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Genomic CpG methylation profiles of peripheral blood mononuclear cells in childhood AD patients and control subjects

ABSTRACT: Peripheral blood samples were taken from a total of 48 individuals (24 AD patients and 24 controls) and subjected to access DNA CpG methylation state using Infinium HumanMethylation450 BeadChips. This array consists of probes to determine the site-specific methylation status of more than 450K CpG loci across the human genome. Approximately 500 ng of bisulfate-converted DNA (BCD) was used per BeadChip for hybridization in accordance with the protocol and instructions of Infinium HD methylation. After completing the whole-genome amplification step and then controlled enzymatic end-point fragmentation, BCD samples were precipitated and re-suspended for hybridization for 16 h at 48C. During this process, the DNA molecules are annealed to two bead types with methylated loci (C)-specific and unmethylated loci (T)-specific oligomers. Afterward, the non-hybridized or mis-hybridized DNA was washed away, followed by single-base extension using 2,4-dinitrophrnol- and biotin-labeled ddNTPs and the annealed BCD as templates.

ORGANISM(S): Homo sapiens

PROVIDER: GSE152084 | GEO | 2020/06/10

REPOSITORIES: GEO

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Genomic CpG methylation profiles of peripheral blood mononuclear cells in KD patients and non-KD normal subjects

Project description:Peripheral blood samples were taken from a total of 48 individuals (24 KD patients and 24 normal controls) and subjected to access DNA CpG methylation state using Infinium HumanMethylation450 BeadChips. This array consists of probes to determine the site-specific methylation status of more than 450K CpG loci across the human genome. Approximately 500 ng of bisulfate-converted DNA (BCD) was used per BeadChip for hybridization in accordance with the protocol and instructions of Infinium HD methylation. After completing the whole-genome amplification step and then controlled enzymatic end-point fragmentation, BCD samples were precipitated and re-suspended for hybridization for 16 h at 48°C. During this process, the DNA molecules are annealed to two bead types with methylated loci (C)-specific and unmethylated loci (T)-specific oligomers. Afterward, the non-hybridized or mis-hybridized DNA was washed away, followed by single-base extension using 2,4-dinitrophrnol- and biotin-labeled ddNTPs and the annealed BCD as templates.

2016-12-31 | GSE84624 | GEO

A Genome-wide DNA Methylation Study in Colorectal Carcinoma

Project description:Genome wide DNA methylation profiling of tumor and surrounding healthy colonic mucosa from patients with colorectal carcinoma. The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across 27,578 CpG loci covering 14,475 genes.

2012-05-23 | GSE29490 | GEO

Array-based DNA methylation profiling in male infertility reveals allele-specific DNA methylation in PIWIL1 and PIWIL2

Project description:Array-based DNA methylation profiling in peripheral blood leukocytes of 30 infertile men with impaired spermatogenesis as compared to 10 fertile men using the Illumina Infinium HumanMethylation 450k Bead Chip reveald 471 CpG sites (287 genes) to be differentially methylated between both groups. These CpG loci were significantly enriched for the gene ontology functions MHC class II receptor activity and piRNA binding. The latter was associated with two methylation-sensitive SNPs in the genes PIWIL1 and PIWIL2, respectivly, which showed significant allele distribution skewing in the infertile cohort. 445/471 differentially methylated CpGs were associated with SNPs, but 26 (15 genes) were not genomically templated and included the ENO1, MTA2, BRSK2 and LBX2 genes previously associated with fertility and spermatogenesis. The study identifies surrogate DNA methylation markers for idiopathic infertility in peripheral blood and suggests allele-specific DNA methylation differences at regulatory sites of genes involved in piRNA regulation to be associated with disturbed spermatogenesis. Bisulfite converted DNA of peripheral blood leukocytes from 30 infertile men and 10 fertile men as controls were hybridized to the Illumina Infinium HumanMethylation 450k Bead Chip.

