Ontology highlight
ABSTRACT:
PROVIDER: PRJNA832971 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18961616.fastq.gz | Fastqsanger.gz | |||
| SRR18961617.fastq.gz | Fastqsanger.gz | |||
| SRR18961618.fastq.gz | Fastqsanger.gz | |||
| SRR18961619.fastq.gz | Fastqsanger.gz | |||
| SRR18961620.fastq.gz | Fastqsanger.gz |
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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: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
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.
2021-04-12 | GSE171856 | GEO
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:Rainbow trout (Oncorhynchus mykiss) is an important aquaculture fish species that is farmed worldwide, and it is also the most widely cultivated cold water fish in China. This species, a member of the salmonidae family, is an ideal model organism for studying the immune system in fish. Two phenotypes of rainbow trout are widely cultured; wild-type rainbow trout with black skin (WR_S) and yellow mutant rainbow trout with yellow skin (YR_S). Fish skin is an important immune organ, however, little is known about the differences in skin immunity between WR_S and YR_S in a natural flowing water pond aquaculture environment, and very few studies were conducted to investigate the ceRNA mechanism for fish skin.
2021-08-17 | GSE181974 | GEO
Project description:Rainbow trout is a typical cold-water fish, with the intensification of global warming, high temperatures severely restrict the development of aquaculture in summer. Understanding the molecular regulation mechanisms of rainbow trout in response to heat stress will be salutary to alleviate heat stress-related damage. In the present study, we performed transcriptome analysis of liver tissues in rainbow trout under heat stress (24℃) and control (18℃) conditions to identify induced lncRNAs and pathways by heat stress. More than 658 million clean reads and 5,916 lncRNAs were identified from six liver libraries. A total of 927 novel lncRNAs were generated and 428 differentially expressed lncRNAs were screened through stringent thresholds. The RNA-seq results were verified by RT-qPCR. In addition, the regulatory network of important functional lncRNA-mRNA were constructed. GO and KEGG enrichment analysis of target gene of differentially expressed lncRNAs were performed. Many target genes involved in maintaining homeostasis or adapting to stress and stimuli were highly induced under heat stress. Several important regulatory pathways were involved in heat stress, including thyroid hormone signaling pathway, PI3K-Akt signaling pathway, estrogen signaling pathway, etc. This result broadens our understanding of lncRNA associated with heat stress and provides new insights into lncRNA-mediated regulation of rainbow trout heat stress.
2019-08-11 | GSE135668 | GEO
Project description:The rainbow trout, Oncorhynchus mykiss, has a male heterogametic XY genetic system, and this knowledge can be used to produce experimentally all male or all female genetic populations using males with new genotypes (XX and YY males). These monosex populations have been widely used for sex differentiation studies because they give the opportunity to work on undifferentiated gonads for which the natural fate as testis or ovary is known a priori. Using as a resource the availability of a lot of expressed sequenced tags (ESTs) sequencing projects in trout, we designed and built a micro-array in order to characterize, at the pangenomic scale, rainbow trout natural gonadal differentiation as well as the mechanisms by which androgen masculinize the embryonic ovary. We choose a Nylon membrane array technique used for large-scale gene expression profiling with low cost, easy customization and high sensitivity, which is important when a limiting amount of RNA is available. Keywords: time course of natural and androgen induced gonadal sex differentiation
2007-12-29 | GSE7018 | GEO