A comprehensive rat transcriptome built from large scale RNA-seq-based annotation
A comprehensive rat transcriptome built from large scale RNA-seq-based annotation
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基于大规模 RNA-seq 注释构建的综合大鼠转录组
DOI：
10.1093/nar/gkaa638
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发表时间：
2020-09-04
影响因子：
14.9
通讯作者：
Shi, Tieliu
中科院分区：
文献类型：
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作者：
Ji, Xiangjun;Li, Peng;Shi, Tieliu
大鼠是生物医学研究中研究人类疾病机制和治疗的重要模式生物，但其注释转录组还很不完整。我们利用SEQC联盟生成的来自11个不同器官的320个样本的RNA-seq数据构建了一个名为RTR的大鼠转录组重新注释。RTR中共有52 807个基因和114 152个转录本。RTR的转录区和外显子分别占基因组的42%和6.5%。在RTR新注释的73 074个转录本中，34 213个为高置信度编码转录本，24 728个为高置信度长非编码转录本。不同组织而非不同阶段对转录本的表达模式有显著影响。11个组织中有11715个基因和15852个转录本表达，849个管家基因在不同组织中表达不同的亚型。这个全面的转录组可在http://www.unimd.org/rtr/免费获得。我们新的大鼠转录组为大鼠疾病和毒性模型的遗传学和基因表达研究提供了重要的参考。
The rat is an important model organism in biomedical research for studying human disease mechanisms and treatments, but its annotated transcriptome is far from complete. We constructed a Rat Transcriptome Re-annotation named RTR using RNA-seq data from 320 samples in 11 different organs generated by the SEQC consortium. Totally, there are 52 807 genes and 114 152 transcripts in RTR. Transcribed regions and exons in RTR account for similar to 42% and similar to 6.5% of the genome, respectively. Of all 73 074 newly annotated transcripts in RTR, 34 213 were annotated as high confident coding transcripts and 24 728 as high confident long noncoding transcripts. Different tissues rather than different stages have a significant influence on the expression patterns of transcripts. We also found that 11 715 genes and 15 852 transcripts were expressed in all 11 tissues and that 849 house-keeping genes expressed different isoforms among tissues. This comprehensive transcriptome is freely available at http://www.unimd.org/rtr/. Our new rat transcriptome provides essential reference for genetics and gene expression studies in rat disease and toxicity models.