Skin immune response of rainbow trout (Oncorhynchus mykiss) infected with infectious hematopoietic necrosis virus
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ABSTRACT:
PROVIDER: PRJNA1059645 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27393375.fastq.gz | Fastqsanger.gz | |||
| SRR27393376.fastq.gz | Fastqsanger.gz | |||
| SRR27393377.fastq.gz | Fastqsanger.gz | |||
| SRR27393378.fastq.gz | Fastqsanger.gz | |||
| SRR27393379.fastq.gz | Fastqsanger.gz |
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Project description:Rainbow trout (Oncorhynchus mykiss) is one of the economically important cold-water fish cultivated in the world. The outbreak of infectious hematopoietic necrosis (IHN) seriously restricted the development of rainbow trout farming industry and caused huge economic losses. Fish skin is the largest mucosal immune organ, providing the first line of defense against pathogen invasion. However, the immune mechanisms associated with fish skin remain unclear. To systematically identify skin mucosal immune genes induced by infectious hematopoietic necrosis virus (IHNV) infection, trout transcriptome profiles following IHNV challenge were examined. Transcriptome analysis identified 6905 differentially expressed genes (DEGs) and revealed numerous immune-related DEGs involved in cytokine-cytokine receptor interactions, NOD-like receptor signaling, RIG-I-like receptor signaling, Toll-like receptor signaling, JAK-STAT signaling, Chemokine signaling pathway, and TNF signaling pathway, and the expression of these DEGs was significantly up-regulated in T48Skm group, including NOD1, NLRC3, NLRC5, TLR3, TLR7/8, TRIM25, DHX58, IFIH1, IRF3/7, STAT1, TRAF3, MX1, and HSP90A1. Additionally, highly interactive DEGs network involving immune-related terms and pathways was shown using protein-protein interaction network. The expression patterns of 12 DEGs were further verified by quantitative real-time PCR, which confirmed the reproducibility and reliability of transcriptome sequencing data. These findings expand our understanding of the innate immune system of rainbow trout skin infected with IHNV, and lay a foundation for further studies of the immune molecular mechanism and disease resistance breeding.
2024-03-11 | GSE252328 | GEO
Project description:Infectious hematopoietic necrosis virus (IHNV) can cause widespread death of rainbow trout (Oncorhynchus mykiss), understanding the molecular mechanisms that occur in the rainbow trout in response to IHNV infection will be useful to decrease IHN-related morbidity and mortality in trout aquaculture. However, the molecular mechanisms of rainbow trout in response to IHNV are very limited. This study performed analysis of mRNAs and miRNAs based on RNA-seq technology on the intestine of rainbow trout infected with IHNV and control. There were 80 differentially expressed miRNAs that regulated 3355 target mRNAs, which overlapped with differentially expressed mRNAs obtained from RNA-seq. The expression patterns of DEGs and miRNAs differentially expressed were validated by qRT-PCR. GO enrichment and KEGG pathway analyses of the potential target genes of the DE miRNAs, revealed DEGs were mainly enriched in immune-related pathways such as Toll-like receptor signaling pathway, RIG-I-like receptor signaling pathway and IL-17 signaling pathway. These findings improve our understanding of the molecular mechanisms of IHNV infection. The study analyzed the immune regulatory target gene pairs and signal pathways of rainbow trout intestine against IHNV infection at the transcriptional level, and provided basic data for the study of rainbow trout against IHNV immune regulatory.
