IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v5y2014i1d10.1038_ncomms4230.html
   My bibliography  Save this article

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

Author

Listed:
  • 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
    National Center for Toxicological Research, Food and Drug Administration
    Fudan-Zhangjiang Center for Clinical Genomics and Zhangjiang Center for Translational Medicine)

  • Charles Wang

    (School of Medicine, Loma Linda University)

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.

Suggested Citation

  • 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, 2014. "A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages," Nature Communications, Nature, vol. 5(1), pages 1-11, May.
    • Handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms4230
    DOI: 10.1038/ncomms4230
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/ncomms4230
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/ncomms4230?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Rizwanul Haque & Sonu Peedikayil Kurien & Hagar Setty & Yehuda Salzberg & Gil Stelzer & Einav Litvak & Hila Gingold & Oded Rechavi & Meital Oren-Suissa, 2024. "Sex-specific developmental gene expression atlas unveils dimorphic gene networks in C. elegans," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    2. Orshay Gabay & Yoav Shoshan & Eli Kopel & Udi Ben-Zvi & Tomer D. Mann & Noam Bressler & Roni Cohen‐Fultheim & Amos A. Schaffer & Shalom Hillel Roth & Ziv Tzur & Erez Y. Levanon & Eli Eisenberg, 2022. "Landscape of adenosine-to-inosine RNA recoding across human tissues," Nature Communications, Nature, vol. 13(1), pages 1-17, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:5:y:2014:i:1:d:10.1038_ncomms4230. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.