Ontology highlight
ABSTRACT:
PROVIDER: PRJNA412626 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6118640_1.fastq.gz | Fastqsanger.gz | |||
| SRR6118640_2.fastq.gz | Fastqsanger.gz | |||
| SRR6118650_1.fastq.gz | Fastqsanger.gz | |||
| SRR6118650_2.fastq.gz | Fastqsanger.gz | |||
| SRR6118641_1.fastq.gz | Fastqsanger.gz |
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Project description:This study consists of 24 genome-wide methylation profiles which have been generated from blood and saliva samples collected from ten volunteers in the Personal Genome Project UK. The Personal Genome Project UK aims to create publicly available genome, health and trait data, and these ten volunteers represent the pilot study (PGP-UK10) and the first three genome donation participants. These samples were bisulphite converted using the EZ DNA methylation kit (Zymo), using the alternative incubation conditions recommended for HumanMethylation450 BeadChip (Illumina). Genome-wide DNA methylation was then profiled using the HumanMethylation450 BeadChip (Illumina).
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Project description:Human saliva microbiota is phylogenetically divergent among host individuals yet their roles in health and disease are poorly appreciated. We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults. Saliva microbiota in the pilot population featured a vast diversity of functional genes. No significant distinction in gene number or diversity indices was observed between healthy and caries-active microbiota. However, co-presence network analysis of functional genes revealed that caries-active microbiota was more divergent in non-core genes than healthy microbiota, despite both groups exhibited a similar degree of conservation at their respective core genes. Furthermore, functional gene structure of saliva microbiota could potentially distinguish caries-active patients from healthy hosts. Microbial functions such as Diaminopimelate epimerase, Prephenate dehydrogenase, Pyruvate-formate lyase and N-acetylmuramoyl-L-alanine amidase were significantly linked to caries. Therefore, saliva microbiota carried disease-associated functional signatures, which could be potentially exploited for caries diagnosis. The DMFT INDEX (Decayed, Missing, Filled [DMF] teeth index used in dental epidemiology) values are provided for each sample
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Project description:Human saliva microbiota is phylogenetically divergent among host individuals yet their roles in health and disease are poorly appreciated. We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults. Saliva microbiota in the pilot population featured a vast diversity of functional genes. No significant distinction in gene number or diversity indices was observed between healthy and caries-active microbiota. However, co-presence network analysis of functional genes revealed that caries-active microbiota was more divergent in non-core genes than healthy microbiota, despite both groups exhibited a similar degree of conservation at their respective core genes. Furthermore, functional gene structure of saliva microbiota could potentially distinguish caries-active patients from healthy hosts. Microbial functions such as Diaminopimelate epimerase, Prephenate dehydrogenase, Pyruvate-formate lyase and N-acetylmuramoyl-L-alanine amidase were significantly linked to caries. Therefore, saliva microbiota carried disease-associated functional signatures, which could be potentially exploited for caries diagnosis. The DMFT INDEX (Decayed, Missing, Filled [DMF] teeth index used in dental epidemiology) values are provided for each sample We employed a microbial functional gene microarray, HuMiChip 1.0, to reconstruct the global functional profiles of human saliva microbiota from ten healthy and ten caries-active adults.
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Project description:Saliva microbiome
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Project description:It has been suggested that the etiology of respiratory allergies (RA) can be partly explained by DNA methylation changes caused by adverse environmental and lifestyle factors experienced early in life. Longitudinal, prospective studies can aid in the unravelment of the epigenetic mechanisms involved in the disease development. High compliance rates can be expected in these studies when data is collected using non-invasive and convenient procedures. Saliva is an attractive biofluid to analyze changes in DNA methylation patterns. We investigated in a pilot study the differential methylation in saliva of RA (n=5) compared to healthy controls (n=5) using the Illumina Methylation 450K BeadChip platform. We evaluated the results against the results obtained in mononuclear blood cells from the same individuals. Differences in methylation patterns from saliva and mononuclear blood cells were clearly distinguishable (PAdj<0.001 and |Δβ|>0.2), though the methylation status of about 96% of the cg-sites was comparable between peripheral blood mononuclear cells and saliva. When comparing RA cases with healthy controls, the number of differentially methylated sites (DMS) in saliva and blood were 485 and 437, respectively, of which 216 were in common. The methylation levels of these sites were significantly correlated between blood and saliva. Pyrosequencing analysis of 3 selected DMS in the PM20D1, STK32C, and FGFR2 genes, confirmed the absolute levels of methylation as well as the differences between cases and controls as observed from the array data. Our findings show that saliva can be used for genome-wide methylation analysis and that it is possible to identify DMS to distinguish RA cases from healthy controls. The results were replicated in blood cells of the same individuals and confirmed by selected pyrosequencing analysis. This study provides a proof-of-concept that the analysis of DNA methylation profiles in saliva may offer distinct opportunities for molecular epidemiology studies of RA.
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