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 muscle transcriptome
| PRJNA122671 | ENA
Project description:Domestication causes large-scale effects on gene expression in rainbow trout: Analysis of the brain transcriptome
| PRJNA122667 | ENA
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:Large-scale temporal gene expression profiling during gonadal differentiation and early gametogenesis in rainbow-trout
| PRJNA91411 | ENA
Project description:Effects of domestication and GH transgenesis on mRNA profiles in rainbow trout
| PRJNA206076 | ENA
Project description:Growth rate can be genetically modified in many vertebrates by domestication and selection, and more recently by transgenesis overexpressing growth factor genes (e.g. growth hormone, GH). While the phenotypic end consequence is similar, it is currently not clear whether the same modifications to physiological pathways are occurring in both genetic processes, nor to what extent they may interact when combined. To examine these questions, we have used rainbow trout as a model species because non-domesticated wild strains are available as comparators to assess genetic and physiological changes that have arisen from domestication and from GH transgenesis. In addition to pure wild and pure domesticated strains, two different GH transgenes with markedly different growth effects were examined, both in a wild background and in hybrids which combined domesticated and wild genomes in addition to the transgene. We find that liver mRNAs show highly concordant changes in levels in both types of fast-growing fish, relative to wild type, for both up- and down-regulated genes. Further, among domesticated, transgenic, and their hybrid genotypes, a strong positive correlation was found between growth rate and the number of genes affected or their levels of mRNA. Functional analysis found that genes involved in immune function, carbohydrate metabolism, detoxification, transcription regulation, growth regulation, and lipid metabolism were affected in common by domestication and GH transgenesis. The common responses of domesticated and GH transgenic strains is consistent with the GH pathway or its downstream effects being upregulated in domesticated animals during their modification from wild-type growth rates. Microarray analyses were performed on five individual rainbow trout per group of pure wild, pure domesticated, GH transgenic strain 1 in wild, GH transgenic strain 2 in wild, GH transgenic strain 1 in wild-domestic hybrid, and GH transgenic strain 2 in wild-domestic hybrid hybridized (one slide per individual) against a common wild-type RNA pool.
2013-12-03 | E-GEOD-47562 | biostudies-arrayexpress
Project description:Domestication has produced faster-growing strains of animals for use in agriculture, but selection has been applied with little knowledge of the underlying genetic changes that arose throughout the process. Mammals and birds have been domesticated for thousands of years whereas fish have been domesticated only recently; therefore, wild progenitor strains remain for comparison. Rainbow trout (Oncorhynchus mykiss) have undergone intensive selection and domesticated strains grow more rapidly than extant wild strains. To assess physiological pathways altered by domestication, whole-genome mRNA expression was measured in brain, muscle and liver of size-matched domestic and wild trout using a 16K (cGRASP) salmonid microarray. A large number of genes differed between strains, ranging from 3% of genes in brain to 9% in muscle. Domestic fish had more down-regulated genes in the brain relative to wild fish, whereas more genes were up-regulated in domestic liver and muscle. Relative to wild fish, there was a down-regulation of cell division and an up-regulation of structural genes in the brain of domestic fish. In liver from domestic fish, there was an up-regulation of genes related to transport with a down-regulation of lipid binding. Analysis of the functional categories for muscle indicated that most pathways, including pathways related to metabolism and catabolism, were up-regulated in domestic fish. Comparison of these results to other genomic studies on transgenic, domestic and wild salmonids suggests that similar physiological pathways are altered systemically to support faster rates of growth, regardless of the underlying genetic alteration that has caused the altered growth. Microarray analyses were performed on six individual fish per group of wild type and domestic rainbow trout hybridized (one slide per individual) against a common wild-type RNA pool.
2010-05-16 | E-GEOD-16901 | biostudies-arrayexpress
Project description:Domestication has produced faster-growing strains of animals for use in agriculture, but selection has been applied with little knowledge of the underlying genetic changes that arose throughout the process. Mammals and birds have been domesticated for thousands of years whereas fish have been domesticated only recently; therefore, wild progenitor strains remain for comparison. Rainbow trout (Oncorhynchus mykiss) have undergone intensive selection and domesticated strains grow more rapidly than extant wild strains. To assess physiological pathways altered by domestication, whole-genome mRNA expression was measured in brain, muscle and liver of size-matched domestic and wild trout using a 16K (cGRASP) salmonid microarray. A large number of genes differed between strains, ranging from 3% of genes in brain to 9% in muscle. Domestic fish had more down-regulated genes in the brain relative to wild fish, whereas more genes were up-regulated in domestic liver and muscle. Relative to wild fish, there was a down-regulation of cell division and an up-regulation of structural genes in the brain of domestic fish. In liver from domestic fish, there was an up-regulation of genes related to transport with a down-regulation of lipid binding. Analysis of the functional categories for muscle indicated that most pathways, including pathways related to metabolism and catabolism, were up-regulated in domestic fish. Comparison of these results to other genomic studies on transgenic, domestic and wild salmonids suggests that similar physiological pathways are altered systemically to support faster rates of growth, regardless of the underlying genetic alteration that has caused the altered growth. Microarray analyses were performed on nine individual fish per group of wild type and domestic rainbow trout hybridized (one slide per individual) against a common wild-type RNA pool.
2010-05-16 | E-GEOD-16889 | biostudies-arrayexpress