsis thaliana
Author(s) -
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.
Publication year - 2015
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/nph.13545
Subject(s) - arabidopsis thaliana , arabidopsis , computational biology , biology , genetics , gene , mutant
SummaryRNA ‐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 (At RTD ) containing over 74 000 transcripts for use with algorithms to quantify AS transcript isoforms in RNA ‐seq. The At RTD was formed by merging transcripts from TAIR 10 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 ailfish and S almon 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 At RTD is a resource that will have immediate utility in analysing Arabidopsis RNA ‐seq data to quantify differential transcript abundance and expression.