Transcriptional and miRNA profiling during rainbow trout ovarian development
Ontology highlight
ABSTRACT:
ORGANISM(S): Oncorhynchus mykiss
PROVIDER: GSE39590 | GEO | 2013/04/11
SECONDARY ACCESSION(S): PRJNA171167
REPOSITORIES: GEO
Similar Datasets
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-04-11 | E-GEOD-39590 | 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).
2013-04-11 | GSE39588 | GEO
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
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).
2013-04-11 | GSE39587 | 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:This SuperSeries is composed of the SubSeries listed below.
2006-12-31 | GSE5813 | GEO
Project description:BACKGROUND: Spermatogenesis is a late developmental process that involves a coordinated expression program in germ cells and a permanent communication between the testicular somatic cells and the germ-line. Current knowledge regarding molecular factors driving male germ cell proliferation and differentiation in vertebrates is still limited and mainly based on existing data from rodents and human. Fish with a marked reproductive cycle and a germ cell development in synchronous cysts have proven to be choice models to study precise stages of the spermatogenetic development and the germ cell-somatic cell communication network. In this study we used 9K cDNA microarrays to investigate the expression profiles underlying testis maturation during the male reproductive cycle of the trout, Oncorhynchus mykiss. RESULTS: Using total testis samples at various developmental stages and isolated spermatogonia, spermatocytes and spermatids, 3379 differentially expressed trout cDNAs were identified and their gene activation or repression patterns throughout the reproductive cycle were reported. We also performed a tissue-profiling analysis and highlighted many genes for which expression signals were restricted to the testes or gonads from both sexes. The search for orthologous genes in genome-sequenced fish species and the use of their mammalian orthologs allowed us to provide accurate annotations for trout cDNAs. The analysis of the GeneOntology terms therefore validated and broadened our interpretation of expression clusters by highlighting enriched functions that are consistent with known sequential events during male gametogenesis. Furthermore, we compared expression profiles of trout and mouse orthologs and identified a complement of genes for which expression during spermatogenesis was maintained throughout evolution. CONCLUSION: A comprehensive study of gene expression and associated functions during testis maturation and germ cell differentiation in the rainbow trout is presented. The study identifies new pathways involved during spermatogonia self-renewal or rapid proliferation, meiosis and gamete differentiation, in fish and potentially in all vertebrates. It also provides the necessary basis to further investigate the hormonal and molecular networks that trigger puberty and annual testicular recrudescence in seasonally breeding species.
| S-EPMC2786911 | biostudies-literature
Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series
2013-06-01 | E-GEOD-32431 | biostudies-arrayexpress
Project description:Carnivorous rainbow trout exhibit prolonged postprandial hyperglycemia when fed a diet exceeding 20% carbohydrate content. This poor capacity to utilize carbohydrates has led to rainbow trout being classified as "glucose-intolerant" (GI). The metabolic phenotype has spurred research to identify the underlying cellular and molecular mechanisms of glucose intolerance, largely because carbohydrate-rich diets provide economic and ecological advantages over traditionally used fish meal, considered unsustainable for rainbow trout aquaculture operations. Evidence points to a contribution of hepatic intermediary carbohydrate and lipid metabolism, as well as upstream insulin signaling. Recently, microRNAs (miRNAs), small noncoding RNAs acting as negative posttranscriptional regulators affecting target mRNA stability and translation, have emerged as critical regulators of hepatic control of glucose-homeostasis in mammals, revealing that dysregulated hepatic miRNAs might play a role in organismal hyperglycemia in metabolic disease. To determine whether hepatic regulatory miRNA networks may contribute to GI in rainbow trout, we induced prolonged postprandial hyperglycemia in rainbow trout by using a carbohydrate-rich diet and profiled genome-wide hepatic miRNAs in hyperglycemic rainbow trout compared with fasted trout and trout fed a diet devoid of carbohydrates. Using small RNA next-generation sequencing and real-time RT-PCR validation, we identified differentially regulated hepatic miRNAs between these groups and used an in silico approach to predict bona fide mRNA targets and enriched pathways. Diet-induced hyperglycemia resulted in differential regulation of hepatic miRNAs compared with fasted fish. Some of the identified miRNAs, such as miRNA-27b-3p and miRNA-200a-3p, are known to be responsive to hyperglycemia in the liver of hyperglycemic glucose-tolerant fish and mammals, suggesting an evolutionary conserved regulation. Using Gene Ontology term-based enrichment analysis, we identify intermediate carbohydrate and lipid metabolism and insulin signaling as potential targets of posttranscriptional regulation by hyperglycemia-regulated miRNAs and provide correlative expression analysis of specific predicted miRNA-target pairs. This study identifies hepatic miRNAs in rainbow trout that exhibit differential postprandial expression in response to diets with different carbohydrate content and predicts posttranscriptionally regulated target mRNAs enriched for pathways involved in glucoregulation. Together, these results provide a framework for testable hypotheses of functional involvement of specific hepatic miRNAs in GI in rainbow trout.
| S-EPMC6766702 | biostudies-literature
Project description:BackgroundMicroRNAs (miRNAs) have emerged as important post-transcriptional regulators of gene expression in a wide variety of physiological processes. They can control both temporal and spatial gene expression and are believed to regulate 30 to 70% of the genes. Data are however limited for fish species, with only 9 out of the 30,000 fish species present in miRBase. The aim of the current study was to discover and characterize rainbow trout (Oncorhynchus mykiss) miRNAs in a large number of tissues using next-generation sequencing in order to provide an extensive repertoire of rainbow trout miRNAs.ResultsA total of 38 different samples corresponding to 16 different tissues or organs were individually sequenced and analyzed independently in order to identify a large number of miRNAs with high confidence. This led to the identification of 2946 miRNA loci in the rainbow trout genome, including 445 already known miRNAs. Differential expression analysis was performed in order to identify miRNAs exhibiting specific or preferential expression among the 16 analyzed tissues. In most cases, miRNAs exhibit a specific pattern of expression in only a few tissues. The expression data from sRNA sequencing were confirmed by RT-qPCR. In addition, novel miRNAs are described in rainbow trout that had not been previously reported in other species.ConclusionThis study represents the first characterization of rainbow trout miRNA transcriptome from a wide variety of tissue and sets an extensive repertoire of rainbow trout miRNAs. It provides a starting point for future studies aimed at understanding the roles of miRNAs in major physiological process such as growth, reproduction or adaptation to stress. These rainbow trout miRNAs repertoire provide a novel resource to advance genomic research in salmonid species.
| S-EPMC4774146 | biostudies-literature