Soil metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJDB12100 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Epstein-Barr virus (EBV) related nasopharyngeal carcinoma (NPC) is an epithelial malignancy with higher incidence in Asian endemic area (EA) than in non-endemic area (NEA), where frequency is below 1/105/year. The causes of such difference are unclear and might be related to viral, environmental (e.g. diet) and genomic factors. We aimed at dissecting the gene expression (GE) and microenvironment landscape in NPC leading to the identification of molecular subtypes explaining the differences between EA and NEA.
2023-12-21 | GSE208281 | GEO
Project description:Monitoring microbial communities can aid in understanding the state of these habitats. Environmental DNA (eDNA) techniques provide efficient and comprehensive monitoring by capturing broader diversity. Besides structural profiling, eDNA methods allow the study of functional profiles, encompassing the genes within the microbial community. In this study, three methodologies were compared for functional profiling of microbial communities in estuarine and coastal sites in the Bay of Biscay. The methodologies included inference from 16S metabarcoding data using Tax4Fun, GeoChip microarrays, and shotgun metagenomics.
2024-04-14 | E-MTAB-13075 | biostudies-arrayexpress
Project description:Sudan I is one of the industry dyes and widely used in cosmetics, wax agent, solvent and textile. Sudan I has multiple toxicity such as carcinogenicity, mutagenicity, genotoxicity and oxidative damage. However, Sudan I has been illegally used as colorant in food products, triggering worldwide attention about food safety. Nevertheless, the toxicity of Sudan I on reproduction, particularly on oocyte maturation is still unclear. In the present study, using mouse in vivo models, we report the toxicity effects of Sudan I on mouse oocyte. The results reflect that Sudan I exposure disrupts spindle organization and chromosomes alignment as well as cortical actin distribution, thus leading to the failure of polar body extrusion. Based on the transcriptome results, it is found that the exposure of Sudan I leads to the change in expression of 764 genes. Moreover, it’s further reflected that the damaging effects of Sudan I are mediated by the destruction of mitochondrial functions, which induces the accumulated ROS to stimulate oxidative stress-induced apoptosis, while in vivo supplementation of melatonin efficaciously suppresses mitochondrial dysfunction and the accompanying apoptosis, thus reverses oocyte meiotic deteriorations. Collectively, our results prove the reproduction toxicity of Sudan I for the exposure of Sudan I reduces the oocyte quality, and demonstrate a feasible solution to mitigating Sudan I-induced meiotic deteriorations.
2021-08-08 | GSE181555 | GEO
Project description:Inflammaging is the name given to this chronic and asymptomatic inflammatory state generated by the aging process and by chronic and infectious diseases. Chronic diseases can alter the epigenetic profile of tissues leading to an increased epigenetic aging and some of the differentially methylated genes can be used to characterize the disease and as disease biomarkers. Leprosy is an infection caused by Mycobacterium leprae and can be lifelong, exposing the individual to a low-grade inflammation environment. In this study, we evaluated the inflammatory profile in 35 individuals from a leprosy endemic area from Brazil by cytokine analysis with a luminex assay. In adition, we investigated the leucocytes genome-wide DNA methylation profile using the Infinium MethylationEPIC BeadChip array. A total number of 31 CpGs were significantly methylated, between cases and controls, which belonged to 8 genes potentially peripherally perturbed in the pathogenesis of the disease. Affected individuals from endemic area were epigenetically aged in relation to control samples and interesting control samples from endemic area were aged in relation to unaffected control samples from non-endemic area. In conclusion, leprosy showed a deregulated methylation profile in comparison with control samples. The epigenetic analysis provided valuable clues for further investigations in understanding peripherical blood leprosy alterations and the use of these genes as biomarkers.
2023-02-21 | GSE197331 | GEO
Project description:Increasing concern about pollution of our environment calls for advanced and rapid methods to estimate ecological toxicity. The use of gene expression microarrays in environmental studies can potentially meet this challenge. We present a novel method to examine soil toxicity. We exposed the collembolan Folsomia candida to soil containing an ecologically relevant cadmium concentration, and found a cumulative total of 1586 differentially expressed transcripts across three exposure durations, including transcripts involved in stress response, detoxification, and hypoxia. Additional enrichment analysis of gene ontology (GO) terms revealed that antibiotic biosynthesis is important at all time points examined. Interestingly, genes involved in the "penicillin and cephalosporin biosynthesis pathway" have never been identified in animals before, but are expressed in F. candida’s tissue. The synthesis of antibiotics can possibly be a response to increased cadmium-induced susceptibility to invading pathogens, which might be caused by repression of genes involved in the immune-system (C-type lectins and Toll receptor). This study presents a first global view on the environmental stress response of an arthropod species exposed to contaminated soil,and provides a mechanistic basis for the development of a gene expression soil quality test. Keywords: cadmium, soil, Collembola, environmental genomics
2008-08-08 | GSE11122 | GEO
Project description:Plankton biodiversity monitoring by environmental DNA: a multiple marker study
| PRJDB12325 | ENA
Project description:Hawai'i coral reef seawater, environmental DNA metabarcoding
| PRJNA607318 | ENA
Project description:16S Metabarcoding of soil bacterial communities from Brazilian karstic area
| PRJNA732183 | ENA