ArticleThe New phytologist2015
AtRTD - a comprehensive reference transcript dataset resource for accurate quantification of transcript-specific expression in Arabidopsis thaliana.
Article in The New phytologist, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- PotatoRTD and TomatoRTD: Comprehensive Reference Transcript Datasets for Accurate Transcriptome Analysis and Isoform Discovery.Scientific data · 2026Article
- The Integration of Data from Different Long-Read Sequencing Platforms Enhances Proteoform Characterization in Arabidopsis.Plants (Basel, Switzerland) · 2023Article
- BaRTv2: a highly resolved barley reference transcriptome for accurate transcript-specific RNA-seq quantification.The Plant journal : for cell and molecular biology · 2022Article
- The value of genotype-specific reference for transcriptome analyses in barley.Life science alliance · 2022Article
- High-quality reference transcriptome construction improves RNA-seq quantification inFrontiers in genetics · 2022Article
- 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists.RNA biology · 2021Article
- A consensus-based ensemble approach to improve transcriptome assembly.BMC bioinformatics · 2021Article
- EORNA, a barley gene and transcript abundance database.Scientific data · 2021Article
- Targeting alternative splicing by RNAi: from the differential impact on splice variants to triggering artificial pre-mRNA splicing.Nucleic acids research · 2021Article
- Integrated multi-omics framework of the plant response to jasmonic acid.Nature plants · 2020Article
- BaRTv1.0: an improved barley reference transcript dataset to determine accurate changes in the barley transcriptome using RNA-seq.BMC genomics · 2019Article
- A junction coverage compatibility score to quantify the reliability of transcript abundance estimates and annotation catalogs.Life science alliance · 2019Article
- Thermo-Sensitive Alternative Splicing ofFrontiers in plant science · 2019Article
- Genome-Wide Identification of Splicing Quantitative Trait Loci (sQTLs) in Diverse Ecotypes ofFrontiers in plant science · 2019Article
- The cyclin-dependent kinase G group defines a thermo-sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU2AF65A.The Plant journal : for cell and molecular biology · 2018Article
- SUPPA2: fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions.Genome biology · 2018Article
- Adaptation of iCLIP to plants determines the binding landscape of the clock-regulated RNA-binding protein AtGRP7.Genome biology · 2017Article
- Article
- A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing.Nucleic acids research · 2017Article
- Light Regulation of Alternative Pre-mRNA Splicing in Plants.Photochemistry and photobiology · 2017Review
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13 authors.
Funding
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.
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