Oncorhynchus mykiss (Rainbow trout)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA551127 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9597140_1.fastq.gz | Fastqsanger.gz | |||
| SRR9597140_2.fastq.gz | Fastqsanger.gz | |||
| SRR9597150_1.fastq.gz | Fastqsanger.gz | |||
| SRR9597150_2.fastq.gz | Fastqsanger.gz | |||
| SRR9597160_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:The objective of this study was to identify and quantify proteomic profiles of spleen 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 spleen was washed three times with sterile phosphate-buffered saline containing a cocktail of mammalian protease inhibitors. Spleen samples were snap-frozen in liquid nitrogen and stored at –80 °C.
2018-08-14 | PXD008478 | Pride
Project description:The aim of this sequencing experiment was to make available tissue expression panels for selected fish species for comparative expression studies between the species. Tissue samples were collected for zebrafish (Danio rerio), medaka (Oryzias latipes), and rainbow trout (Oncorhynchus mykiss). Tissue types included liver, skin, muscle, heart, gut, gill, eye, brain for all three species, with additionally pyloric caeca, kidney, head kidney, and spleen for rainbow trout. Only liver samples were taken in replicate of four or three for rainbow trout. All fish were raised under standard rearing conditions for the species. Total RNA was extracted from the tissue samples and paired‐end sequencing of sample libraries was completed on an Illumina HiSeq 2500 with 125‐bp reads. Processed count tables per species as raw counts, FPKM, or TPM, were generated from read alignment to the Ensembl genomes of the respective species using STAR and gene level counting using RSEM and Ensembl gene annotation.
2020-04-30 | E-MTAB-8959 | biostudies-arrayexpress
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 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: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:Purpose: a transcriptomic analysis was performed to extend our understanding on the immune response picture of rainbow trout exposed to I. multifiliis. Methods: Gill samples were collected from fish in each tank (control and infected group) at day 8 after infection. Total RNA was extracted using RTN350 (Sigma-Aldrich), according to the manufacturer’s instruction and subsequently, DNase treated with DNase I (Thermo Scientific, USA). Quality and integrity of the total RNA were checked on an Agilent Bioanalyzer 2100 total RNA Nano series II chip (Agilent, Amstelveen, Netherlands). Illumina RNAseq libraries were prepared from 500 ng total RNA using the Illumina TruSeqTM Stranded mRNA LT Sample Prep Kit according to the manufacturer’s instructions (Illumina Inc. San Diego, CA, USA). All RNAseq libraries (150-750 bp inserts) were sequenced on an Illumina HiSeq2500 sequencer as 1 x 50 nucleotides single-end reads according to the manufacturer’s protocol. Image analysis and base calling were done using the Illumina pipeline. Reads were aligned to the Rainbow trout reference genome (http://www.genoscope.cns.fr/trout/data/) using TopHat (version 2.0.5) and on average 53.4% of the RNAseq reads could be mapped. The resulting files were filtered using SAMtools (version 0.1.18) to exclude secondary alignment of reads. For statistical comparison of gene expression levels between groups, aligned fragments per predicted gene were counted from SAM alignment files using the Python package HTSeq (version 0.5.3p9). To make comparisons across samples possible, these fragment counts were corrected for the total amount of sequencing performed for each sample. As a correction scalling factor, we employed library size estimates determined using the R/Bioconductor (release 2.11) package DESeq. Read counts were normalized by dividing the raw counts obtained from HTSeq by its scale factor. Correction for false positives is included in the statistical analysis of gene expression through DESeq. The cut-off for significance was set to adjusted p<0.05 and at least 2-fold change. Results: a transcriptomic analysis was performed on infected rainbow trout gills and it showed that a total of 3,352 (7.2%) out of 46,585 identified genes were revealed significantly expressed after parasite infection. Of differentially expressed genes, 1.796 genes were up-regulated and 1.556 genes down-regulated. These were classified into 61 Gene Ontology (GO) terms and mapped to 282 reference canonical pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Infection of I. multifiliis induced a clear differential expression of immune genes, related to both innate and adaptive immunity. A total of 268 (6.86%) regulated genes was known to take part in 16 immune-related pathways. These involved pathways related to the innate immune system such as Chemokine signaling pathway, Platelet activation, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, and Leukocyte transendothelial migration. Conclusion: a transcriptomic profile of rainbow trout gills exposed to the parasitic I. multifiliis was reported for the first time. A total of 3,355 differentially expressed unigenes were identified. Of these were 1,184 unigenes (mapped to 952 genes) annotated 282 KEGG pathways and 268 unigenes were associated with 16 immune pathways. Most unigenes were related to innate immune system pathways (Chemokine signaling pathway, Platelet activation, Toll-like receptor signaling pathway, NOD-like receptor signaling pathway, and Leukocyte transendothelial migration) although a number of unigenes was related to adaptive responses (antigen processing and presentation, T and B cell receptor signaling pathway). The present study gave a far better resolution of the immune response of rainbow trout exposed to a parasitic protozoan than has ever been presented previously. The identification of a series of immune genes involved in several but important was useful for understanding of immune mechanism of the rainbow trout responding to the parasite I. multifiliis. Our results provide tools to link innate and adaptive immune elements in the process and present basic information which will be useful in the future studies related to immunoprophylaxis.
2018-06-13 | GSE115675 | GEO
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: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
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: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