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Selected Publication:

Zhang, R; Calixto, CP; Tzioutziou, NA; James, AB; Simpson, CG; Guo, W; Marquez, Y; Kalyna, M; Patro, R; Eyras, E; Barta, A; Nimmo, HG; Brown, JW; .
(2015): AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.
New Phytol. 2015; 208(1):96-101 FullText FullText_BOKU

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 74000 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.
Authors BOKU Wien:
Kalyna Mariya
BOKU Gendermonitor:


Find related publications in this database (Keywords)
alternative splicing
Arabidopsis thaliana
high resolution reverse transcription (HR RT)-PCR
RNA-sequencing (RNA-seq)
Sailfish
Salmon
transcripts per million


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