Ontology highlight
ABSTRACT:
PROVIDER: PRJNA376561 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5280480_1.fastq.gz | Fastqsanger.gz | |||
| SRR5280480_2.fastq.gz | Fastqsanger.gz | |||
| SRR5280490_1.fastq.gz | Fastqsanger.gz | |||
| SRR5280490_2.fastq.gz | Fastqsanger.gz | |||
| SRR5280510_1.fastq.gz | Fastqsanger.gz |
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Project description:Comparison of brain gene expression between silver foxes selected for tame behavior and non-selected silver fox.
2005-12-31 | E-MEXP-451 | biostudies-arrayexpress
Project description:Domestication leads to a spectrum of striking behavioral changes whose genetic basis remains largely unknown. Silver foxes have been selectively bred for tame and aggressive behaviors for over 50 years at the Institute for Cytology and Genetics in Novosibirsk, Russia. To further understand the genetic basis and molecular mechanisms underlying tame and aggressive behavioral phenotypes segregating in selected strains of the silver fox, we quantified genome-wide gene expression levels using RNA-seq in two selected brain tissues, right prefrontal cortex and basal forebrain, from 12 aggressive and 12 tame individuals. Expression analysis reveals 146 differentially expressed genes in prefrontal cortex between tame and aggressive individuals at a 5% FDR, and 33 hits were found in basal forebrain. These candidates include genes in key pathways known to be critical to neurological processing, such as serotonin and glutamate receptor pathways. The data relate in interesting ways to neurological and pharmacological effects that are actively being studied to understand human aggression. In addition, we identified 31,000 high quality exonic SNPs, 295 of which show significant allele frequency differences between tame and aggressive individuals at an adjust P-value < 0.05 level from gene dropping simulation based on the entire pedigrees. A non-synonymous change in a glutamate receptor, GRM3, is among these significant SNPs, indicating that expression and allele-frequency changes are hitting the same pathways. These changes in expression level and allele frequency might be the direct response to the artificial selection and will help understand the genetic basis of mammalian domestication process.
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Project description:Transcriptome responses to selection for tame/aggressive behaviors in silver foxes (Vulpes vulpes)
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Project description:mRNA Sequencing was done in whole brain hemispheres of the 75 most tame and 75 most aggressive rats of an F2 intercross of rat lines selected for tame and aggressive behavior towards humans. The brain gene expression levels are associated with 1728 genetic markers across the genome to identify expression QTL (eQTL). Genes whose expression is influenced by the same genetic loci that also influence tameness are candidate genes for tame and aggressive behavior. The list of genetic markers can be found in the supplementary materials of the paper for this study. A series of genotype data spreadsheets and associated data processing protocol are available from http://www.ebi.ac.uk/arrayexpress/files/E-MTAB-2544/E-MTAB-2544.additional.1.zip.
2014-08-27 | E-MTAB-2544 | biostudies-arrayexpress
Project description:Dogs infected with the cardiopulmonary nematode Angiostrongylus vasorum may suffer respiratory distress and/or bleeding disorders. Descriptions of clinical signs in foxes are rare, despite high prevalence. To evaluate the impact of infection on coagulation and immune response, serum proteins from eight experimentally infected foxes before and after inoculation (day 0, 35, 84, 154) were subjected to quantitative proteomic analysis and compared to available data from dogs. The number of differentially expressed proteins compared to uninfected baseline increased with chronicity of the infection. Bone marrow proteoglycan, chitinase 3-like protein 1 and pulmonary surfactant-associated protein B were among strongly upregulated proteins. Several proteins involved in coagulation were downregulated. Enriched pathways obtained from both up- and downregulated proteins included among others ‘platelet degranulation‘ and ‘haemostasis’, and indicated both activation and suppression of coagulation. Qualitative comparison to dog data suggests some parallel serum proteomic alterations. The comparison, however, highlights that foxes have a more balanced immunopathological response to A. vasorum infection compared to dogs, facilitating parasite survival in foxes. Our findings imply that foxes may cope better with an A. vasorum infection and that A. vasorum is likely more adapted to foxes as compared to dogs, explaining the relevant role of foxes as wildlife reservoir.
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Project description:Due to multi-generation domestication selection, farmed and wild Atlantic salmon diverge genetically, which raises concerns about potential genetic interactions among escaped farmed and wild populations and disrupts local adaptation through introgression. When farmed strains of distant geographic origin are used, it is unknown whether the genetic risks posed by escaped farmed fish will be greater than if more locally derived strains are used. Quantifying gene expression differences among divergent farmed, wild and F1 hybrids under controlled conditions is one of the ways to explore the consequences of hybridization. We compared the transcriptomes of late sac fry of a European (EO) farmed (“StofnFiskur”, Norwegian strain), a North American (NA) farmed (Saint John River, NB strain), a Newfoundland (NF) wild population with EO ancestry, and related F1 hybrids using 44K microarrays. Our findings indicate that the wild population showed greater transcriptome differences from the EO farmed strain than that of the NA farmed strain. We also found the largest differences in global gene expression between the two farmed strains. We detected fewer differentially expressed transcripts between F1 hybrids and domesticated/wild maternal strains. We also found that the differentially expressed genes between cross types over-represented GO terms associated with metabolism, development, growth, immune response, and redox homeostasis processes. These findings suggest that the interbreeding of escaped EO/NA farmed and NF wild population would alter gene transcription, and the consequences of hybridization would be greater from escaped EO farmed than NA farmed salmon, resulting in potential effects on the fitness of wild populations.
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