Homo sapiens
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PROVIDER: PRJNA151817 | ENA |
REPOSITORIES: ENA
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Project description:Methylation Profiling of Blood DNA from Healthy Children
| PRJNA151669 | ENA
Project description:Analysis of the DNA methylation level in peripheral blood leukocytes from healthy children using the Illumina HumanMethylation450 BeadChip Groupings by family membership requested but not provided by submitter DNA methylation association study in healthy children
2012-02-24 | E-GEOD-36064 | biostudies-arrayexpress
Project description:Analysis of the DNA methylation level in peripheral blood leukocytes from healthy children using the Illumina HumanMethylation450 BeadChip Groupings by family membership requested but not provided by submitter DNA methylation association study in healthy children
2015-02-16 | E-GEOD-36054 | biostudies-arrayexpress
Project description:Methylome-wide DNA methylation profiling of whole blood samples in health children to find age-associated methylation sites. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 485,000 CpGs in 48 samples. Samples included 29 boys and 19girls.
2017-10-12 | GSE104812 | GEO
Project description:Age-related changes in DNA methylation occurring in blood leukocytes during early childhood may reflect epigenetic maturation. We hypothesized that some of these changes involve gene networks of critical relevance in leukocyte biology and conducted a prospective study to elucidate the dynamics of DNA methylation. Serial blood samples were collected at 3, 6, 12, 24, 36, 48 and 60 months after birth in 10 healthy girls born in Finland and participating in the Type 1 Diabetes Prediction and Prevention Study. DNA methylation was measured using the HumanMethylation450 BeadChip. After filtering for the presence of polymorphisms and cell-lineage-specific signatures, 794 CpGs showed significant DNA methylation differences as a function of age in all children (41.5% age-methylated and 58.4% age-demethylated, bonferroni corrected p-value <0.001). Age-methylated CpGs were more frequently located in gene bodies and within +5 to +50 kilobases (kb) of transcription start sites (TSS), and enriched in developmental, neuronal and plasma membrane genes. Age-demethylated CpGs were associated to promoters and DNAse-I hypersensitivity sites, located within -5 to +5 kb of the nearest TSS, and enriched in genes related to immunity, antigen presentation, the polycomb-group protein complex and cytoplasm. This study reveals that susceptibility loci for complex inflammatory diseases (e.g. IRF5, NOD2, PTGER4) and genes encoding histone modifiers and chromatin remodeling factors (e.g. HDAC4, KDM2A, KDM2B, JARID2, ARID3A, SMARCD3) undergo DNA methylation changes in leukocytes during early childhood. These results open new perspectives to understand leukocyte maturation and provide a catalog of CpGs that may need to be corrected for age effects when performing DNA methylation studies in children. We analysed the longitudinal changes in DNA methylation in a total of 60 samples at 3, 6, 12, 24, 36, 48, and 60 months after birth, using serial DNA samples extracted from peripheral blood leukocytes of 10 healthy girls of the Diabetes Prediction and Prevention Study (DIPP).
2015-04-01 | E-GEOD-62219 | biostudies-arrayexpress
Project description:Developmental language disorder (DLD), previously known as specific language impairment, is a neurodevelopmental disorder. It affects approximately 7% of school-age children. The affected children fail to develop normal speech and language skills. This is a major public health concern as it adversely impacts the communication, academic, and social skills of the affected individual. The human brain development is a complex process that involves the accurate orchestration of the expression of multiple genes. Precise temporal and spatial regulation of gene expression is essential for proper brain development. Epigenetic factors such as DNA methylation can modulate gene expression without altering the DNA sequence. They are, therefore, considered as key regulators of the expression of genes involved in neurodevelopment. In this study, we examined any altered DNA methylation between children affected with DLD and healthy control subjects. We looked into genome-wide methylation differences between the DLD and control groups using Infinium HumanMethylation850 (EPICarray). Twelve children with DLD and 12 healthy controls were recruited for the study. Five milliliters of peripheral blood samples were collected from the study subjects in EDTA vials. Genomic DNA (gDNA) was extracted from the blood samples using the standard salting out protocol. Five micrograms of each DNA at 50 ng/µl concentration were used for genome-wide methylation analysis. The gDNA samples were bisulfite-treated with EpiTect Bisulfite Kit. Further to this, the DNA samples were subjected to whole genome amplification and enzymatic fragmentation. Human Infinium Methylation EPIC BeadChip (Illumina), which covers more than 850,000 genome-wide methylation sites, was used for genome-wide methylation analysis. The DNA methylation profiles of each sample were visualized at the single-CpG level and for the genomic regions of interest.
