Oncorhynchus mykiss
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA80097 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR316698.fastq.gz | Fastqsanger.gz | |||
| SRR316699.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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:Stress represents a major factor negatively affecting fish welfare in aquaculture. The objective of the present study was to identify and evaluate informative indicators for the welfare of rainbow trout Oncorhynchus mykiss exposed to (A) a critical water temperature of 27 °C and (B) acute crowding of 100 kg/m3 combined with water temperature of 27 °C. In order to make an approximate assessment of the overall condition, we determined health index, spleen-somatic index and haematocrit and recorded the blood concentrations of haemoglobin, cortisol and glucose of rainbow trout under challenging versus control conditions. Moreover, we analysed the transcriptomic profiles of the spleen of the two stress-treatment and the reference groups to identify gene sets, which are specific for temperature stress alone or combined temperature and crowding stress.
2019-04-04 | GSE129271 | GEO
Project description:The hypoxia frequently occurs in natural aquatic systems and aquaculture environment due to the natural reasons and human factors such as extreme climate, high density farming, environmental pollution and global warming, which have gradually become a huge threat to aquatic ecosystem functions and aquatic organism survival, causing serious ecological damage and enormous economic losses. Rainbow trout (Oncorhynchus mykiss), as a hypoxia-sensitive fish species, is a good model to study hypoxia stress. The molecular regulation and oxidative stress of rainbow trout still remains unknown in response to environmental hypoxia and reoxygenation stress. In this study, the transcriptome and biochemical indexes of rainbow trout liver in response to hypoxia for different durations were analyzed to highlight the changes in the molecular regulation and oxidative stress.
2021-02-25 | GSE167386 | 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:Stocking density is considered as a key factor determining the productivity of fish aquaculture systems. The transcriptomic response to crowding stress is, however, still poorly investigated. We aimed at the identification of potential biomarker genes via microarray analyses to get insight into molecular pathways modulated through density-induced stress in farmed rainbow trout Oncorhynchus mykiss. Transcriptome profiling in liver, kidney, and gills was complemented with behaviarol observation and analysis of classical plasma parameters. Individuals of two trout strains were exposed for eight days to definite stocking densities, 1 kg/m³ (low density); 10 kg/m³ (moderate); 18 kg/m³ (elevated); and 35 kg/m³ (high). Whereas stocking density had no significant effect on cortisol levels, plasma glucose levels were elevated in trout kept at high density. Pathway enrichment analyses confirmed the upregulation of HIF1a signaling in liver contributing to glucose homeostasis during stress conditions, while mTOR and PI3K/AKT signaling pathways were downregulated. Further perturbed hepatic pathways were involved in protein ubiquitination and the biosynthesis of cholesterol, retinol and glutathione. Three stocking density conditions were investigated: an uncrowded âmoderateâ density (MD: 10 kg trout/m³) , an elevated density (ED: 18 kg/m³ ), and high density (HD: 35 kg/m³). The experiment was performed twice with two strains of Steelhead rainbow trout (Troutlodge and Born trout), randomly assigned to identical glass tanks with MD (30 and 34 individuals), ED (60 and 64 individuals), and HD (120 and 140 individuals). Trout were sampled 8 d after experimental onset.
2015-10-24 | E-GEOD-74332 | biostudies-arrayexpress
Project description:Gynogenetic development in fish is induced by activation of eggs with irradiated spermatozoa followed by exposure of the activated eggs to the temperature or high hydrostatic pressure (HHP) shock that prevents 1st cell cleavage. Produced specimens are fully homozygous fish also known as Doubled Haploids. Gynogenetic DH individuals might be used aquaculture and developmental biology unfortunately; the potential application of DHs is limited by a rather low survival rate of such specimens. However, observed variation in the survival rates of the gynogenetic embryos originated from different clutches suggests that eggs from some females have increased ability for gynogenetic development than others. Taking into account that first 10 cell cleavages in the fish embryos rely on the maternal RNA, it is tempting to assume that the ova showing such a vast difference in potential for gynogenesis may have also had different biological characteristics including alterations in maternal gene expression profiles. If so, then genes that up- or down –regulated expression in eggs increases competence for gynogenetic development in trout might be considered as candidate genes for gynogenesis in rainbow trout. Thus, the main goal of the project is identification of genes that increase ability of rainbow trout eggs for gynogenetic development. Within the project, we tried to verify following hypotheses: 1. Eggs from different females have different potential for gynogenesis in rainbow trout. 2. Eggs with different ability for gynogenetic development with all maternal inheritance have different biological characteristics including morphology and anti-ROS enzyme activities. 3. Eggs with increased competence for gynogenesis have altered transcriptomic profiles. 4. There are some particular genes that altered expression in trout eggs enable development of gynogenetic embryos. Gynogenetic rainbow trout specimens were produced in the course of activation of eggs with UV-irradiated spermatozoa and High Hydrostatic Pressure shock (HHP) applied around 1st cell cleavage. Eggs from several females were used in the experiment. Survival rates of gynogenetic rainbow trout was monitored since fertilization. Quality of eggs was examined by assessment of their morphology and activity of anti-ROS (reactive oxygene species) enzymes. Transcriptome of eggs showing increased and decreased developmental competence for gynogenesis was analyzed using RNA-seq approach and results compared to find out any alterations related to survival of gynogenetic trout.
2023-02-28 | GSE225353 | GEO
Project description:Rainbow trout (Oncorhynchus mykiss) is a typical cold-water fish, the development of rainbow trout aquaculture was severely hampered via the high temperature in summer. Understanding the regulatory mechanism of rainbow trout response to chronic heat stress can provide a theoretical basis for formulating measures to relieve heat stress. In the study, changes in the biochemical parameters revealed that a strong stress response occurred in rainbow trout at 24 °C, the organisms stress defense system was activated, and the immune system was also affected. Proteome of rainbow trout liver tissues under heat stress (24 °C) and control conditions (18 °C) were performed using DIA/SWATH. A total of 390 DEPs were identified by strict threshold (q-value <0.05 and fold changes >1.5), among them 175 were up-regulated and 225 were down-regulated. Some proteins related to HSP, metabolism and immunity were identified. GO analysis showed that some proteins that were highly induced to express at high temperature were involved in the regulation of cell homeostasis, metabolism, adaptive stress and stimulation. KEGG analysis shows that some pathways play an important role in the regulation of heat stress, such as metabolic pathway, protein processing in endoplasmic reticulum pathway, PPAR signaling pathway and complement and coagulation cascades pathway, etc. PPI network analysis shows HSP90b1 and C3 maybe cooperative to protect the integrity of cell membrane function under heat stress. Our finding provide a comprehensive review of protein expression of rainbow trout liver under heat stress, which helps to formulate strategies for rainbow trout to relieve heat stress during high temperature in summer.
2020-07-06 | PXD020206 |
Project description:Transcriptional profiling of rainbow trout liver cells comparing liver cells from small fish with liver cells from large fish at two time periods.
2012-11-29 | GSE42583 | GEO
Project description:Transcriptional profiling of rainbow trout muscle cells comparing muscle cells from small fish with muscle cells from large fish at two time periods.
2012-11-29 | GSE42582 | GEO