ArticleNucleic acids research2017
A high quality Arabidopsis transcriptome for accurate transcript-level analysis of alternative splicing.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 147 papers.
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Who cites it
147 citing papers in PubMed, 318 citations in OpenAlex.
- Domain compositions of Arabidopsis Toll/Interleukin-1 Receptor/Resistance domain-containing TX14 proteins affect localization and induction of the hypersensitive response.Journal of experimental botany · 2026Article
- PotatoRTD and TomatoRTD: Comprehensive Reference Transcript Datasets for Accurate Transcriptome Analysis and Isoform Discovery.Scientific data · 2026Article
- Hexokinase 1 facilitates post-germinative seedling growth through its catalytic function.The Plant journal : for cell and molecular biology · 2026Article
- MASQ: A multiplex qPCR platform for quantitative alternative splicing analysis in clinical specimens.Molecular therapy. Nucleic acids · 2026Article
- Plant hormone and peptide signaling converge in the genetic network regulating cambium activation in Arabidopsis roots.The Plant cell · 2026Article
- Global profiling of alternative splicing landscapes in response to cold stress during the cotyledon stage in cotton.BMC genomics · 2026Article
- Alternative splicing: an underexplored layer in immune receptor regulation, systemic resistance and priming.Frontiers in plant science · 2026Article
- Transcriptome and weighted gene co-enrichment analysis revealed modules and candidate genes associated with barley response to low potassium stress.Frontiers in plant science · 2026Article
- Article
- Conservation and Remodeling of Alternative Splicing Landscapes in the Evolution ofPlants (Basel, Switzerland) · 2025Article
- At-RS31 orchestrates hierarchical cross-regulation of splicing factors and integrates alternative splicing with TOR-ABA pathways.The New phytologist · 2025Article
- Exploring Alternative Splicing in Response to Salinity: A Tissue-Level Comparative Analysis UsingPlants (Basel, Switzerland) · 2025Article
- Sporophyte-directed gametogenesis in Arabidopsis.Nature plants · 2025Article
- A barley pan-transcriptome reveals layers of genotype-dependent transcriptional complexity.Nature genetics · 2025Article
- Integrated morphophysiological, transcriptomic, and metabolomic data uncover the molecular mechanism of environmental adaptation ofFrontiers in plant science · 2025Article
- ZmHSFA2B self-regulatory loop is critical for heat tolerance in maize.Plant biotechnology journal · 2025Article
- The nuclear exosome subunit HEN2 acts independently of the core exosome to assist transcription in Arabidopsis.Plant physiology · 2024Article
- The Negative Regulators of the Basal Defence WRKY7, WRKY11 and WRKY17 Modulate the Jasmonic Acid Pathway and an Alternative Splicing Regulatory Network in Response to Pseudomonas syringae in Arabidopsis thaliana.Molecular plant pathology · 2024Article
- Differences in alternative splicing and their potential underlying factors between animals and plants.Journal of advanced research · 2024Review
- Transcriptional and hormonal profiling uncovers the interactions between plant developmental stages and RNA virus infection.The Journal of general virology · 2024Article
87 more citing papers are in PubMed but not listed here.
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Authors and funding
17 authors at 7 institutions in 6 countries.
Funding
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.