title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages.
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.
authors: 1] 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].
authors: Ying
authors: Y
authors: Yu
authors: 1] National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA [2].
authors: James C
authors: JC
authors: Fuscoe
authors: 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.
authors: Chen
authors: C
authors: Zhao
authors: Functional Genomics Core, Beckman Research Institute, City of Hope, Duarte, California 91010, USA.
authors: Chao
authors: C
authors: Guo
authors: 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.
authors: Meiwen
authors: M
authors: Jia
authors: 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.
authors: Tao
authors: T
authors: Qing
authors: Army Institute of Public Health, U.S. Army Public Health Command, Aberdeen Proving Ground, Maryland 21010, USA.
authors: Desmond I
authors: DI
authors: Bannon
authors: Computation Biology and Bioinformatics, IP & Science, Thomson Reuters, London EC1N 8JS, UK.
authors: Lee
authors: L
authors: Lancashire
authors: SAS Institute Inc., Cary, North Carolina 27513, USA.
authors: Wenjun
authors: W
authors: Bao
authors: 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.
authors: Tingting
authors: T
authors: Du
authors: 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.
authors: Heng
authors: H
authors: Luo
authors: National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
authors: Zhenqiang
authors: Z
authors: Su
authors: Expression Analysis Inc., Durham, North Carolina 27713, USA.
authors: Wendell D
authors: WD
authors: Jones
authors: National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
authors: Carrie L
authors: CL
authors: Moland
authors: National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
authors: William S
authors: WS
authors: Branham
authors: National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
authors: Feng
authors: F
authors: Qian
authors: National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
authors: Baitang
authors: B
authors: Ning
authors: National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
authors: Yan
authors: Y
authors: Li
authors: National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
authors: Huixiao
authors: H
authors: Hong
authors: National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
authors: Lei
authors: L
authors: Guo
authors: National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
authors: Nan
authors: N
authors: Mei
authors: The Center for Bioinformatics and The Institute of Biomedical Sciences, College of Life Science, Shanghai 200241, China.
authors: Tieliu
authors: T
authors: Shi
authors: Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
authors: Kevin Y
authors: KY
authors: Wang
authors: SAS Institute Inc., Cary, North Carolina 27513, USA.
authors: Russell D
authors: RD
authors: Wolfinger
authors: Computation Biology and Bioinformatics, IP & Science, Thomson Reuters, London EC1N 8JS, UK.
authors: Yuri
authors: Y
authors: Nikolsky
authors: Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina 27157, USA.
authors: Stephen J
authors: SJ
authors: Walker
authors: Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA.
authors: Penelope
authors: P
authors: Duerksen-Hughes
authors: Department of Physiology & Biophysics and the Institute for Computational Biomedicine, Cornell University, New York, New York 10021, USA.
authors: Christopher E
authors: CE
authors: Mason
authors: National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
authors: Weida
authors: W
authors: Tong
authors: National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA.
authors: Jean
authors: J
authors: Thierry-Mieg
authors: National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA.
authors: Danielle
authors: D
authors: Thierry-Mieg
authors: 1] 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.
authors: Leming
authors: L
authors: Shi
authors: Center for Genomics and Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA.
authors: Charles
authors: C
authors: Wang
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D005260:Female; D020869:Gene Expression Profiling; D008297:Male; D020033:Protein Isoforms / Q000378:metabolism; D011916:Rats, Inbred F344 / Q000254:growth & development / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D012727:Sex Characteristics; D059467:Transcriptome
chemical_list: D020033:Protein Isoforms