2024-01-10 | E-MTAB-13583 | biostudies-arrayexpress
Project description:Age-related changes in DNA methylation occurring in blood leukocytes during early childhood may reflect epigenetic maturation. We hypothesized that some of these changes involve gene networks of critical relevance in leukocyte biology and conducted a prospective study to elucidate the dynamics of DNA methylation. Serial blood samples were collected at 3, 6, 12, 24, 36, 48 and 60 months after birth in 10 healthy girls born in Finland and participating in the Type 1 Diabetes Prediction and Prevention Study. DNA methylation was measured using the HumanMethylation450 BeadChip. After filtering for the presence of polymorphisms and cell-lineage-specific signatures, 794 CpGs showed significant DNA methylation differences as a function of age in all children (41.5% age-methylated and 58.4% age-demethylated, bonferroni corrected p-value <0.001). Age-methylated CpGs were more frequently located in gene bodies and within +5 to +50 kilobases (kb) of transcription start sites (TSS), and enriched in developmental, neuronal and plasma membrane genes. Age-demethylated CpGs were associated to promoters and DNAse-I hypersensitivity sites, located within -5 to +5 kb of the nearest TSS, and enriched in genes related to immunity, antigen presentation, the polycomb-group protein complex and cytoplasm. This study reveals that susceptibility loci for complex inflammatory diseases (e.g. IRF5, NOD2, PTGER4) and genes encoding histone modifiers and chromatin remodeling factors (e.g. HDAC4, KDM2A, KDM2B, JARID2, ARID3A, SMARCD3) undergo DNA methylation changes in leukocytes during early childhood. These results open new perspectives to understand leukocyte maturation and provide a catalog of CpGs that may need to be corrected for age effects when performing DNA methylation studies in children.
2015-04-01 | GSE62219 | GEO
Project description:Genome wide DNA methylation profiling of isolated monocyte samples from healthy Kenyan children, the same children during an episode of acute malaria, healthy Kenyan adults, and healthy adults from the United States. The Illumina Infinium MethylationEPIC BeadChip microarray was used to obtain DNA methylation profiles across approximately 860,000 CpGs in negatively selected monocyte samples. Samples included monocytes from 8 children from western Kenya obtained while healthy and matching samples from the same 8 Kenyan children obtained during an episode of acute uncomplicated Plasmodium falciparum malaria, 8 healthy malaria-immune adults from western Kenya, and 8 healthy malaria-naive adults from the US. Abstract -- Background: Age-related changes in adaptive and innate immune cells have been associated with a decline in effective immunity and chronic, low-grade inflammation. Epigenetic, transcriptional, and functional changes in monocytes occur with aging, though most studies to date have focused on differences between young adults and the elderly in populations with European ancestry; few data exist regarding changes that occur in circulating monocytes during the first few decades of life or in African populations. We analyzed DNA methylation profiles, cytokine production, and inflammatory gene expression profiles in monocytes from young adults and children from western Kenya. Results: We identified several hypo- and hyper-methylated CpG sites in monocytes from Kenyan young adults vs. children that replicated findings in the current literature of differential DNA methylation in monocytes from elderly persons vs. young adults across diverse populations. Differentially methylated CpG sites were also noted in gene regions important to inflammation and innate immune responses. Monocytes from Kenyan young adults vs. children displayed increased production of IL-8, IL-10, and IL-12p70 in response to TLR4 and TLR2/1 stimulation as well as distinct inflammatory gene expression profiles. Conclusions: These findings complement previous reports of age-related methylation changes in isolated monocytes and provide novel insights into the role of age-associated changes in innate immune functions.
2021-03-11 | GSE157611 | GEO
Project description:Using DNA microarray as a global approach to understanding the molecular basis of autism, we examined gene expression profiling in peripheral blood from 21 young adults with autism spectrum disorder (ASD) and healthy mothers having children with ASD, between whom there was no blood relationship. Several genes which were significantly changed in the ASD group comparing with their age- and gender-matched healthy subjects were mainly involved in cell morphology, cellular assembly and organization, and nerve system development and function. In addition, mothers having children with ASD possessed a unique gene expression signature shown as significant alterations of protein synthesis despite of their nonautistic diagnostic status. Moreover, an ASD-associated gene expression signature was commonly observed in both individuals with ASD and healthy mothers having children with ASD. Total RNA was prepared from venous blood which was taken from each subject. Gene expression profiling of venous blood from subjects with ASD (21), the healthy women who had children with ASD (21) and their age- and gender-matched healthy subjects (42) were obtained using a whole human genome oligonucleotide microarray (Agilent 44K Human whole genome array G4112F, GPL6480) to measure gene expression in these samples according to the manufacture’s protocol. The one GSM sample of microarray analysis was made by individual subject. Differentially expressed genes were determined across all rationed expression values for age- and gender-matched pairs (ASD vs. control, asdMO vs. ctrlMO) using Genespling analysis.
2011-01-13 | E-GEOD-26415 | biostudies-arrayexpress
Project description:Purpose:we'd like to provide the first DNA methylation profiling for ITP. Methods:Peripheral blood CD4+ T lymphocytes samples were collected from 4 primary refractory ITP cases and 4 age-matched healthy controls, and DNA methylome profiling was performed using Illumina Human Methylation850K. Results:The DNA methylome profiling identified a total of 260 differentially methylated CpG sites mapping to 72 hypermethylated and 64 hypomethylated genes. Conclusions:we performed genome-wide DNA methylation profiling of primary refractory ITP and healthy controls, and identified a set of differentially methylated genes and pathways.
2023-06-14 | GSE205495 | GEO