Ontology highlight
ABSTRACT:
PROVIDER: PRJNA117683 | ENA |
REPOSITORIES: ENA
Similar Datasets
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:Domestication causes large-scale effects on gene expression in rainbow trout: Analysis of the liver transcriptome
| PRJNA122669 | ENA
Project description:Domestication causes large-scale effects on gene expression in rainbow trout: Analysis of the brain transcriptome
| PRJNA122667 | ENA
Project description:Domestication causes large-scale effects on gene expression in rainbow trout: Analysis of the muscle transcriptome
| PRJNA122671 | ENA
Project description:Over the last century, rainbow trout (RBT) has been widely used as a biological model in many biological disciplines and has become one of the best-studied fish. For example, RBT is an excellent model to study gene evolution as it is a partially tetraploid organism that underwent a whole-genome duplication (salmonid-specific 4th WGD) followed by a partial re-diploidization and significant genome rearrangements. In the meantime, RBT domestication spread quickly and globally to six continents for aquaculture and recreation. Efforts to sequence a pangenome reference have begun, and genome sequence is available for at least three rainbow trout clonal lines. However, epigenome reference annotations are needed to understand the functional genomic basis of RBT's phenotypic, environmental, and evolutional variations. This study provides a comprehensive catalog and epigenome annotation tracks of the rainbow trout. Gene regulatory elements, including chromatin histone modifications, chromatin accessibility, and DNA methylation, were identified by integrating data from ChIP-seq, ATAC-seq, and Methyl Mini-seq across RBT tissues together with RNA-seq gene expression data sets.
2024-10-03 | GSE245212 | 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
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