Ontology highlight
ABSTRACT:
PROVIDER: PRJNA897820 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR22164760_1.fastq.gz | Fastqsanger.gz | |||
| SRR22164760_2.fastq.gz | Fastqsanger.gz | |||
| SRR22164761_1.fastq.gz | Fastqsanger.gz | |||
| SRR22164761_2.fastq.gz | Fastqsanger.gz | |||
| SRR22164762_1.fastq.gz | Fastqsanger.gz |
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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
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:To date, little is known about the proteomic changes at the portals of entry in rainbow trout after infection with the myxozoans, Myxobolus cerebralis, and Tetracapsuloides bryosalmonae the causative agents of whirling disease and proliferative kidney disease, respectively. Therefore, the aim of this study was to provide the first proteomic profiles of the host in the search for evasion strategies against single and coinfection with M. cerebralis and T. bryosalmonae. One group of fish was initially infected with M. cerebralis and another group with T. bryosalmonae. After 30 days, half of the fish in each group were co-infected with the other parasite. Using a quantitative proteomic approach, we investigated proteomic changes in the caudal fins and gills of rainbow trout before and after co-infection. In the caudal fins, 16 proteins were differentially regulated post exposure to M. cerebralis, whereas 27 proteins were differentially modulated in the gills of the infected rainbow trout post exposure to T. bryosalmonae. After co-infection, 4 proteins involved in parasite recognition and the regulation of host immune responses were differentially modulated between the groups in the caudal fin. In the gills, 11 proteins involved in parasite recognition and host immunity, including 4 myxozoan proteins predicted to be virulence factors, were differentially modulated. The results of this study increase our knowledge on rainbow trout co-infections by myxozoan parasites and rainbow trout immune responses against myxozoa at the portals of entry, supporting a better understanding of these host-parasite interactions.
2024-05-06 | PXD050412 | Pride
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:As an important cold-water economic fish species, rainbow trout (Oncorhynchus mykiss) exhibits several intra-specific variation in skin pigmentation that can give rise to distinctive phenotypes, and wild-type rainbow trout with black skin (WR) and yellow mutant rainbow trout with yellow skin (YR) are the major two types in the farms, whose distinct skin colors make them suitable model for elucidating the skin pigmentation process. Skin color as a key indicator for selection in rainbow trout farming as well as has a strong visual impact on the consumer when rainbow trout are marketed. Previously, extensive studies have been conducted on skin color in rainbow trout, including the observation of skin spots and the expression analysis of some important pigment genes. However, up to date, no studies have systematically examined the molecular regulation mechanism of skin color difference between WR and YR through a high throughput method. Therefore, the aim of this study was to reveal the molecular regulation mechanism of skin color difference between these two strains at the mRNA and miRNA transcriptome level, and candidate genes, miRNAs and miRNA-mRNA pairs that may be responsible for rainbow trout albinism were obtained.
2022-04-21 | GSE172482 | 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 aquaculture fish species that is farmed worldwide, and it is also the most widely cultivated cold water fish in China. This species, a member of the salmonidae family, is an ideal model organism for studying the immune system in fish. Two phenotypes of rainbow trout are widely cultured; wild-type rainbow trout with black skin (WR_S) and yellow mutant rainbow trout with yellow skin (YR_S). Fish skin is an important immune organ, however, little is known about the differences in skin immunity between WR_S and YR_S in a natural flowing water pond aquaculture environment, and very few studies were conducted to investigate the ceRNA mechanism for fish skin.
2021-08-17 | GSE181974 | GEO
Project description:Purpose:Our data significantly advance understanding of heat stress regulatory mechanism of miRNA in the head kidney of rainbow trout Methods:miRNAs of rainbow trout were involved in heat stress were identified by high-throughput sequencing of six small RNA libraries of the kidney tissues under control (18℃) and heat-treated (24℃) conditions Results:high-throughput sequencing was performed to identify miRNAs responsive to heat stress. We obtained 41,991,119 and 43,882,123 raw reads and 39,756,736 and 42,538,331 clean reads from under control (18℃) and heat-treated (24℃) .A total of 392 conserved miRNAs and 989 novel miRNAs were identified, of which 78 miRNAs were expressed in different response to heat stress. In addition to, including 393 negative correlation miRNA-target gene pairs Conclusions:through high-throughput sequencing of the six libraries from head kidney tissue of rainbow trout, the expression level of miRNA has significant changes after heat stress.
2018-03-16 | GSE111816 | GEO
Project description:The objective of this study was to identify and quantify proteomic profiles of head kidney 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 9 aquaria, 18 fish per aquarium. The test groups were infected by immersion of Yersinia ruckeri strains: CSF007-82 (biotype 1) and 7959-11 (biotype 2). The control group was immersed similar with sterile broth medium. There were 3 aquaria per each group (CSF007-82-infected, 7959-11-infected and control). Nine fish from infected and control fish groups were anaesthetized with MS-222 at 3, 9 and 28 days post exposure and sampled aseptically. Each head kidney was washed three times with sterile phosphate-buffered saline containing a cocktail of mammalian protease inhibitors. Head kidney samples were snap-frozen in liquid nitrogen and stored at –80 °C.
2018-08-14 | PXD008473 | Pride