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

Zhang, R. et al. (2015) AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana. New Phytologist, 208(1), pp. 96-101. (doi: 10.1111/nph.13545) (PMID:26111100) (PMCID:PMC4744958)

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.

• Item Type: Articles
• Status: Published
• Refereed: Yes
• Glasgow Author(s) Enlighten ID: Nimmo, Professor Hugh and James, Dr Allan
• Authors: Zhang, R., Calixto, C. P. G., Tzioutziou, N. A., James, A. B., Simpson, C. G., Guo, W., Marquez, Y., Kalyna, M., Patro, R., Eyras, E., Barta, A., Nimmo, H. G., and Brown, J. W. S.
• College/School: College of Medical Veterinary and Life Sciences > School of Molecular Biosciences
• Journal Name: New Phytologist
• Publisher: Wiley
• ISSN: 0028-646X
• ISSN (Online): 1469-8137
• Copyright Holders: Copyright © 2015 The Authors
• First Published: First published in New Phytologist
• Publisher Policy: Reproduced under a Creative Commons License

Project Code	Award No	Project Name	Principal Investigator	Funder's Name	Funder Ref	Lead Dept
60704	1	Mechanisms and function of alternative splicing in the plant circadian clock	Hugh Nimmo	Biotechnology and Biological Sciences Research Council (BBSRC)	BB/K006835/1	RI MOLECULAR CELL & SYSTEMS BIOLOGY