Ontology highlight
ABSTRACT:
PROVIDER: PRJNA547678 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Escaped domesticated individuals can introduce disadvantageous traits into wild populations due to both adaptive differences between population ancestors and human-induced changes during domestication. In contrast to their domesticated counterparts, some endangered wild Atlantic salmon populations encounter during their marine stage large amounts of suspended sediments, which may act as a selective agent. We used microarrays to elucidate quantitative transcriptional differences between a domesticated salmon strain, a wild population and their first-generation hybrids during their marine life stage, to describe transcriptional responses to natural suspended sediments, and to test for adaptive genetic variation in plasticity relating to a history of natural exposure or nonexposure to suspended sediments. We identified 67 genes differing in transcription level among salmon groups. Among these genes, processes related to energy metabolism and ion homoeostasis were over-represented, while genes contributing to immunity and actin-/myosin-related processes were also involved in strain differentiation. Domestic–wild hybrids exhibited intermediate transcription patterns relative to their parents for two-thirds of all genes that differed between their parents; however, genes deviating from additivity tended to have similar levels to those expressed by the wild parent. Sediments induced increases in transcription levels of eight genes, some of which are known to contribute to external or intracellular damage mitigation. Although genetic variation in plasticity did not differ significantly between groups after correcting for multiple comparisons, two genes (metallothionein and glutathione reductase) tended to be more plastic in response to suspended sediments in wild and hybrid salmon, and merit further examination as candidate genes under natural selection.
2012-04-23 | GSE30555 | GEO
Project description:Analysis of gene expression in human macrophages infected with influenza A viruses expressing wild type NS1 protein or its mutant R38A, K41A. The hypothesis tested was that R38 and K41 residues within viral NS1 protein are essential fro transctiptional control of cellluar gene expression. Cells were infected with influenza A/WSN/33 viruses expressing wild type NS1 protein (WT), its R38A, K41A mutant (RK/AA) or non-infected (Mock)
2015-02-07 | GSE65702 | GEO
Project description:Analysis of gene expression in human retinal pigment epithelium cell line (RPE) infected with influenza A viruses expressing wild type NS1 protein or its mutant R38A, K41A. The hypothesis tested was that R38 and K41 residues within viral NS1 protein are essential fro transctiptional control of cellluar gene expression. Cells were infected with influenza A/WSN/33 viruses expressing wild type NS1 protein (WT), its R38A, K41A mutant (RK/AA) or non-infected (Mock)
2015-02-07 | GSE65699 | GEO
Project description:Lepeophtheirus salmonis (sea lice) and bacterial co-infection threatens wild and farmed Atlantic salmon performance and welfare. The present microarray-based study examined the dorsal skin transcriptome response to formalin-killed Aeromonas salmonicida bacterin (ASAL) in pre-adult sea lice-infected and non-infected Atlantic salmon to fill the existing knowledge gap and aid in developing anti-co-infection strategies. To this aim, sea lice-infected and non-infected salmon were intraperitoneally injected with either phosphate-buffered saline (PBS) or ASAL (i.e., 4 injection/infection groups: PBS/no lice, PBS/lice, ASAL/no lice, and ASAL/lice). The analysis of the dorsal skin transcriptome data [Significance Analysis of Microarrays (5% FDR)] identified 345 up-regulated and 2,189 down-regulated DEPs in the comparison PBS/lice vs. PBS/no lice, and 82 up-regulated and 3 down-regulated DEPs in the comparison ASAL/lice vs. ASAL/no lice. The comparison ASAL/lice vs. PBS/lice identified 272 up-regulated and 11 down-regulated DEPs, whereas ASAL/no lice vs. PBS/no lice revealed 27 up-regulated DEPs. The skin transcriptome differences between the co-stimulated salmon (i.e., ASAL/lice) and PBS/no lice salmon accounted for 1,878 up-regulated and 3,120 down-regulated DEPs.
