Ontology highlight
ABSTRACT:
PROVIDER: PRJNA386519 | ENA |
REPOSITORIES: ENA
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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: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: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
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: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 | GSE176396 | GEO
Project description:In rainbow trout (Oncorhynchus mykiss), the effect of a paternal and a maternal high carbohydrate/low protein diet was assessed on progeny. To this purpose, two-year old males and females rainbow trout were fed either a control diet or a high carbohydrate/low protein diet for an entire reproductive cycle for females and for 5 months for males. Crossed-fertilizations were carried out in order to obtain 4 groups of offspring. Before the first feeding, whole fry transcriptomes were compared to detect any impact of the parental diet on offspring metabolism.
2021-07-08 | GSE171310 | 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:The study aimed to characterize gene expression in rainbow trout ovary during ovarian development from immature to mature stages. Whole ovary were collected at the following stages: immature pre-vitelogenesis (IMM), mid-vitellogenesis (MV), late vitellogenesis (LV), post-vitellogenesis (PV) and mature while meiotic maturation is in progress (MAT). Gene expression in rainbow trout ovary was measured at 5 different stages (immature, mid-vitellogenesis, late vitellogenesis, post-vitellogenesis and mature). Three to four biological replicates were used for each stages.
2013-04-11 | E-GEOD-39587 | biostudies-arrayexpress
Project description:The study aimed to characterize miRNA expression in rainbow trout ovary during ovarian development from immature to mature stages. Whole ovary were collected at the following stages: immature pre-vitelogenesis (IMM), mid-vitellogenesis (MV), late vitellogenesis (LV), post-vitellogenesis (PV) and mature while meiotic maturation is in progress (MAT). miRNA expression in rainbow trout ovary was measured at 5 different stages (immature, mid-vitellogenesis, late vitellogenesis, post-vitellogenesis and mature). Two to three biological replicates were used for each stages.
2013-04-11 | E-GEOD-39588 | biostudies-arrayexpress