Zhang, R. et al. (2017) A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing. Nucleic Acids Research, 45(9), pp. 5061-5073. (doi: 10.1093/nar/gkx267) (PMID:28402429) (PMCID:PMC5435985)
|
Text
139918.pdf - Published Version Available under License Creative Commons Attribution. 1MB |
Abstract
Alternative splicing generates multiple transcript and protein isoforms from the same gene and thus is important in gene expression regulation. To date, RNA-sequencing (RNA-seq) is the standard method for quantifying changes in alternative splicing on a genome-wide scale. Understanding the current limitations of RNA-seq is crucial for reliable analysis and the lack of high quality, comprehensive transcriptomes for most species, including model organisms such as Arabidopsis, is a major constraint in accurate quantification of transcript isoforms. To address this, we designed a novel pipeline with stringent filters and assembled a comprehensive Reference Transcript Dataset for Arabidopsis (AtRTD2) containing 82,190 non-redundant transcripts from 34 212 genes. Extensive experimental validation showed that AtRTD2 and its modified version, AtRTD2-QUASI, for use in Quantification of Alternatively Spliced Isoforms, outperform other available transcriptomes in RNA-seq analysis. This strategy can be implemented in other species to build a pipeline for transcript-level expression and alternative splicing analyses.
| 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., Marquez, Y., Venhuizen, P., Tzioutziou, N. A., Guo, W., Spensley, M., Entizne, J. C., Lewandowska, D., ten Have, S., Frei dit Frey, N., Hirt, H., James, A. B., Nimmo, H. G., Barta, A., Kalyna, M., and Brown, J. W.S. |
| College/School: | College of Medical Veterinary and Life Sciences > School of Molecular Biosciences |
| Journal Name: | Nucleic Acids Research |
| Publisher: | Oxford University Press |
| ISSN: | 0305-1048 |
| ISSN (Online): | 1362-4962 |
| Published Online: | 11 April 2017 |
| Copyright Holders: | Copyright © 2017 The Authors |
| First Published: | First published in Nucleic Acids Research 45(9):5061-5073 |
| Publisher Policy: | Reproduced under a Creative Commons License |
University Staff: Request a correction | Enlighten Editors: Update this record
Altmetric
Altmetric