2022-02-28 | GSE186292 | GEO
Project description:Escaped domesticated individuals can introduce disadvantageous traits into wild populations due to both adaptive differences between population ancestors and human-induced changes during domestication. In contrast to their domesticated counterparts, some endangered wild Atlantic salmon populations encounter during their marine stage large amounts of suspended sediments, which may act as a selective agent. We used microarrays to elucidate quantitative transcriptional differences between a domesticated salmon strain, a wild population and their first-generation hybrids during their marine life stage, to describe transcriptional responses to natural suspended sediments, and to test for adaptive genetic variation in plasticity relating to a history of natural exposure or nonexposure to suspended sediments. We identified 67 genes differing in transcription level among salmon groups. Among these genes, processes related to energy metabolism and ion homoeostasis were over-represented, while genes contributing to immunity and actin-/myosin-related processes were also involved in strain differentiation. DomesticM-bM-^@M-^Swild hybrids exhibited intermediate transcription patterns relative to their parents for two-thirds of all genes that differed between their parents; however, genes deviating from additivity tended to have similar levels to those expressed by the wild parent. Sediments induced increases in transcription levels of eight genes, some of which are known to contribute to external or intracellular damage mitigation. Although genetic variation in plasticity did not differ significantly between groups after correcting for multiple comparisons, two genes (metallothionein and glutathione reductase) tended to be more plastic in response to suspended sediments in wild and hybrid salmon, and merit further examination as candidate genes under natural selection. Salmon of three genotypes (strains: 1. wild (Stewiacke River salmon), 2. domesticated (Saint John River salmon), and 3. first generation hybrids between the two strains, were exposed to two environments (treatment: 1. suspended sediments, 2. control: clear water), using eight biological replicates (individuals) of each of the six experimental groups, summing up to 48 individuals, each individual has two technical replicates , each technical replicate has been labelled with a different dye, each technical replicate appears on a different array, dye swaps are equilibrated for arrays that combine individuals from different genotypes and for arrays that combine individuals from the same genotype but different environments. Technical replicates of individuals always appear once on arrays that compare between environments and once on arrays that compare among genotypes. In total there are 48 arrays.
2012-04-22 | E-GEOD-30555 | biostudies-arrayexpress
Project description:This purpose of this experiment was to investigate the transcriptional differences between mice infected with icSARS CoV, SARS MA15 wild type or SARS BatSRBD viruses.
2014-02-15 | GSE50000 | GEO
Project description:Analysis of gene expression in human macrophages infected with influenza A viruses expressing full length or truncated NS1 protein. The hypothesis tested was that C-terminal truncations of viral NS1 protein attenuate the capability of NS1 to limit activation of host antiviral and immune response genes. Cells were infected with influenza A/WSN/33 viruses expressing wild type NS1 protein (WSN-230), NS1 protein of 220 aa long (WSN-220) and NS1 protein of 202 aa long (WSN-202) on non-infected (Mock)
2014-10-08 | GSE62127 | GEO
Project description:Analysis of gene expression in human macrophages infected with influenza A viruses expressing wild type NS1 protein or its mutant R38A, K41A. The hypothesis tested was that R38 and K41 residues within viral NS1 protein are essential fro transctiptional control of cellluar gene expression. Cells were infected with influenza A/WSN/33 viruses expressing wild type NS1 protein (WT), its R38A, K41A mutant (RK/AA) or non-infected (Mock) Total RNA isolated from macrophages after 10 hours of infection with wild type or mutant influenza A virus (multiplicity of infection = 1)
2015-02-07 | E-GEOD-65702 | biostudies-arrayexpress
Project description:Analysis of gene expression in macrophages infected with influenza A virus or non-infected and treated with the saliphenylhalamide, obatoclax, expressing wild type NS1 protein or its mutant R38A, K41A. The hypothesis tested was that R38 and K41 residues within viral NS1 protein are essential for transctiptional control of cellluar gene expression. Cells were infected with influenza A/WSN/33 viruses expressing wild type NS1 protein (WT), its R38A, K41A mutant (RK/AA) or non-infected (Mock)
2015-02-18 | GSE66015 | GEO