A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing.
Nucleic Acids Res
; 45(9): 5061-5073, 2017 May 19.
Article
em En
| MEDLINE
| ID: mdl-28402429
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.
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Base de dados:
MEDLINE
Assunto principal:
Genes de Insetos
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Arabidopsis
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Processamento Alternativo
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Transcriptoma
Idioma:
En
Ano de publicação:
2017
Tipo de documento:
Article