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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.
- Arabidopsis thaliana
- Alternative splicing
- High resolution reverse transcription (HR RT)-PCR
- RNA-sequencing (RNA-seq)
- Transcripts per million
ASJC Scopus subject areas
- Plant Science
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- 1 Finished
Computational analysis and method development for high throughput transcriptomics and transcriptional regulatory inference in plantsAuthor: Guo, W., 2018
Student thesis: Doctoral Thesis › Doctor of Philosophy