A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages.
A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages.
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DOI：
10.1038/ncomms4230
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发表时间：
2014
影响因子：
16.6
通讯作者：
Wang, Charles
中科院分区：
文献类型：
--
作者：
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
大鼠已被广泛用作评估化学毒性和理解药物机制的模型。然而，它的转录组跨多个器官，或发育阶段，尚未报道。在这里，我们显示，作为SEQC联盟努力的一部分，通过对来自青少年，青少年，成年和老年Fischer 344大鼠的11个器官的320个样本进行RNA-Seq创建了一个全面的大鼠转录组BodyMap。我们对AceView中注释的40，064个基因、65，167个转录本、31，909个可变剪接转录本变体和2，367个非编码基因/非编码RNA（ncRNA）的表达谱进行了编目。我们发现器官富集的差异表达基因反映了已知的器官特异性生物活性。大量的转录本表现出器官特异性、年龄依赖性或性别特异性的差异表达模式。我们创建了一个基于网络的，开放访问的大鼠BodyMap数据库的表达谱与其他广泛使用的数据库的交叉链接，预计它将作为使用大鼠模型的生物医学研究的主要资源。 基因表达在组织之间高度可变，并且在发育期间和随着年龄变化。在这里，作者提供了大鼠转录组的全面RNA-Seq分析，跨越11个器官，4个发育阶段和两种性别。
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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影响因子：
4.4
作者：
Kwekel JC;Desai VG;Moland CL;Branham WS;Fuscoe JC
通讯作者：
Fuscoe JC
影响因子：
48
作者：
Katz, Yarden;Wang, Eric T.;Airoldi, Edoardo M.;Burge, Christopher B.
通讯作者：
Burge, Christopher B.
影响因子：
7.3
作者：
Cookson, Mark R.
通讯作者：
Cookson, Mark R.
影响因子：
2.5
作者：
Henry, Alex M.;Hohmann, John G.
通讯作者：
Hohmann, John G.
影响因子：
64.8
作者：
Graveley BR;Brooks AN;Carlson JW;Duff MO;Landolin JM;Yang L;Artieri CG;van Baren MJ;Boley N;Booth BW;Brown JB;Cherbas L;Davis CA;Dobin A;Li R;Lin W;Malone JH;Mattiuzzo NR;Miller D;Sturgill D;Tuch BB;Zaleski C;Zhang D;Blanchette M;Dudoit S;Eads B;Green RE;Hammonds A;Jiang L;Kapranov P;Langton L;Perrimon N;Sandler JE;Wan KH;Willingham A;Zhang Y;Zou Y;Andrews J;Bickel PJ;Brenner SE;Brent MR;Cherbas P;Gingeras TR;Hoskins RA;Kaufman TC;Oliver B;Celniker SE
通讯作者：
Celniker SE