ArticleNucleic acids research2020
A comprehensive rat transcriptome built from large scale RNA-seq-based annotation.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 31 citations in OpenAlex.
- Characterizing Infiltrating Macrophages in Intracranial Aneurysm with IA Animal Models and Spatial Transcriptomics.Translational stroke research · 2026Review
- Manual curation for improved genome annotation of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni).PloS one · 2026Article
- Integrated analysis reveals NLRC4 as a potential biomarker in sepsis pathogenesis.Genes and immunity · 2024Article
- Rat Models of Hormone Receptor-Positive Breast Cancer.Journal of mammary gland biology and neoplasia · 2024Review
- Transcriptomic profiling of early synucleinopathy in rats induced with preformed fibrils.NPJ Parkinson's disease · 2024Article
- Gene expression variability across cells and species shapes the relationship between renal resident macrophages and infiltrated macrophages.BMC bioinformatics · 2023Article
- Integrative analysis of Iso-Seq and RNA-seq reveals dynamic changes of alternative promoter, alternative splicing and alternative polyadenylation during Angiotensin II-induced senescence in rat primary aortic endothelial cells.Frontiers in genetics · 2023Article
- Comprehensive microRNA-seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats.Scientific data · 2022Article
- Generation and network analysis of an RNA-seq transcriptional atlas for the rat.NAR genomics and bioinformatics · 2022Article
- Preclinical species gene expression database: Development and meta-analysis.Frontiers in genetics · 2022Article
- Beyond Genes: Inclusion of Alternative Splicing and Alternative Polyadenylation to Assess the Genetic Architecture of Predisposition to Voluntary Alcohol Consumption in Brain of the HXB/BXH Recombinant Inbred Rat Panel.Frontiers in genetics · 2022Article
- Current status and trends in forest genomics.Forestry research · 2022Review
- Multi-Omic Approaches to Identify Genetic Factors in Metabolic Syndrome.Comprehensive Physiology · 2021Article
- Comprehensive annotation of the Chinese tree shrew genome by large-scale RNA sequencing and long-read isoform sequencing.Zoological research · 2021Article
- CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure.PLoS computational biology · 2021Article
- Alternative Animal Models of Aging Research.Frontiers in molecular biosciences · 2021Review
- A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium.Nature biotechnology · 2014Article
Corrections and comments
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Authors and funding
21 authors at 10 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rat is an important model organism in biomedical research for studying human disease mechanisms and treatments, but its annotated transcriptome is far from complete. We constructed a Rat Transcriptome Re-annotation named RTR using RNA-seq data from 320 samples in 11 different organs generated by the SEQC consortium. Totally, there are 52 807 genes and 114 152 transcripts in RTR. Transcribed regions and exons in RTR account for ∼42% and ∼6.5% of the genome, respectively. Of all 73 074 newly annotated transcripts in RTR, 34 213 were annotated as high confident coding transcripts and 24 728 as high confident long noncoding transcripts. Different tissues rather than different stages have a significant influence on the expression patterns of transcripts. We also found that 11 715 genes and 15 852 transcripts were expressed in all 11 tissues and that 849 house-keeping genes expressed different isoforms among tissues. This comprehensive transcriptome is freely available at http://www.unimd.org/rtr/. Our new rat transcriptome provides essential reference for genetics and gene expression studies in rat disease and toxicity models.
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