RNA-seq profiles from grass carp tissues after reovirus (GCRV) infection based on singular and modular enrichment analyses.
RNA-seq profiles from grass carp tissues after reovirus (GCRV) infection based on singular and modular enrichment analyses.
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DOI：
10.1016/j.molimm.2014.05.004
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发表时间：
2014-09
影响因子：
3.6
通讯作者：
Mijuan Shi;Rong Huang;F. Du;Y. Pei;L. Liao;Zuoyan Zhu;Yaping Wang
中科院分区：
文献类型：
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作者：
Mijuan Shi;Rong Huang;F. Du;Y. Pei;L. Liao;Zuoyan Zhu;Yaping Wang
草鱼出血病是由一种呼肠孤病毒引起的草鱼鱼种和一岁鱼的致死性疾病。在GCRV攻击前2 h和攻击后6个时间点（2 h、24 h、48 h、72 h、96 h和120 h）获得了草鱼鳃、肠、肝和脾4种患病组织的RNA-seq数据。每个RNA-seq分析获得总共7.25 ± 0.18百万（M）个干净读段和3.53 ± 0.37 M个独特读段。与对照组相比，在GCRV攻击后的六个时间点，四种组织中有9060个独特的差异表达基因（DEG）。系统聚类分析显示，6个时间点的数据可分为3个分支：2 h、24 h/48 h和72 h/96 h/120 h。基于基因本体进行每个RNA-seq数据集的DEG的奇异（SEA）和模块富集分析。结果表明，免疫反应发生在所有四个组织中，表明GCRV可能不特异性靶向任何组织。此外，在疾病过程中，观察到每个器官的脂质和碳水化合物代谢紊乱。同时对京都基因和基因组百科全书数据库中的DEG进行了SEA分析，结果表明补体系统和细胞免疫在出血性疾病的发病过程中起着重要作用。使用一式两份攻击实验的合并样品的qPCR来确认我们的RNA-seq方法。
Hemorrhagic disease of the grass carp,Ctenopharyngodon idella, is a fatal disease in fingerlings and yearlings caused by a reovirus, GCRV. RNA-seq data from four diseased grass carp tissues (gill, intestine, liver and spleen) were obtained at 2 h before and six times after (2 h, 24 h, 48 h, 72 h, 96 h and 120 h) GCRV challenge. A total of 7.25 ± 0.18 million (M) clean reads and 3.53 ± 0.37 M unique reads were obtained per RNA-seq analysis. Compared with controls, there were 9060 unique differentially expressed genes (DEGs) in the four tissues at the six time points post-GCRV challenge. Hierarchical clustering analysis of the DEGs showed that the data from the six time points fell into three branches: 2 h, 24 h/48 h, and 72 h/96 h/120 h. Singular (SEA) and modular enrichment analyses of DEGs per RNA-seq dataset were performed based on gene ontology. The results showed that immune responses occurred in all four tissues, indicating that GCRV probably does not target any tissue specifically. Moreover, during the course of disease, disturbances were observed in lipid and carbohydrate metabolism in each of the organs. SEA of DEGs based on the Kyoto Encyclopedia of Genes and Genomes database was also performed, and this indicated that the complement system and cellular immunity played an important role during the course of hemorrhagic disease. The qPCR of pooled samples of duplicate challenge experiment were used to confirm our RNA-seq approach.