Oncorhynchus spp
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA774772 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR16876500.fastq.gz | Fastqsanger.gz | |||
| SRR16876600.fastq.gz | Fastqsanger.gz | |||
| SRR16876700.fastq.gz | Fastqsanger.gz | |||
| SRR16876800.fastq.gz | Fastqsanger.gz | |||
| SRR16876900.fastq.gz | Fastqsanger.gz |
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Project description:Transcriptional profiling of rainbow trout liver and muscle cells comparing small fish with large fish within a population of neomale offspring.
2013-11-20 | GSE52507 | GEO
Project description:Transcriptional profiling of rainbow trout liver and muscle cells comparing small fish with large fish within a population of neomale offspring. Small vs. large-fish liver and muscle cells from neomale offspring. Biological replicates: 4 small replicates, 4 large replicates.
2013-11-20 | E-GEOD-52507 | biostudies-arrayexpress
Project description:Metabolic processes and sexual maturation closely interact during the long-distance reproductive migration of many fish species to their spawning grounds. In the present study, we have for the first time used exercise experimentally to investigate the effects on sexual maturation in rainbow trout. Pubertal autumn-spawning seawater-raised female rainbow trout Oncorhynchus mykiss (n=26; 50-cm, 1.5-kg) were rested or swum at a near optimal speed of 0.75 body-lengths per second in a 6,000 L swim-flume under natural reproductive conditions (16 °C fresh-water, starvation, 8h-light:16h-dark photoperiod). Fish were sampled after arrival and subsequently after 10 days (resting or swimming 307 km) and 20 days (resting or swimming 636 km). Ovarian development was significantly reduced in the swimmers. Analysis of the expression of key factors in the reproductive axis included pituitary kiss1-receptor, lh and fsh and ovarian lh-receptor, fsh-receptor, aromatase and vitellogenin-receptor (vtgr). Swimmers had lower pituitary lh and ovarian vtgr expression than resters. Furthermore, the number of late vitellogenic oocytes was lower in swimmers than in resters, probably resulting from the lower vtgr expression, and vitellogenin plasma levels were higher. Therefore, swimming exercise suppresses oocyte development possibly by inhibiting vitellogenin uptake. Transcriptomic changes that occurred in the ovary of exercised fish were investigated using a salmonid cDNA microarray platform. Protein biosynthesis and energy provision were among the sixteen functional categories that were all down-regulated in the ovary. Down-regulation of the transcriptomic response in the ovary illustrates the priority of energy reallocation and will save energy to fuel exercise. A swimming-induced ovarian developmental suppression at the start of vitellogenesis during long-term reproductive migration may be a strategy to avoid precocious muscle atrophy.
2010-02-05 | GSE20131 | GEO
Project description:Sex steroids play a key role in triggering sec differentiation in fish and the use of exogenous hormone treatment leads to partial or complete sex reversal. This phenomenon has attracted attention since the discovery taht even low environmental doses of exogenous steroids can adversely affect gonad morphology (ovotestis development) and induce reproductive failure. Modern genomic-based technologies have enhanced opportunities to find mechanisms of action (MOA) and dentify biomarkers for the toxic action of a compound. The goal of this study are to improve the understanding of feminization in fish by analyzing gene expression patterns in the gonads of rainbow trout fry after a chronic exposure to several doses (0.01, 0.1, 1 and 10 ?g/L) of ethynylestradiol (EE2) and to offer target genes as potential biomarkers of ovotestis development. An all-male population of Rainbow trout fry was exposed during 76 days (from 60 to 136 days post-fertilization (dpf)) to five nominal concentrations of 17?-ethynylestradiol (0-solvent control-, 0.01, 0.1, 1 and 10 ?g EE2/L of water), using 3 tanks per condition. In total, 30 samples were analyzed independantly: 6 samples per concentration tested (two samples per tank, three tanks per concentration), each sample being a pool of 10 pairs of gonads.
