Fish metagenome strain:Rainbow trout
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB18020 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| DRR549602_1.fastq.gz | Fastqsanger.gz | |||
| DRR549602_2.fastq.gz | Fastqsanger.gz | |||
| DRR549603_1.fastq.gz | Fastqsanger.gz | |||
| DRR549603_2.fastq.gz | Fastqsanger.gz | |||
| DRR549604_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
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:In the context of replacing fish meal and fish oil in feeds for aquaculture, rainbow trout alevins received from first-feeding onwards, one of the three experimental diets: V (100% plant-based), C (mix of FM-FO & plant ingredients) or M (100% FM-FO based). The long term effects of such dietary replacement on the intestinal (mid gut) and hepatic transcriptome were studied in juveniles after a 7-month feeding trial at 7°C.
2018-02-14 | GSE84985 | GEO
Project description:Rainbow Trout metagenome Raw sequence reads
| PRJNA937442 | ENA
Project description:Gut bacteria of rainbow trout fed diets supplemented with Cellobiose
| PRJNA868155 | ENA
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:This SuperSeries is composed of the following subset Series: GSE16889: Domestication causes large-scale effects on gene expression in rainbow trout: Analysis of the brain transcriptome GSE16897: Domestication causes large-scale effects on gene expression in rainbow trout: Analysis of the liver transcriptome GSE16901: Domestication causes large-scale effects on gene expression in rainbow trout: Analysis of the muscle transcriptome Refer to individual Series
2010-05-16 | E-GEOD-16903 | biostudies-arrayexpress
Project description:Erythromycin (ERY) is a commonly used antibiotic that can be found in wastewater effluents globally. Due to the mechanisms by which they kill and prevent bacterial growth, antibiotics can have significant unwanted impacts on the fish gut microbiome. The overall objective of this project was to assess the effects of erythromycin and an antibiotic mixture on fish gut microbiomes. The project was split into two experiments to assess gut microbiome in response to exposure with ERY alone or in mixture with other common antibiotics. The objectives of experiment 1 were to understand uptake and depuration of ERY in juvenile rainbow trout (RBT) over a 7 d uptake followed by a 7 d depuration period using three concentrations of ERY. Furthermore, throughout the study changes in gut microbiome response were assessed. In experiment 2, a follow-up study was conducted using an identical experimental design to assess the impacts of an antibiotic-mixture (ERY, ampicillin, metronidazole, and ciprofloxacin at 100 µg/g each). Here, three matrices were analyzed, with gut collected for 16s metabarcoding, plasma for untargeted metabolomics, and brain for mRNA-seq analysis. ERY was depurated from the fish relatively quickly and gut microbiome dysbiosis was observed at 7 d after exposure, with a slight recovery after the 7 d depuration period. A greater number of plasma metabolites was dysregulated at 14 d compared to 7 d revealing temporality compared to gut microbiome dysbiosis. Furthermore, several transformation products of antibiotics and biomarker metabolites were observed in plasma due to antibiotic exposure. Brain transcriptome revealed only slight alterations due to antibiotic exposure. The results of these studies will help inform aquaculture practitioners and risk assessors when assessing the potential impacts of antibiotics in fish feed and the environment, with implications for host health.
2024-02-07 | GSE253746 | GEO
Project description:Through 8 generations of selection, our group has developed a strain of rainbow trout that exhibits high growth rates on an economically and environmentally sustainable all plant protein, high-soy diet. The selected strain is resistant to development of soy-induced enteritis, an inflammatory intestinal pathology that occurs often in high-value carnivorous aquaculture species. To better characterize the physiological mechanism behind the superior performance of the selected strain we compared the homeostatic intestinal gene expression of the select strain to that of a commercial control line of trout. Samples were collected at early life stages known to be critical in the development of host-microbe interactions in the gut of rainbow trout. All female cohorts of both strains were reared alongside starting from eggs. Intestinal samples from 5 fish per group (2 fish strains; 2 developmental stages; 20 samples total) were used to generate mRNA selected stranded RNA-seq libraries for high throughput sequencing. Reads were quantified at the transcript level prior to evaluating differential transcript usage and differential gene expression between the two strains of trout and the developmental stages.
2020-12-15 | GSE156372 | GEO
Project description:In the present study the combination of protein fractionation by one-dimensional gel electrophoresis and high performance liquid chromatography electrospray ionization tandem mass spectrometry was used to characterize the rainbow trout seminal plasma proteome. Our results led to the creation of a catalogue of rainbow trout seminal plasma proteins and significantly contributed to the current knowledge regarding the protein composition of fish seminal plasma. The major proteins of rainbow trout seminal plasma, such as transferrin, apolipoproteins, complement C3, serum albumin, hemopexin-like protein, alpha-1-antiproteinase-like and precerebellin-like protein were recognized as acute phase proteins (proteins which plasma concentration changes in response to inflammation). This study provides the basis for further functional studies of fish seminal plasma proteins, as well as for the identification of novel biomarkers for sperm quality.
2014-01-31 | PXD000306 | Pride
Project description:We have constructed a rainbow trout high-density oligonucleotide microarray by using all the available tentative consensus (TC) sequences from the Rainbow Trout Gene Index database (The Computational Biology and Functional Genomics Lab., Dana Farber Cancer Institute and Harvard School of Public Health). The Rainbow Trout Gene Index integrates research data from all available international rainbow trout genomic research projects. The newly designed microarray incorporates 37,394 unique transcript-specific oligonucleotide probes, 60-mer long each. The microarray was printed according to our design by Agilent Technologies using the 4 X 44-design format and contains 1417 Agilent control spots. The performance of the new microarray platform was evaluated by analyzing gene expression associated with the rainbow trout vitellogenesis-induced muscle atrophy. These chips can be ordered from Agilent using design number 016320. This microarray is anticipated to open new avenues of research that will aid in the development of novel strategies to enhance growth efficiency and quality in salmonid species. Keywords: Development of an oligo-array for rainbow trout
2008-06-01 | GSE9380 | GEO