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A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages.
Yu, Ying; Fuscoe, James C; Zhao, Chen; Guo, Chao; Jia, Meiwen; Qing, Tao; Bannon, Desmond I; Lancashire, Lee; Bao, Wenjun; Du, Tingting; Luo, Heng; Su, Zhenqiang; Jones, Wendell D; Moland, Carrie L; Branham, William S; Qian, Feng; Ning, Baitang; Li, Yan; Hong, Huixiao; Guo, Lei; Mei, Nan; Shi, Tieliu; Wang, Kevin Y; Wolfinger, Russell D; Nikolsky, Yuri; Walker, Stephen J; Duerksen-Hughes, Penelope; Mason, Christopher E; Tong, Weida; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Shi, Leming; Wang, Charles.
Afiliación
  • Yu Y; 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].
  • Fuscoe JC; 1] National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA [2].
  • Zhao C; 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.
  • Guo C; Functional Genomics Core, Beckman Research Institute, City of Hope, Duarte, California 91010, USA.
  • Jia M; 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.
  • Qing T; 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.
  • Bannon DI; Army Institute of Public Health, U.S. Army Public Health Command, Aberdeen Proving Ground, Maryland 21010, USA.
  • Lancashire L; Computation Biology and Bioinformatics, IP & Science, Thomson Reuters, London EC1N 8JS, UK.
  • Bao W; SAS Institute Inc., Cary, North Carolina 27513, USA.
  • Du T; 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.
  • Luo H; 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.
  • Su Z; National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
  • Jones WD; Expression Analysis Inc., Durham, North Carolina 27713, USA.
  • Moland CL; National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
  • Branham WS; National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
  • Qian F; National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
  • Ning B; National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
  • Li Y; National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
  • Hong H; National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
  • Guo L; National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
  • Mei N; National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
  • Shi T; The Center for Bioinformatics and The Institute of Biomedical Sciences, College of Life Science, Shanghai 200241, China.
  • Wang KY; Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
  • Wolfinger RD; SAS Institute Inc., Cary, North Carolina 27513, USA.
  • Nikolsky Y; Computation Biology and Bioinformatics, IP & Science, Thomson Reuters, London EC1N 8JS, UK.
  • Walker SJ; Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences, Winston-Salem, North Carolina 27157, USA.
  • Duerksen-Hughes P; Department of Basic Sciences, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA.
  • Mason CE; Department of Physiology & Biophysics and the Institute for Computational Biomedicine, Cornell University, New York, New York 10021, USA.
  • Tong W; National Center for Toxicological Research, Food and Drug Administration, Jefferson, Arkansas 92079, USA.
  • Thierry-Mieg J; National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA.
  • Thierry-Mieg D; National Center for Biotechnology Information, National Institutes of Health, Bethesda, Maryland 20894, USA.
  • Shi L; 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, Ar
  • Wang C; Center for Genomics and Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University, Loma Linda, California 92350, USA.
Nat Commun ; 5: 3230, 2014.
Article en En | MEDLINE | ID: mdl-24510058
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.
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Ratas Endogámicas F344 / Transcriptoma Tipo de estudio: Prognostic_studies Límite: Animals Idioma: En Revista: Nat Commun Asunto de la revista: BIOLOGIA / CIENCIA Año: 2014 Tipo del documento: Article
Texto completo
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Ratas Endogámicas F344 / Transcriptoma Tipo de estudio: Prognostic_studies Límite: Animals Idioma: En Revista: Nat Commun Asunto de la revista: BIOLOGIA / CIENCIA Año: 2014 Tipo del documento: Article