title: RNA-seq profiles from grass carp tissues after reovirus (GCRV) infection based on singular and modular enrichment analyses.
abstract: 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 2h before and six times after (2h, 24h, 48h, 72h, 96h and 120h) GCRV challenge. A total of 7.25±0.18 million (M) clean reads and 3.53±0.37M 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: 2h, 24h/48h, and 72h/96h/120h. 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.
authors.affiliation: State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China.
authors.forename: Mijuan
authors.initials: M
authors.lastname: Shi
authors.affiliation: State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
authors.forename: Rong
authors.initials: R
authors.lastname: Huang
authors.affiliation: State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
authors.forename: Fukuan
authors.initials: F
authors.lastname: Du
authors.affiliation: State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
authors.forename: Yongyan
authors.initials: Y
authors.lastname: Pei
authors.affiliation: State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100039, China.
authors.forename: Lanjie
authors.initials: L
authors.lastname: Liao
authors.affiliation: State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
authors.forename: Zuoyan
authors.initials: Z
authors.lastname: Zhu
authors.affiliation: State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China. Electronic address: wangyp.ihb@gmail.com.
authors.forename: Yaping
authors.initials: Y
authors.lastname: Wang
mesh_terms: D000818:Animals; D002347:Carps / Q000235:genetics / Q000276:immunology* / Q000821:virology; D016000:Cluster Analysis; D005393:Fish Diseases / Q000235:genetics / Q000276:immunology* / Q000821:virology; D020869:Gene Expression Profiling / Q000379:methods*; D063990:Gene Ontology; D005880:Gills / Q000276:immunology / Q000378:metabolism / Q000821:virology; D054884:Host-Pathogen Interactions / Q000276:immunology; D007413:Intestinal Mucosa / Q000378:metabolism; D007422:Intestines / Q000276:immunology / Q000821:virology; D008099:Liver / Q000276:immunology / Q000378:metabolism / Q000821:virology; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012087:Reoviridae / Q000276:immunology* / Q000502:physiology; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013154:Spleen / Q000276:immunology / Q000378:metabolism / Q000821:virology; D013997:Time Factors; D059467:Transcriptome / Q000276:immunology*
chemical_list: D012333:RNA, Messenger
keywords: Cellular immunity; Complement; Ctenopharyngodon idella; Hemorrhagic disease; Innate immunity; Metabolic disturbances