2021-06-09 | GSE176398 | GEO
Project description:Infectious hematopoietic necrosis virus (IHNV) can cause widespread death of rainbow trout (Oncorhynchus mykiss), understanding the molecular mechanisms that occur in the rainbow trout in response to IHNV infection will be useful to decrease IHN-related morbidity and mortality in trout aquaculture. However, the molecular mechanisms of rainbow trout in response to IHNV are very limited. This study performed analysis of mRNAs and miRNAs based on RNA-seq technology on the intestine of rainbow trout infected with IHNV and control. There were 80 differentially expressed miRNAs that regulated 3355 target mRNAs, which overlapped with differentially expressed mRNAs obtained from RNA-seq. The expression patterns of DEGs and miRNAs differentially expressed were validated by qRT-PCR. GO enrichment and KEGG pathway analyses of the potential target genes of the DE miRNAs, revealed DEGs were mainly enriched in immune-related pathways such as Toll-like receptor signaling pathway, RIG-I-like receptor signaling pathway and IL-17 signaling pathway. These findings improve our understanding of the molecular mechanisms of IHNV infection. The study analyzed the immune regulatory target gene pairs and signal pathways of rainbow trout intestine against IHNV infection at the transcriptional level, and provided basic data for the study of rainbow trout against IHNV immune regulatory.
2021-06-09 | GSE176396 | GEO
Project description:Rainbow trout (Oncorhynchus mykiss), an economically important cold-water fish cultured worldwide, suffers from infectious hematopoietic necrosis virus (IHNV) infection, resulting in huge financial losses. In order to understand the immune response of rainbow trout during virus infection, we explored trout skin transcriptome profiles following IHNV challenge, and identified 6905 differentially expressed genes (DEGs). Transcriptome analysis revealed numerous DEGs involved in immune responses, such as NOD1, NLRC3, NLRC5, TLR3, TLR7/8, TRIM25, DHX58, IFIH1, IRF3/7, STAT1, TRAF3, MX1 and HSP90A1. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses showed that DEGs were significantly enriched in various immune-related terms including immune system process, innate immune response and regulation of immune effector process and pathways of cytokine-cytokine receptor interactions, NOD-like receptor signaling, RIG-I-like receptor signaling, Toll-like receptor signaling, JAK-STAT signaling, Chemokine signaling pathway, and TNF signaling pathway. In addition, protein-protein interaction network (PPI) was used to display highly interactive DEG networks involving immune-related pathways. The expression trends of 16 DEGs were further verified by quantitative real-time PCR, which confirmed the reliability of the transcriptome sequencing results. This study expands our understanding of the immune response of rainbow trout infected with IHNV, and provides valuable resources for future studies on the immune molecular mechanism and disease resistance breeding.
2022-12-28 | GSE221722 | GEO
Project description:Rainbow trout (Oncorhynchus mykiss) is an important cold-water fish widely cultivated in China. The frequent occurrence of viral diseases caused by infectious hematopoietic necrosis virus (IHNV) seriously restricted the healthy development of the rainbow trout farming industry. However, the immune defense mechanism induced by IHNV in rainbow trout has not been fully elucidated. In the present study, we detected mRNA and miRNA expression profiles in rainbow trout head kidney after IHNV infection and the expression patterns of key immune-related genes at different post-infection periods (0-, 6-, 12-, 24-, 48-, 72-, 96-, 120- and 144 hours post-infection (hpi)) using RNA-seq and qRT-PCR. The results showed that a total of 7486 genes and 277 miRNAs were differentially expressed, and numerous differentially expressed genes (DEGs) enriched in the immune-related pathways such as Toll-like receptor signaling pathway, RIG-I-like receptor signaling pathway, NOD-like receptor signaling pathway, cytokine-cytokine receptor interaction and JAK-STAT signaling pathway were significantly up-regulated, including LGP2, MDA5, TRIM25, IRF3, IRF7, TLR3, TLR7, TLR8, MYD88, IFN1, MX1 and VIG-1. Integration analysis identified six miRNAs (miR-141-y, miR-200-y, miR-144-y, miR-2188-y, miR-725-y and miR-203-y) that target at least four key immune-related genes (TRIM25, LGP2, TLR3, TLR7, IRF3 and IRF7). Expression analysis showed that TRIM25, MDA5, LGP2, TLR3, TLR7, IRF3, IRF7, IFN1, MX1 and VIG-1 genes increased firstly and then decreased, and reached peak expression at 48 hpi. These findings improve our understanding of the immune mechanism of rainbow trout infected with IHNV, and provide a basic data for future breeding for disease resistance in rainbow trout.
