对 Fischer 344 大鼠的 11 种器官、4 个年龄和 2 个性别进行全面的 RNA-Seq 转录组谱分析。
Comprehensive RNA-Seq transcriptomic profiling across 11 organs, 4 ages, and 2 sexes of Fischer 344 rats.
机构信息
Center for Pharmacogenomics, State Key Laboratory of Genetic Engineering and MOE Key Laboratory of Contemporary Anthropology, Schools of Life Sciences and Pharmacy, Fudan University , Shanghai 201203, China.
National Center for Toxicological Research, Food and Drug Administration , Jefferson, Arkansas 72079, USA.
出版信息
Sci Data. 2014 Jun 24;1:140013. doi: 10.1038/sdata.2014.13. eCollection 2014.
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.
大鼠被制药、监管和学术团体广泛用于药物和化学物质的安全性评估，以及研究人类疾病；然而，其转录组尚未得到很好的研究。作为 SEQC（即 MAQC-III）联盟努力的一部分，使用来自 10 个器官（肾上腺、脑、心、肾、肝、肺、肌肉、脾、胸腺和睾丸或子宫）的 320 个 RNA 样本构建了一个全面的 RNA-Seq 数据集，这些样本来自四个年龄段（2 周、6 周、21 周和 104 周）的雌雄两性 Fischer 344 大鼠，每个样本组（器官-性别-年龄）有四个生物学重复。通过 Ribo-Zero rRNA 去除和 Illumina RNA-Seq 方案，每个样本生成了 4100 万个 50 个碱基的单端读数，总共产生了 134 亿个读数。该数据集可用于鉴定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型基因调控网络，并发现与疾病和药物毒性和疗效相关的基因。
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