Comprehensive RNA-Seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats.
Comprehensive RNA-Seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats.
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DOI：
10.1038/sdata.2014.13
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发表时间：
2014
期刊：
影响因子：
9.8
通讯作者：
Shi, Leming
中科院分区：
文献类型：
--
作者：
Yu, Ying;Zhao, Chen;Su, Zhenqiang;Wang, Charles;Fuscoe, James C.;Tong, Weida;Shi, Leming
大鼠被制药、监管和学术界广泛用于药物和化学品的安全性评估以及人类疾病的研究;然而，其转录组尚未得到很好的研究。作为SEQC的一部分（即，MAQC-III）联盟的努力，使用从10个器官分离的320个RNA样品构建了综合RNA-Seq数据集（肾上腺、脑、心脏、肾脏、肝脏、肺、肌肉、脾脏、胸腺和睾丸或子宫）（2、6、21和104周龄），80个样品组（器官-性别-年龄）中的每一个具有四个生物学重复。通过Ribo-Zero rRNA去除和Illumina RNA-Seq方案，每个样品产生4100万个50 bp单端读段，总共产生134亿个读段。该数据集可用于识别和验证新的大鼠基因和转录本，开发更全面的大鼠转录组注释系统，识别与组织特异性基因表达和发育相关的新基因调控网络，并发现负责疾病和药物毒性和疗效的基因。
The rat is used extensively by the pharmaceutical, regulatory, and academic communities for safety assessment of drugs and chemicals and for studying human diseases; however, its transcriptome has not been well studied. As part of the SEQC (i.e., MAQC-III) consortium efforts, a comprehensive RNA-Seq data set was constructed using 320 RNA samples isolated from 10 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four ages (2-, 6-, 21-, and 104-week-old) with four biological replicates for each of the 80 sample groups (organ-sex-age). With the Ribo-Zero rRNA removal and Illumina RNA-Seq protocols, 41 million 50 bp single-end reads were generated per sample, yielding a total of 13.4 billion reads. This data set could be used to identify and validate new rat genes and transcripts, develop a more comprehensive rat transcriptome annotation system, identify novel gene regulatory networks related to tissue specific gene expression and development, and discover genes responsible for disease and drug toxicity and efficacy.
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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：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
14.9
作者：
Hansen KD;Brenner SE;Dudoit S
通讯作者：
Dudoit S
影响因子：
16.6
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
通讯作者：
Wang, Charles
影响因子：
14.9
作者：
Lohse M;Bolger AM;Nagel A;Fernie AR;Lunn JE;Stitt M;Usadel B
通讯作者：
Usadel B