2015-06-25 | E-GEOD-58519 | biostudies-arrayexpress
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
Project description:Metabolic processes and sexual maturation closely interact during the long-distance reproductive migration of many fish species to their spawning grounds. In the present study, we have for the first time used exercise experimentally to investigate the effects on sexual maturation in rainbow trout. Pubertal autumn-spawning seawater-raised female rainbow trout Oncorhynchus mykiss (n=26; 50-cm, 1.5-kg) were rested or swum at a near optimal speed of 0.75 body-lengths per second in a 6,000 L swim-flume under natural reproductive conditions (16 °C fresh-water, starvation, 8h-light:16h-dark photoperiod). Fish were sampled after arrival and subsequently after 10 days (resting or swimming 307 km) and 20 days (resting or swimming 636 km). Ovarian development was significantly reduced in the swimmers. Analysis of the expression of key factors in the reproductive axis included pituitary kiss1-receptor, lh and fsh and ovarian lh-receptor, fsh-receptor, aromatase and vitellogenin-receptor (vtgr). Swimmers had lower pituitary lh and ovarian vtgr expression than resters. Furthermore, the number of late vitellogenic oocytes was lower in swimmers than in resters, probably resulting from the lower vtgr expression, and vitellogenin plasma levels were higher. Therefore, swimming exercise suppresses oocyte development possibly by inhibiting vitellogenin uptake. Transcriptomic changes that occurred in the ovary of exercised fish were investigated using a salmonid cDNA microarray platform. Protein biosynthesis and energy provision were among the sixteen functional categories that were all down-regulated in the ovary. Down-regulation of the transcriptomic response in the ovary illustrates the priority of energy reallocation and will save energy to fuel exercise. A swimming-induced ovarian developmental suppression at the start of vitellogenesis during long-term reproductive migration may be a strategy to avoid precocious muscle atrophy. In order to simulate the natural reproductive conditions of anadromous salmonids, experiments were performed with sea water-raised rainbow trout, Oncorhynchus mykiss. Resters and swimmers were starved during the experiment, seawater was replaced by fresh water and photoperiod was changed. These changes were expected to affect reproductive parameters but as âbackgroundâ effect because both resters as swimmers were experiencing these conditions at the same time in the same set-up. Any additional effects in swimming fish would thus be caused by swimming only. Pubertal autumn spawning rainbow trout (n=26; ~50 cm, ~1.5 kg) were purchased from a Danish exporter (Frederiksvaerk Aleexport) where they had been raised for 2 years in freshwater followed by 4 months in sea water cages at 10 â°. They were transferred by truck within 16 h to Spakenburg (Spakenburg Paling, The Netherlands) and subsequently in the same water in a similar holding tank to the swim-flume at Leiden University (The Netherlands). The next day, 5 randomly chosen fish were sampled as âstartâ-group while others were randomly divided into a ârestâ-group (n=10) and a âswimâ-group (n=11). During the following 4 days, the brackish 10 â° water was stepwise replaced by freshwater at 16 °C and photoperiod was changed from 16L:8D to 8L:16D. Fish were then acclimatized for two days to their new conditions. Subsequently, swimmers were first swum at a speed of 0.33 body-lengths per second (BL/s) which was increased the next day to the final, near optimal speed of 0.75 BL/s (0.34 m/s or 29.4 km/day). Fish were sampled after 10 days (5 resters and 5 swimmers) and 20 days (5 resters and 6 swimmers). At sampling, fish were anesthetized using oil of cloves that was commercially purchased from a drugstore (diluted 1:10 in ethanol and used at a dosage of 1.5 ml/l). Fish were euthanized by decapitation and dissected for the ovary which was flash frozen in liquid nitrogen. RNA was isolated from pituitary and ovary samples according to the TRIZOL reagent protocol by Invitrogen (Baro, Spain). Isolated RNA was DNAse treated using RQ1 DNAse Promega (Madison, USA) and reverse transcribed using Superscript IIITM (Baro, Spain) according to the manufacturerâs protocol. Microarray analyses were performed on ovarian tissue for 20-days-swimmers vs. 20-days-resters. A rainbow trout cDNA microarray platform was used that was previously validated and described by Koskinen et al., 2004ab, Krasnov et al., 2005, MacKenzie et al., 2006ab, 2008 and Djordjevic et al., 2009, and deposited in GEO under accession number GPL1212, the original cDNA microarray (SFA2.0 chip), and GPL6154; the updated 1.8 K platform. This platform compromises 1818 genes representing 366 functional categories. Total RNA was extracted from flash frozen samples from experimental fish of the 20-days-swim group (n=5) and 20-days-rest group (n=5) like described before. Total RNA corresponding to pooled samples from the swim or rest groups was labeled with Cye3 and Cye5-dCTP (GE Healthcare, Barcelona, Spain) using SuperScript III reverse transcriptase (Invitrogen, Baro, Spain) and oligo(dT) primer. In our experience, reverse labeling combined with multiple replication of spots provide robust normalization and high statistical power of analyses. cDNA was purified with MicroconYM30 (Millipore). The slides were pretreated with 1% BSA(fraction V), 20 à SSC, 10% SDS (30 min at 50°C) and washed with 2 à SSC (3 min) and 0.2 à SSC (3 min) and hybridized overnight in cocktail containing 50 à Denhardt's, 20 à SSC, 10% SDS, 10μg/μl polyadenylate and 10 μg/μl yeast tRNA. All chemicals were from Sigma-Aldrich. Scanning was performed with ScanArray 5000 and images were processed with QuantArray (GSI Luminomics). The measurements in spots were filtered by criteria I/B ⥠3 and (I-B)/(SI + SB) ⥠0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations. After subtraction of mean background, LOWESS normalization was performed. To assess differential expression of genes, the normalized log intensity ratios (expression ratio) were analyzed with Student's t-test (P <0.05). Validation of the microarray was performed by Q-PCR of 6 differentially expressed genes (DEGs) as described above. The used primers were either published (Alpha-globin I-1: Donate Jimeno, 2008) or designed, again by using the Genamics software.
2010-06-24 | E-GEOD-20131 | biostudies-arrayexpress
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: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