RGD Reference Report - A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages. - Rat Genome Database

Send us a Message

Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   

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

Authors: 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 
Citation: Yu Y, etal., Nat Commun. 2014;5:3230. doi: 10.1038/ncomms4230.
RGD ID: 13506920
Pubmed: PMID:24510058   (View Abstract at PubMed)
PMCID: PMC3926002   (View Article at PubMed Central)
DOI: DOI:10.1038/ncomms4230   (Journal Full-text)

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.

Objects referenced in this article
Strain F344/Nctr Fischer Rattus norvegicus

Additional Information