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

Ying Yu, James C. Fuscoe, Chen Zhao, Chao Guo, Meiwen Jia, Tao Qing, Desmond I. Bannon, Lee Lancashire, Wenjun Bao, Tingting Du, Heng Luo, Zhenqiang Su, Wendell D. Jones, Carrie L. Moland, William S. Branham, Feng Qian, Baitang Ning, Yan Li, Huixiao Hong, Lei Guo, Nan Mei, Tieliu Shi, Kevin Y. Wang, Russell D. Wolfinger, Yuri Nikolsky, Stephen J. Walker, Penelope Duerksen-Hughes, Christopher E. Mason, Weida Tong, Jean Thierry-Mieg, Danielle Thierry-Mieg, Leming Shi () and Charles Wang ()
Additional contact information
Ying Yu: Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University
James C. Fuscoe: National Center for Toxicological Research, Food and Drug Administration
Chen Zhao: Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University
Chao Guo: Functional Genomics Core, Beckman Research Institute, City of Hope
Meiwen Jia: Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University
Tao Qing: Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University
Desmond I. Bannon: Army Institute of Public Health, U.S. Army Public Health Command, Aberdeen Proving Ground
Lee Lancashire: Computation Biology and Bioinformatics, IP & Science, Thomson Reuters
Wenjun Bao: SAS Institute Inc.
Tingting Du: Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University
Heng Luo: Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University
Zhenqiang Su: National Center for Toxicological Research, Food and Drug Administration
Wendell D. Jones: Expression Analysis Inc.
Carrie L. Moland: National Center for Toxicological Research, Food and Drug Administration
William S. Branham: National Center for Toxicological Research, Food and Drug Administration
Feng Qian: National Center for Toxicological Research, Food and Drug Administration
Baitang Ning: National Center for Toxicological Research, Food and Drug Administration
Yan Li: National Center for Toxicological Research, Food and Drug Administration
Huixiao Hong: National Center for Toxicological Research, Food and Drug Administration
Lei Guo: National Center for Toxicological Research, Food and Drug Administration
Nan Mei: National Center for Toxicological Research, Food and Drug Administration
Tieliu Shi: The Center for Bioinformatics and The Institute of Biomedical Sciences, College of Life Science
Kevin Y. Wang: Johns Hopkins University School of Medicine
Russell D. Wolfinger: SAS Institute Inc.
Yuri Nikolsky: Computation Biology and Bioinformatics, IP & Science, Thomson Reuters
Stephen J. Walker: Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences
Penelope Duerksen-Hughes: School of Medicine, Loma Linda University
Christopher E. Mason: Cornell University
Weida Tong: National Center for Toxicological Research, Food and Drug Administration
Jean Thierry-Mieg: National Center for Biotechnology Information, National Institutes of Health
Danielle Thierry-Mieg: National Center for Biotechnology Information, National Institutes of Health
Leming Shi: Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University
Charles Wang: School of Medicine, Loma Linda University

Nature Communications, 2014, vol. 5, issue 1, 1-11

Abstract: 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.

Date: 2014
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DOI: 10.1038/ncomms4230

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