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ABSTRACT:
PROVIDER: PRJEB13496 | ENA |
REPOSITORIES: ENA
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Project description:Purpose: We studied dioxin exposures and DNA methylation in sperm in 37 men from the Air Force Health Study Methods: We compared methylation levels in subjects with no, low, medium, and high dioxin levels using EWAS and looking at regions of DNA. We compared our results to those from a Russian study Results: No loci were found to be significantly associated with dioxin exposure in the EWAS when controlling for false discovery rate. Region H19 was found to have significant associations. Five of our loci of interest overlapped with significant findings from the Russian study
2019-10-24 | GSE139307 | GEO
Project description:The aim for this study was to compare the differences in the methylome of three Russian wheat aphid populations that differ in virulence and bacterial load. Differences in the methylome of US Russian wheat aphid biotype 2 (US-RWA2) that have undergone removal of their phytobiomes through isolation of newly born nymphs from their mothers compared to nymphs who stayed in close proximity to their progenitors. US-RWA1 is the least virulent biotype and US-RWA2 is the most virulent biotype. The isolated US-RWA2 population (with a reduced bacterial load) has been shown to be less virulent than the co-fed population (Luna et al., 2018). The corresponding two methylomes were then compared to the methylome of US Russian wheat aphid biotype 1 (US-RWA1 is less virulent than US-RWA2) to ascertain the contribution (or lack thereof) of the phytobiome in regards to the increased/decreased virulence of phytobiome present and absent aphids. We investigated the overall, genic, intergenic, exonic and intronic methylation - as well as genic and intergenic hemimethylation -all three available contexts ( CpG, CHG and CHH) through use of the Bismark pipeline. These findings were used to ascertain to what effect the phytobiome (bacterial load) had on methylation within the US Russian wheat aphid biotypes.
2022-06-30 | GSE185975 | GEO
Project description:The fate of the carbon stocked in permafrost soils following global warming and permafrost thaw is of major concern in view of the potential for increased CH4 and CO2 emissions from these soils. Complex carbon compound degradation and greenhouse gas emissions are due to soil microbial communities, but their composition and functional potential in permafrost soils are largely unknown. Here, a 2 m deep permafrost and its overlying active layer soil were subjected to metagenome sequencing, quantitative PCR, and microarray analyses. The active layer soil and 2 m permafrost soil microbial community structures were very similar, with Actinobacteria being the dominant phylum. The two soils also possessed a highly similar spectrum of functional genes, especially when compared to other already published metagenomes. Key genes related to methane generation, methane oxidation and organic matter degradation were highly diverse for both soils in the metagenomic libraries and some (e.g. pmoA) showed relatively high abundance in qPCR assays. Genes related to nitrogen fixation and ammonia oxidation, which could have important roles following climatic change in these nitrogen-limited environments, showed low diversity but high abundance. The 2 m permafrost soil showed lower abundance and diversity for all the assessed genes and taxa. Experimental biases were also evaluated and showed that the whole community genome amplification technique used caused large representational biases in the metagenomic libraries. This study described for the first time the detailed functional potential of permafrost-affected soils and detected several genes and microorganisms that could have crucial importance following permafrost thaw. A 2m deep permafrost sample and it overlying active layer were sampled and their metagenome analysed. For microarray analyses, 8 other soil samples from the same region were used for comparison purposes.
2010-05-06 | E-GEOD-20073 | biostudies-arrayexpress
Project description:The aim for this study was to compare the differences in the methylome of 2 Russian wheat aphid biotypes that are genealogically linked, but at opposite ends of the virulence scale. We studied genic as well as intergenic methylation in all three available contexts in the Bismark pipeline, CpG, CHG and CHH. We were also interested to see how methylation patterns in the Russian wheat aphid compares to that of other investigated insects. Specifically the ratio of genic to intergenic methylation and to what extent contexts other than CpG are methylated. Grant number: CPR20110615000019459 Funding body: National Science Foundation ZA Grantholders name: Anna-Maria Botha-Oberholster
2020-07-15 | GSE119504 | GEO
Project description:The fate of the carbon stocked in permafrost soils following global warming and permafrost thaw is of major concern in view of the potential for increased CH4 and CO2 emissions from these soils. Complex carbon compound degradation and greenhouse gas emissions are due to soil microbial communities, but their composition and functional potential in permafrost soils are largely unknown. Here, a 2 m deep permafrost and its overlying active layer soil were subjected to metagenome sequencing, quantitative PCR, and microarray analyses. The active layer soil and 2 m permafrost soil microbial community structures were very similar, with Actinobacteria being the dominant phylum. The two soils also possessed a highly similar spectrum of functional genes, especially when compared to other already published metagenomes. Key genes related to methane generation, methane oxidation and organic matter degradation were highly diverse for both soils in the metagenomic libraries and some (e.g. pmoA) showed relatively high abundance in qPCR assays. Genes related to nitrogen fixation and ammonia oxidation, which could have important roles following climatic change in these nitrogen-limited environments, showed low diversity but high abundance. The 2 m permafrost soil showed lower abundance and diversity for all the assessed genes and taxa. Experimental biases were also evaluated and showed that the whole community genome amplification technique used caused large representational biases in the metagenomic libraries. This study described for the first time the detailed functional potential of permafrost-affected soils and detected several genes and microorganisms that could have crucial importance following permafrost thaw.
2010-03-08 | GSE20073 | GEO
Project description:This experiment explored the transcriptional response of human peripheral blood mononuclear cells (PBMC) isolated from BCG-vaccinated individuals following 6 days of in vitro stimulation with 2x10^5 cfu of different Bacillus Calmette-Guérin (BCG) strains or 100 ng/ml Mycobacterium tuberculosis-derived purified protein derivative (PPD). The BCG strains used were BCG Russia (Russian BCG-I sub-strain), BCG Japan (Tokyo 172 sub-strain), BCG Denmark (Danish 1331 sub-strain) & BCG Pasteur.
2022-01-26 | E-MTAB-11345 | biostudies-arrayexpress