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

• Published in: Nature communications Vol. 5; no. 1; p. 3230
• Main 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
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 10.02.2014; Nature Publishing Group; Nature Pub. Group
• Subjects: 38/23; 38/39; 38/91; 631/114; 631/337/2019; 692/308; Alternative Splicing; Animals; Developmental stages; Female; Gene Expression Profiling; Humanities and Social Sciences; Male; multidisciplinary; Protein Isoforms - metabolism; Rats, Inbred F344 - growth & development; Rats, Inbred F344 - metabolism; Science; Science (multidisciplinary); Sequence Analysis, RNA; Sex Characteristics; Transcriptome
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/ncomms4230

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.