Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1300819 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:We used the scRNA-seq to characterize disease-related heterogeneity within cell populations of macrophages/monocytes in the bronchoalveolar lavage fluid from West Highland white terriers either healthy or affected with canine idioapthic pulmonary fibrosis. The disease is still not well understood, occurs in old West Highland white terriers and results from deposition of fibrotic tissue in the lung parenchyma causing respiratory failure.
2020-12-02 | E-MTAB-9623 | biostudies-arrayexpress
Project description:SNP genotyping was used to determine if the free living Highland Wild dogs of Papua, Indonesia are the ansestors of captive New Guinea Singing Dogs.
2020-03-31 | GSE143824 | GEO
Project description:Tibetan chickens exhibit specific adaptations to high-altitude conditions compared with their lowland counterparts. To illustrate the genetic mechanisms of such adaptations in highland chickens, the genomes of four highland and four lowland chicken populations were resequenced. Our results showed that genes under positive selection in highland populations were related to cardiovascular and respiratory system development, DNA repair, response to radiation, inflammation, and immune response, indicating a strong adaptation to oxygen scarcity and high-intensity solar radiation. The distribution of allele frequencies of non-synonymous single nucleotide polymorphisms between highland and lowland populations was also analyzed by chi-square test. The results showed that several differentially distributed genes with missense mutations were enriched in several functional categories, especially in blood vessel development, which were related to adaptations to hypoxia and intense radiation. RNA sequencing also revealed that several differentially expressed genes were enriched in gene ontology terms related to blood vessel and respiratory system development. Additionally, an evident admixture found in Tibetan chickens suggested a history of introgression from lowland gene pools. Overall, our data provided new insights into the unique adaptation of highland animals to extreme environments.
2016-01-26 | GSE77166 | GEO
Project description:The process of commercial catching, transport and slaughter (CTS) is known to be an acute stressful event in broiler chickens. Corticosteroid concentrations increase, impacting measures of IGF-1, growth hormone and metabolites of the immune system from blood plasma samples. We used ARK-Genomics chicken 20K oligo array, a two channel DNA microarray, to investigate the significantly differentially expressed genes in the livers of chickens during CTS. We investigate the differences of gene expression profiles in hepatic tissues between control birds (n=10) and birds experiencing CTS (n=10) using an ARK-Genomics chicken 20K oligo array, a two channel DNA array (http://www.ark-genomics.orgmicroarray) with full dye swap.
2010-05-05 | E-GEOD-20953 | biostudies-arrayexpress
Project description:Using comparative genomics, we discovered that a previously uncharacterized gene (1700011H14RIK/C14ORF105/CCDC198) hereby named FAME (Factor Associated with Metabolism and Energy) shows an unusually high rate of evolutionary divergence in birds and mammals. By comparing SNVs, we identified gene-flow of FAME from Neandertals into modern humans. FAME knockout animals demonstrated increased body weight and decreased energy expenditure, corresponding to GWAS linking FAME with higher BMI, diabetes-related pathologies, and macular degeneration in humans. The analysis of gene expression and subcellular localization revealed that FAME is a membrane-bound protein enriched in kidneys. Although a gene knockout resulted in structurally normal kidneys, we detected higher Albumin in urine and lowered ferritin in the blood. The experiment confirmed interactions between FAME and ferritin and showed co-localization in vesicular and plasma membranes. Overall, our results show that FAME plays a role in tuning metabolite excretion and energy expenditure, partly explaining why it evolves at a high rate in birds and mammals. Here, we provide data related to identification of FAME interactome using the co-immunoprecipitation method.
2023-07-20 | PXD039259 | Pride
Project description:Spatially varying environments can pose distinct costs and benefits on traits under selection, such that a beneficial trait in one environment may be counter-productive in another. As an example, lowland and highland Peromyscus maniculatus populations display divergent, locally adapted physiological mechanisms shaped by altitudinal differences in oxygen availability. Particularly, lowland mice leverage ancestral plasticity derived from acute episodic bouts of low internal oxygen triggered by causes such as blood loss, anemia or tissue ischemia. These responses can be maladaptive under persistent low-oxygen conditions, as they could lead to physiological complications such as pulmonary hypertension. Therefore, highland ancestry is associated with traits promoting chronic hypoxia tolerance. Given each population’s distinct adaptive histories and reliance on plasticity for hypoxia tolerance, we hypothesized that upon hypoxia exposure lowland mice would have a more robust epigenetic response, driving trait plasticity, than highland mice. Using DNA methylation data collected from left ventricle tissues, we show that upon hypoxia exposure, lowland mice can chemically modulate the epigenetic landscape to a greater extent than highland mice, especially at key hypoxia-relevant genes such as Egln3, a regulator of Epas1- a gene frequently targeted for positive selection at high elevation. In addition, lowland mice show greater enrichment of DNA methylation change concentrated at hypoxia-relevant biological pathways, particularly those related to Notch ligands. These findings exemplify each population’s distinct reliance on molecular plasticity driven by their unique evolutionary histories.
2025-04-30 | GSE270202 | GEO