Rainbow Trout metagenome
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ABSTRACT:
PROVIDER: PRJNA937442 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Rainbow trout skeletal muscle challenging with IPNV - Raw sequence reads
| PRJNA629987 | ENA
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:Rainbow trout myotubes treated with cortisol and/or infected with Piscirickettsia salmonis - Raw sequence reads
| PRJNA732666 | ENA
Project description:Proteomics represents a powerful tool for the analysis of fish spermatozoa, since these cells are transcriptionally inactive. The aim of the present study was to generate an inventory of the most prominent rainbow trout sperm proteins with the use of one-dimensional electrophoresis prefractionation combined with performance liquid chromatography electrospray ionization tandem mass spectrometry. This study provides the first in-depth analysis of the rainbow trout sperm proteome, with a total of 204 identified proteins. We found that rainbow trout spermatozoa are equipped with functionally diverse proteins related to energetic metabolism, signal transduction, protein turnover, transport, cytoskeleton, oxidative injures and stress and reproduction. The availability of a catalogue of rainbow trout sperm proteins provides a crucial tool for the understanding of fundamental molecular processes in fish spermatozoa for ongoing research in the development of novel markers of sperm quality and for the optimization of short- and long-term sperm preservation procedures.
2013-11-04 | PXD000355 | Pride
Project description:Raw read data from rainbow trout spleen and NALT libraries Raw sequence reads
| PRJNA551127 | ENA
Project description:Gut microbiota composition of rainbow trout Raw sequence reads
| PRJNA783153 | ENA
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: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:Rainbow trout (Oncorhynchus mykiss) and other salmonids are piscivorous fish. In aquaculture, fish-based feed ingredients are rapidly becoming unsustainable due to increased demand and diminishing supply. Total replacement of fishmeal with plant proteins causes severe intestinal enteritis, leading to reduced growth and lower feed efficiency. Through selective breeding, we have developed a strain of rainbow trout that does not develop distal intestine enteritis when reared on a high soy plant protein-based feed and also shows increased growth compared to other strains. Since central metabolism plays a major role in dietary alterations, and as growth was a major factor in the selection program, both muscle and liver gene expression were examined for differential regulation between commercial and selected trout strains when fed alternative diets. After three months of rearing on either a fishmeal (FM) or plant protein-based (PM) diet, muscle and liver tissues from a domestic non-selected strain (House Creek; develops enteritis) and the selected strain (ARS-KO; no enteritis) were extracted and prepped for Illumina RNA-seq. Raw reads were screened for quality then aligned to the rainbow trout transcriptome. Read-counts were used to assess differential expression between strains and treatments. Significant differentially expressed genes between comparisons were assessed.
2017-09-05 | GSE79531 | GEO
Project description:Rainbow trout (Oncorhynchus mykiss) and other salmonids are piscivorous fish. In aquaculture, fish-based feed ingredients are rapidly becoming unsustainable due to increased demand and diminishing supply. Total replacement of fishmeal with plant proteins causes severe intestinal enteritis, leading to reduced growth and lower feed efficiency. Through selective breeding, we have developed a strain of rainbow trout that does not develop distal intestine enteritis when reared on a high soy plant protein-based feed and also shows increased growth compared to other strains. Since central metabolism plays a major role in dietary alterations, liver RNA was examined for differential expression of long non-coding RNAs (lncRNAs) between commercial and selected trout strains when fed an alternative diet. These types of non-coding RNA have been previously shown to have a potential role in regulation of gene expression; however, most identified lncRNAs have not been functionally characterized and/or lack definition in many non-model organisms. Their roles in gene regulation and their responsiveness to dietary changes in trout are to be explored. After three months of rearing on a plant protein-based (PM) diet, liver tissues from a domestic non-selected strain (House Creek; develops enteritis) and the plant-diet tolerant selected strain (ARS-KO; no enteritis) were extracted and prepped for Illumina RNA-seq. Raw reads were screened for quality then assembled into transcripts using Trinity. Assembled transcripts were then submitted to the Annocript pipeline to determine their potential as lncRNAs. RNA-seq reads were mapped to putative lncRNAs. Read-counts were used to assess differential expression between strains.
2018-04-10 | GSE85104 | GEO