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Nat Commun. 2014;5:3230. doi: 10.1038/ncomms4230.

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages.

Author information

  • 11] Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China [2].
  • 21] National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA [2].
  • 3Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China.
  • 4Functional Genomics Core, Beckman Research Institute, City of Hope, Duarte, California 91010, USA.
  • 5Army Institute of Public Health, U.S. Army Public Health Command, Aberdeen Proving Ground, Maryland 21010, USA.
  • 6Computation Biology and Bioinformatics, IP & Science, Thomson Reuters, London EC1N 8JS, UK.
  • 7SAS Institute Inc., Cary, North Carolina 27513, USA.
  • 8National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
  • 9Expression Analysis Inc., Durham, North Carolina 27713, USA.
  • 10The Center for Bioinformatics and The Institute of Biomedical Sciences, College of Life Science, Shanghai 200241, China.
  • 11Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
  • 12Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina 27157, USA.
  • 13Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA.
  • 14Department of Physiology & Biophysics and the Institute for Computational Biomedicine, Cornell University, New York, New York 10021, USA.
  • 15National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA.
  • 161] Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, Shanghai 201203, China [2] National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA [3] Fudan-Zhangjiang Center for Clinical Genomics and Zhangjiang Center for Translational Medicine, Shanghai 201203, China.
  • 17Center for Genomics and Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA.

Abstract

The rat has been used extensively as a model for evaluating chemical toxicities and for understanding drug mechanisms. However, its transcriptome across multiple organs, or developmental stages, has not yet been reported. Here we show, as part of the SEQC consortium efforts, a comprehensive rat transcriptomic BodyMap created by performing RNA-Seq on 320 samples from 11 organs of both sexes of juvenile, adolescent, adult and aged Fischer 344 rats. We catalogue the expression profiles of 40,064 genes, 65,167 transcripts, 31,909 alternatively spliced transcript variants and 2,367 non-coding genes/non-coding RNAs (ncRNAs) annotated in AceView. We find that organ-enriched, differentially expressed genes reflect the known organ-specific biological activities. A large number of transcripts show organ-specific, age-dependent or sex-specific differential expression patterns. We create a web-based, open-access rat BodyMap database of expression profiles with crosslinks to other widely used databases, anticipating that it will serve as a primary resource for biomedical research using the rat model.

PMID:
24510058
[PubMed - in process]
PMCID:
PMC3926002
Free PMC Article
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