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New Phytol. 2015 Oct;208(1):96-101. doi: 10.1111/nph.13545. Epub 2015 Jun 25.

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

Author information

1
Informatics and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
2
Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee, DD2 5DA, UK.
3
Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
4
Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
5
Max F. Perutz Laboratories, Medical University of Vienna, Dr Bohrgasse 9/3, 1030, Vienna, Austria.
6
Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
7
Computer Science Department, 1422 Computer Science, Stony Brook University, Stony Brook, NY, 11794-4400, USA.
8
Computational Genomics, Universitat Pompeu Fabra, 08002, Barcelona, Spain.
9
Catalan Institution of Research and Advanced Studies (ICREA), 08010, Barcelona, Spain.

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.

KEYWORDS:

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

PMID:
26111100
PMCID:
PMC4744958
DOI:
10.1111/nph.13545
[Indexed for MEDLINE]
Free PMC Article

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