A comprehensive rat transcriptome built from large scale RNA-seq-based annotation Article Swipe
Xiangjun Ji
,
Peng Li
,
James C. Fuscoe
,
Geng Chen
,
Wenzhong Xiao
,
Leming Shi
,
Baitang Ning
,
Zhichao Liu
,
Huixiao Hong
,
Jun Wu
,
Jinghua Liu
,
Lei Guo
,
David P. Kreil
,
Paweł P. Łabaj
,
Liping Zhong
,
Wenjun Bao
,
Yong Huang
,
Jian He
,
Yongxiang Zhao
,
Weida Tong
,
Tieliu Shi
·
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkaa638
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkaa638
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.
Related Topics
Concepts
Transcriptome
Biology
Gene
RNA-Seq
Genetics
Genome
Computational biology
Exon
Genome project
Annotation
Gene Annotation
Gene expression
Model organism
De novo transcriptome assembly
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/nar/gkaa638
- https://academic.oup.com/nar/article-pdf/48/15/8320/33697162/gkaa638.pdf
- OA Status
- gold
- Cited By
- 30
- References
- 62
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3046937172
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W3046937172Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1093/nar/gkaa638Digital Object Identifier
- Title
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A comprehensive rat transcriptome built from large scale RNA-seq-based annotationWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
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2020Year of publication
- Publication date
-
2020-07-22Full publication date if available
- Authors
-
Xiangjun Ji, Peng Li, James C. Fuscoe, Geng Chen, Wenzhong Xiao, Leming Shi, Baitang Ning, Zhichao Liu, Huixiao Hong, Jun Wu, Jinghua Liu, Lei Guo, David P. Kreil, Paweł P. Łabaj, Liping Zhong, Wenjun Bao, Yong Huang, Jian He, Yongxiang Zhao, Weida Tong, Tieliu ShiList of authors in order
- Landing page
-
https://doi.org/10.1093/nar/gkaa638Publisher landing page
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-
https://academic.oup.com/nar/article-pdf/48/15/8320/33697162/gkaa638.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
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https://academic.oup.com/nar/article-pdf/48/15/8320/33697162/gkaa638.pdfDirect OA link when available
- Concepts
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Transcriptome, Biology, Gene, RNA-Seq, Genetics, Genome, Computational biology, Exon, Genome project, Annotation, Gene Annotation, Gene expression, Model organism, De novo transcriptome assemblyTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
30Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 1, 2024: 9, 2023: 6, 2022: 6, 2021: 7Per-year citation counts (last 5 years)
- References (count)
-
62Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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