AtRTD - a comprehensive reference transcript dataset resource foraccurate quantification of transcript-specific expression in Arabidopsis thaliana

作者：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^*

来源：NEW PHYTOLOGIST, 2015, 208(1): 96-101.

DOI：10.1111/nph.13545

• alternative splicing
• Arabidopsis thaliana
• high resolution reverse transcription (HR RT)-PCR
• RNA-sequencing (RNA-seq)
• Sailfish
• Salmon
• transcripts per million

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 74000 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.

• 出版日期2015-10