2014-02-16 | E-GEOD-51245 | biostudies-arrayexpress

Comprehensive Analysis of Preeclampsia-Associated DNA Methylation in the Placenta

Project description:Background: A small number of recent reports have suggested that altered placental DNA methylation may be associated with early onset preeclampsia. It is important that further studies be undertaken to confirm and develop these findings. We therefore undertook a systematic analysis of DNA methylation patterns in placental tissue from 24 women with preeclampsia and 24 with uncomplicated pregnancy outcome. Methods: We analyzed the DNA methylation status of approximately 27,000 CpG sites in placental tissues in a massively parallel fashion using an oligonucleotide microarray. Follow up analysis of DNA methylation at specific CpG loci was performed using the Epityper MassArray approach and high-throughput bisulfite sequencing. Results: Preeclampsia-specific DNA methylation changes were identified in placental tissue samples irrespective of gestational age of delivery. In addition, we identified a group of CpG sites within specific gene sequences that were only altered in early onset-preeclampsia (EOPET) although these DNA methylation changes did not correlate with altered mRNA transcription. We found evidence that fetal gender influences DNA methylation at autosomal loci but could find no clear association between DNA methylation and gestational age. Conclusion: Preeclampsia is associated with altered placental DNA methylation. Fetal gender should be carefully considered during the design of future studies in which placental DNA is analyzed at the level of DNA methylation. Further large-scale analyses of preeclampsia-associated DNA methylation are necessary. Bisulphite converted DNA from the 48 samples were hybridized to the Illumina Infinium 27k Human Methylation Beadchip v1.2

2014-07-12 | E-GEOD-59274 | biostudies-arrayexpress

A Genome-wide DNA Methylation Study in Colorectal Carcinoma

2012-05-22 | E-GEOD-29490 | biostudies-arrayexpress

Genome-wide DNA methylation profiling in tongue squamous cell carcinoma

Project description:DNA methylation is one of the most studied epigenetic alterations in cancer. Genome-wide DNA methylation profiling was conducted in 6 oral tongue squamous cell carcinomas and matched normal tissues. In the present study, the Illumina Infinium HumanMethylationEPIC BeadChip (EPIC array) was used to characterize the DNA methylation pattern across approximately 850,000 CpG dinucleotide methylation loci using DNA isolated of formalin-fixed and paraffin-embedded tissue sections.

2023-03-20 | GSE210443 | GEO

Genome-wide DNA methylation study in bladder cancer

Project description:Genome-wide DNA methylation profiles were determined on a set of fresh 44 bladder cancer tissues using normal blood as control. DNA amplicons were prepared using Differential Methylation Hybridization (DMH) method, subsequently hybridized on to the Agilent Human CpG island Microarray. The goal was to unravel the DNA methylation patterns in different subgropus of bladder cancer along with finding markers for progresssion and early diagnosis.

2012-02-16 | GSE35824 | GEO

Comparison of the DNA methylation profiles of CD19+ B lymphocytes of a pair of monozygotic twins discordant for common variable immunodeficiency

Project description:The methylation profiles of bisulfite-modified DNA of CD19+ cells from MZ twins discordant for CVID were compared using the Infinium HumanMethylation450 BeadChips (Illumina, Inc., San Diego, CA,). This platform allows the interrogation of >485,000 methylation sites per sample at single-nucleotide resolution, and comprises an average of 17 CpG sites per gene in the 99% of RefSeq genes. 96% of CpG islands are covered, with additional coverage in CpG island shores and the regions flanking them. The samples were hybridized in the array following the manufacturer’s instructions.

2015-06-17 | GSE63849 | GEO

Epigenome analysis of normal colon mucosa samples

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

2014-07-01 | E-GEOD-48988 | biostudies-arrayexpress

Methylation analysis in monozygotic(MZ) twins with differences in TSH

Project description:Genome wide DNA methylation profiling of MZ twins whose within-pair difference in TSH were discordant. the Illumina Infinium HumanMethylation450 Bead Chip Kit (approximately 480,000 CpG sites) and the Illumina Infinium Methylation EPIC Bead Chip (approximately 900,000 CpG sites) were used to obtain DNA methylation profiles in peripheral blood samples.

2024-01-04 | GSE252408 | GEO

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