title: AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.
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.
authors.affiliation: Informatics and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
authors.forename: Runxuan
authors.initials: R
authors.lastname: Zhang
authors.affiliation: Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee, DD2 5DA, UK.
authors.forename: Cristiane P G
authors.initials: CP
authors.lastname: Calixto
authors.affiliation: Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee, DD2 5DA, UK.
authors.forename: Nikoleta A
authors.initials: NA
authors.lastname: Tzioutziou
authors.affiliation: Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
authors.forename: Allan B
authors.initials: AB
authors.lastname: James
authors.affiliation: Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
authors.forename: Craig G
authors.initials: CG
authors.lastname: Simpson
authors.affiliation: Informatics and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.|Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee, DD2 5DA, UK.
authors.forename: Wenbin
authors.initials: W
authors.lastname: Guo
authors.affiliation: Max F. Perutz Laboratories, Medical University of Vienna, Dr Bohrgasse 9/3, 1030, Vienna, Austria.
authors.forename: Yamile
authors.initials: Y
authors.lastname: Marquez
authors.affiliation: Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190, Vienna, Austria.
authors.forename: Maria
authors.initials: M
authors.lastname: Kalyna
authors.affiliation: Computer Science Department, 1422 Computer Science, Stony Brook University, Stony Brook, NY, 11794-4400, USA.
authors.forename: Rob
authors.initials: R
authors.lastname: Patro
authors.affiliation: Computational Genomics, Universitat Pompeu Fabra, 08002, Barcelona, Spain.|Catalan Institution of Research and Advanced Studies (ICREA), 08010, Barcelona, Spain.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Eyras
authors.affiliation: Max F. Perutz Laboratories, Medical University of Vienna, Dr Bohrgasse 9/3, 1030, Vienna, Austria.
authors.forename: Andrea
authors.initials: A
authors.lastname: Barta
authors.affiliation: Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
authors.forename: Hugh G
authors.initials: HG
authors.lastname: Nimmo
authors.affiliation: Plant Sciences Division, College of Life Sciences, University of Dundee, Invergowrie, Dundee, DD2 5DA, UK.|Cell and Molecular Sciences, The James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK.
authors.forename: John W S
authors.initials: JW
authors.lastname: Brown
mesh_terms: D000465:Algorithms; D017398:Alternative Splicing; D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D066264:Datasets as Topic; D020869:Gene Expression Profiling / Q000379:methods*; D017343:Genes, Plant; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D020033:Protein Isoforms / Q000032:analysis*; D012326:RNA Splicing; D012333:RNA, Messenger / Q000032:analysis*; D012016:Reference Values; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software; D059467:Transcriptome
chemical_list: D020033:Protein Isoforms; D012333:RNA, Messenger
keywords: Arabidopsis thaliana; RNA-sequencing (RNA-seq); Sailfish; Salmon; alternative splicing; high resolution reverse transcription (HR RT)-PCR; transcripts per million