A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
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 tran...
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| Published in | Nature communications Vol. 5; no. 1; p. 3230 |
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| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
London
Nature Publishing Group UK
10.02.2014
Nature Publishing Group Nature Pub. Group |
| Subjects | |
| Online Access | Get full text |
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| 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.
Gene expression is highly variable between tissues, and changes during development and with age. Here, the authors provide a comprehensive RNA-Seq analysis of the rat transcriptome, spanning eleven organs, four developmental stages and both sexes. |
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| AbstractList | 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.
Gene expression is highly variable between tissues, and changes during development and with age. Here, the authors provide a comprehensive RNA-Seq analysis of the rat transcriptome, spanning eleven organs, four developmental stages and both sexes. 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. 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.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. |
| ArticleNumber | 3230 |
| Author | Branham, William S. Wang, Kevin Y. Wolfinger, Russell D. Jones, Wendell D. Walker, Stephen J. Shi, Leming Bao, Wenjun Mei, Nan Su, Zhenqiang Qing, Tao Bannon, Desmond I. Li, Yan Yu, Ying Lancashire, Lee Zhao, Chen Hong, Huixiao Shi, Tieliu Mason, Christopher E. Guo, Lei Ning, Baitang Du, Tingting Duerksen-Hughes, Penelope Fuscoe, James C. Jia, Meiwen Qian, Feng Thierry-Mieg, Jean Guo, Chao Luo, Heng Moland, Carrie L. Tong, Weida Wang, Charles Nikolsky, Yuri Thierry-Mieg, Danielle |
| Author_xml | – sequence: 1 givenname: Ying surname: Yu fullname: Yu, Ying organization: Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University – sequence: 2 givenname: James C. surname: Fuscoe fullname: Fuscoe, James C. organization: National Center for Toxicological Research, Food and Drug Administration – sequence: 3 givenname: Chen surname: Zhao fullname: Zhao, Chen organization: Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University – sequence: 4 givenname: Chao surname: Guo fullname: Guo, Chao organization: Functional Genomics Core, Beckman Research Institute, City of Hope – sequence: 5 givenname: Meiwen surname: Jia fullname: Jia, Meiwen organization: Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University – sequence: 6 givenname: Tao surname: Qing fullname: Qing, Tao organization: Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University – sequence: 7 givenname: Desmond I. surname: Bannon fullname: Bannon, Desmond I. organization: Army Institute of Public Health, U.S. Army Public Health Command, Aberdeen Proving Ground – sequence: 8 givenname: Lee surname: Lancashire fullname: Lancashire, Lee organization: Computation Biology and Bioinformatics, IP & Science, Thomson Reuters – sequence: 9 givenname: Wenjun surname: Bao fullname: Bao, Wenjun organization: SAS Institute Inc – sequence: 10 givenname: Tingting surname: Du fullname: Du, Tingting organization: Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University – sequence: 11 givenname: Heng surname: Luo fullname: Luo, Heng organization: Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University – sequence: 12 givenname: Zhenqiang surname: Su fullname: Su, Zhenqiang organization: National Center for Toxicological Research, Food and Drug Administration – sequence: 13 givenname: Wendell D. surname: Jones fullname: Jones, Wendell D. organization: Expression Analysis Inc – sequence: 14 givenname: Carrie L. surname: Moland fullname: Moland, Carrie L. organization: National Center for Toxicological Research, Food and Drug Administration – sequence: 15 givenname: William S. surname: Branham fullname: Branham, William S. organization: National Center for Toxicological Research, Food and Drug Administration – sequence: 16 givenname: Feng surname: Qian fullname: Qian, Feng organization: National Center for Toxicological Research, Food and Drug Administration – sequence: 17 givenname: Baitang surname: Ning fullname: Ning, Baitang organization: National Center for Toxicological Research, Food and Drug Administration – sequence: 18 givenname: Yan surname: Li fullname: Li, Yan organization: National Center for Toxicological Research, Food and Drug Administration – sequence: 19 givenname: Huixiao surname: Hong fullname: Hong, Huixiao organization: National Center for Toxicological Research, Food and Drug Administration – sequence: 20 givenname: Lei surname: Guo fullname: Guo, Lei organization: National Center for Toxicological Research, Food and Drug Administration – sequence: 21 givenname: Nan surname: Mei fullname: Mei, Nan organization: National Center for Toxicological Research, Food and Drug Administration – sequence: 22 givenname: Tieliu surname: Shi fullname: Shi, Tieliu organization: The Center for Bioinformatics and The Institute of Biomedical Sciences, College of Life Science – sequence: 23 givenname: Kevin Y. surname: Wang fullname: Wang, Kevin Y. organization: Johns Hopkins University School of Medicine – sequence: 24 givenname: Russell D. surname: Wolfinger fullname: Wolfinger, Russell D. organization: SAS Institute Inc – sequence: 25 givenname: Yuri surname: Nikolsky fullname: Nikolsky, Yuri organization: Computation Biology and Bioinformatics, IP & Science, Thomson Reuters – sequence: 26 givenname: Stephen J. surname: Walker fullname: Walker, Stephen J. organization: Wake Forest Institute for Regenerative Medicine, Wake Forest University Health Sciences – sequence: 27 givenname: Penelope surname: Duerksen-Hughes fullname: Duerksen-Hughes, Penelope organization: Department of Basic Sciences, School of Medicine, Loma Linda University – sequence: 28 givenname: Christopher E. surname: Mason fullname: Mason, Christopher E. organization: Department of Physiology & Biophysics and the Institute for Computational Biomedicine, Cornell University – sequence: 29 givenname: Weida surname: Tong fullname: Tong, Weida organization: National Center for Toxicological Research, Food and Drug Administration – sequence: 30 givenname: Jean surname: Thierry-Mieg fullname: Thierry-Mieg, Jean organization: National Center for Biotechnology Information, National Institutes of Health – sequence: 31 givenname: Danielle surname: Thierry-Mieg fullname: Thierry-Mieg, Danielle organization: National Center for Biotechnology Information, National Institutes of Health – sequence: 32 givenname: Leming surname: Shi fullname: Shi, Leming email: leming.shi@gmail.com organization: Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University, National Center for Toxicological Research, Food and Drug Administration, Fudan-Zhangjiang Center for Clinical Genomics and Zhangjiang Center for Translational Medicine – sequence: 33 givenname: Charles surname: Wang fullname: Wang, Charles email: oxwang@gmail.com organization: Center for Genomics and Division of Microbiology & Molecular Genetics, School of Medicine, Loma Linda University |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/24510058$$D View this record in MEDLINE/PubMed |
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| Title | A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages |
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