TY - JOUR
T1 - A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
AU - Yu, Ying
AU - Fuscoe, James C.
AU - Zhao, Chen
AU - Guo, Chao
AU - Jia, Meiwen
AU - Qing, Tao
AU - Bannon, Desmond I.
AU - Lancashire, Lee
AU - Bao, Wenjun
AU - Du, Tingting
AU - Luo, Heng
AU - Su, Zhenqiang
AU - Jones, Wendell D.
AU - Moland, Carrie L.
AU - Branham, William S.
AU - Qian, Feng
AU - Ning, Baitang
AU - Li, Yan
AU - Hong, Huixiao
AU - Guo, Lei
AU - Mei, Nan
AU - Shi, Tieliu
AU - Wang, Kevin Y.
AU - Wolfinger, Russell D.
AU - Nikolsky, Yuri
AU - Walker, Stephen J.
AU - Duerksen-Hughes, Penelope
AU - Mason, Christopher E.
AU - Tong, Weida
AU - Thierry-Mieg, Jean
AU - Thierry-Mieg, Danielle
AU - Shi, Leming
AU - Wang, Charles
PY - 2014
Y1 - 2014
N2 - 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.
AB - 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.
UR - https://www.scopus.com/pages/publications/84907492839
U2 - 10.1038/ncomms4230
DO - 10.1038/ncomms4230
M3 - 文章
C2 - 24510058
AN - SCOPUS:84907492839
SN - 2041-1723
VL - 5
SP - 3230
JO - Nature Communications
JF - Nature Communications
M1 - 3230
ER -