2022-11-29 | GSE218752 | GEO
Project description:Rainbow trout (Oncorhynchus mykiss) is an important cold-water fish widely cultivated in China. The frequent occurrence of viral diseases caused by infectious hematopoietic necrosis virus (IHNV) seriously restricted the healthy development of the rainbow trout farming industry. However, the immune defense mechanism induced by IHNV in rainbow trout has not been fully elucidated. In the present study, we detected mRNA and miRNA expression profiles in rainbow trout head kidney after IHNV infection and the expression patterns of key immune-related genes at different post-infection periods (0-, 6-, 12-, 24-, 48-, 72-, 96-, 120- and 144 hours post-infection (hpi)) using RNA-seq and qRT-PCR. The results showed that a total of 7486 genes and 277 miRNAs were differentially expressed, and numerous differentially expressed genes (DEGs) enriched in the immune-related pathways such as Toll-like receptor signaling pathway, RIG-I-like receptor signaling pathway, NOD-like receptor signaling pathway, cytokine-cytokine receptor interaction and JAK-STAT signaling pathway were significantly up-regulated, including LGP2, MDA5, TRIM25, IRF3, IRF7, TLR3, TLR7, TLR8, MYD88, IFN1, MX1 and VIG-1. Integration analysis identified six miRNAs (miR-141-y, miR-200-y, miR-144-y, miR-2188-y, miR-725-y and miR-203-y) that target at least four key immune-related genes (TRIM25, LGP2, TLR3, TLR7, IRF3 and IRF7). Expression analysis showed that TRIM25, MDA5, LGP2, TLR3, TLR7, IRF3, IRF7, IFN1, MX1 and VIG-1 genes increased firstly and then decreased, and reached peak expression at 48 hpi. These findings improve our understanding of the immune mechanism of rainbow trout infected with IHNV, and provide a basic data for future breeding for disease resistance in rainbow trout.
2022-11-28 | GSE218831 | GEO
Project description:The aim of present study is to identify and quantify proteins involved in the events of fertilization and early embryo development using a label-free protein quantification method in rainbow trout (Oncorhynchus mykiss) as an economically important fish species in aquaculture.
2020-01-16 | PXD013329 | Pride
Project description:A rapid decline in temperature poses a major challenge for poikilothermic fish. The gene expression of rainbow trout Oncorhynchus mykiss having undergone such a cold shock (0 °C) and a control (5 °C) were compared in a microarray-based study.
2015-12-02 | GSE75563 | GEO
Project description:The objective of this study was to identify and quantify proteomic profiles of intestine of rainbow trout (Oncorhynchus mykiss). Specific pathogen free rainbow trout (mean length 15 ± 1 cm) were maintained in recirculating de-chlorinated water at 19±1 °C. Prior to the experiment, fish were distributed between aquaria. The test groups were infected by immersion of Yersinia ruckeri CSF007-82 (biotype 1) and 7959-11 (biotype 2) strains. The control group was immersed similar with sterile broth medium. Fish were anaesthetized and sampled aseptically at different time points. Each intestine was washed three times with sterile phosphate-buffered saline containing a cocktail of mammalian protease inhibitors. Intestinal mucosa was scraped with a sterile large scalpel blade. Intestinal samples were snap-frozen in liquid nitrogen and stored at –80 °C.
2019-11-12 | PXD011087 | Pride
Project description:The rainbow trout (Oncorhynchus mykiss) is one of the most important aquaculture species worlwide. In this study, transcriptional profiling of skin by oligonucleotide microarray was applied to rainbow trout individuals infected with A. salmonicida, to identified enriched genes involved in pathogen response.
2023-11-28 | GSE230658 | GEO