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Fish metagenome

ABSTRACT: Microbiome analysis of rainbow trout

PROVIDER: PRJDB10074 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR236194_1.fastq.gz	Fastqsanger.gz
	DRR236194_2.fastq.gz	Fastqsanger.gz
	DRR236195_1.fastq.gz	Fastqsanger.gz
	DRR236195_2.fastq.gz	Fastqsanger.gz
	DRR236196_1.fastq.gz	Fastqsanger.gz

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fish metagenome strain:Rainbow trout

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Waterborne beclomethasone diproprionate affects fish while its metabolite beclomethasone is not taken up

Project description:Investigation of transcriptome expression changes in liver tissue of rainbow trout exposed beclomethasone diproprionate (1 µg/L nominal concentration) in a flow through set up for 2 weeks

2014-12-10 | GSE57219 | GEO

Integrated mRNA and miRNA expression profile analyses reveal the potential roles of miRNA–mRNA pairs in skin color variation between wild-type and yellow mutant rainbow trout

Project description:As an important cold-water economic fish species, rainbow trout (Oncorhynchus mykiss) exhibits several intra-specific variation in skin pigmentation that can give rise to distinctive phenotypes, and wild-type rainbow trout with black skin (WR) and yellow mutant rainbow trout with yellow skin (YR) are the major two types in the farms, whose distinct skin colors make them suitable model for elucidating the skin pigmentation process. Skin color as a key indicator for selection in rainbow trout farming as well as has a strong visual impact on the consumer when rainbow trout are marketed. Previously, extensive studies have been conducted on skin color in rainbow trout, including the observation of skin spots and the expression analysis of some important pigment genes. However, up to date, no studies have systematically examined the molecular regulation mechanism of skin color difference between WR and YR through a high throughput method. Therefore, the aim of this study was to reveal the molecular regulation mechanism of skin color difference between these two strains at the mRNA and miRNA transcriptome level, and candidate genes, miRNAs and miRNA-mRNA pairs that may be responsible for rainbow trout albinism were obtained.

2022-04-21 | GSE172482 | GEO

Fish coelomic fluid proteomic analysis by LC-MSMS

Project description:The aim of this study was to complete and fully characterize the proteome of rainbow trout coelomic fluid (CF). Furthermore, we intended to identify the proteins responsible for the extension of egg viability in salmonids coelomic fluid. For this, the proteomic composition of different salmonids CF and non-salmonids CF were compared to identify proteins specifically present in salmonids CF. Those proteins could be responsible for the egg conservation property of the salmonids CF. In parallel, rainbow trout CF has been fractionated using HPLC coupled to gel filtration or ion exchange columns. We have then tested the egg conservation properties of the different fractions obtained. Proteins present in the fractions allowing egg quality preservation were identified. Identifying the CF components involved in egg viability would have important applied outputs with various biotechnological applications for aquaculture. It could help understanding egg quality preservation mechanisms, and consequently improving egg storage condition.

2024-05-21 | PXD034989 | Pride

Identification of gonadotropin-responsive genes in fish testis

Project description:In all vertebrates, the dual function of testis (production of sexual steroids and production of gametes) is mainly regulated by two gonadotropic pituitary hormones, FSH and LH. However, in fish the biological activities of the two hormones are not still clearly delineated and moreover, their molecular mechanisms are yet poorly understood. In this study we investigated the effects of FSH and LH on testicular gene expression, in the rainbow trout, at two developmental stages I-II and III (I: spermatogonia only, II: active spermatogonia proliferation, III: meiosis onset with the appearance of spermatocytes and round spermatids). Testes were collected from all-male population rainbow trout and incubated in six replicates for 96 hours, at 12Â°C, in the absence or presence of purified salmonid gonadotropins, FSH and LH (500 ng/mL).

2012-10-22 | E-GEOD-39465 | biostudies-arrayexpress

Integrative mRNA-miRNA interaction analysis associated with the immune response of rainbow trout Oncorhynchus mykiss to infectious hematopoietic necrosis virus infection [miRNA-seq]

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

Oncorhynchus mykiss muscle cells: Small vs. Large fish

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. Two-condition experiment, small vs. large-fish muscle cells. Sept. and Dec. spawning fish. Biological replicates: 4 small replicates, 4 large replicates for each time period.

2012-11-29 | E-GEOD-42582 | biostudies-arrayexpress

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