Human Microbiome Samples
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA746977 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17246300_1.fastq.gz | Fastqsanger.gz | |||
| SRR17246300_2.fastq.gz | Fastqsanger.gz | |||
| SRR17246400.fastq.gz | Fastqsanger.gz | |||
| SRR17246500.fastq.gz | Fastqsanger.gz | |||
| SRR17246301.fastq.gz | Fastqsanger.gz |
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Project description:Genome wide DNA methylation profiling of epidermal and dermal samples obtained from sun-exposed and sun-protected body sites from younger (<35 years old) and older (>60 years old) individuals. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in dermal and epidermal samples. Samples included 10 younger sun protected dermal samples, 10 younger sun exposed dermal samples, 10 older sun protected dermal samples, 10 older sun exposed dermal samples, 9 younger sun protected epidermal samples, 9 younger sun exposed epidermal samples, 10 older sun protected epidermal sample, 10 older sun exposed epidermal samples.
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Project description:To investigate whether lifestyle factors modulate the stability of gene promoter methylation in the normal aging colonic mucosa, we performed genome-scale DNA methylation profiling of 178 normal colon biopsies using the Illumina Infinium DNA methylation assay, which assesses the DNA methylation status of 27,578 CpG sites located at the promoter regions of 14,495 protein-coding genes. We identified Aspirin use and hormonal replacement therapy (HRT) suppress, whereas a high body mass index (BMI) and smoking promote age-related hyermethylation. Many of these loci modulated by lifestyle in the healthy colon mucosa coincide with loci hypermethylated in colorectal cancers and down-regulated in adenomas. The data show that lifestyle modulates the stability of DNA methylation in the aging colonic epithelium and thereby impacts the rate of evolution of cancer methylomes.
2014-07-01 | GSE48988 | GEO
Project description:To investigate whether lifestyle factors modulate the stability of gene promoter methylation in the normal aging colonic mucosa, we performed genome-scale DNA methylation profiling of 178 normal colon biopsies using the Illumina Infinium DNA methylation assay, which assesses the DNA methylation status of 27,578 CpG sites located at the promoter regions of 14,495 protein-coding genes. We identified Aspirin use and hormonal replacement therapy (HRT) suppress, whereas a high body mass index (BMI) and smoking promote age-related hyermethylation. Many of these loci modulated by lifestyle in the healthy colon mucosa coincide with loci hypermethylated in colorectal cancers and down-regulated in adenomas. The data show that lifestyle modulates the stability of DNA methylation in the aging colonic epithelium and thereby impacts the rate of evolution of cancer methylomes. Bisulphite converted DNA from the 178 samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2
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Project description:Genome wide DNA methylation profiling of epidermal samples obtained from sum-exposed and sun-protected body sites from younger (<35 years old) and older (>60 years old) individuals.
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Project description:Background - Prepregnancy overweight and obesity promote deleterious health impacts on both mothers during pregnancy and the offspring. Significant changes in the maternal peripheral blood mononuclear cells (PBMCs) gene expression due to obesity are well-known. However, during pregnancy the impact of overweight on immune cell gene expression and its association with maternal and infant outcomes is not well explored. Methods – Blood samples were collected from healthy normal weight (NW, BMI 18.5-24.9) or overweight (OW, BMI 25-29.9) 2nd parity pregnant women at 12, 24 and 36 weeks of pregnancy. PBMCs were isolated from the blood and subjected to mRNA sequencing. Maternal and infant microbiota were analyzed by 16S rRNA gene sequencing. Integrative multi-omics data analysis was performed to evaluate the association of gene expression with maternal diet, gut microbiota, milk composition, and infant gut microbiota. Results - Gene expression analysis revealed that 453 genes were differentially expressed in the OW women compared to NW women at 12 weeks of pregnancy, out of which 354 were upregulated and 99 were downregulated. Several up-regulated genes in the OW group were enriched in inflammatory, chemokine-mediated signaling and regulation of interleukin-8 production-related pathways. At 36 weeks of pregnancy healthy eating index score was positively associated with several genes that include, DTD1, ELOC, GALNT8, ITGA6-AS1, KRT17P2, NPW, POT1-AS1 and RPL26. In addition, at 36 weeks of pregnancy, genes involved in adipocyte functions, such as NG2 and SMTNL1, were negatively correlated to human milk 2’FL and total fucosylated oligosaccharides content collected at 1 month postnatally. Furthermore, infant Akkermansia was positively associated with maternal PBMC anti-inflammatory genes that include CPS1 and RAB7B, at 12 and 36 weeks of pregnancy. Conclusions – These findings suggest that prepregnancy overweight impacts the immune cell gene expression profile, particularly at 12 weeks of pregnancy. Further, deciphering the complex association of PBMC’s gene expression levels with maternal gut microbiome and milk composition and infant gut microbiome may aid in developing strategies to mitigate obesity-mediated effects.
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