Project description:Genome wide DNA methylation profiling of smokers and non-smokers in PBMC samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.1 was used to obtain DNA methylation profiles across 485,577 CpGs in PBMC samples. Samples included 24 smokers and 28 non-smokers.
Project description:Genome wide DNA methylation profiling of smokers and non-smokers in PBMC samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.1 was used to obtain DNA methylation profiles across 485,577 CpGs in PBMC samples. Samples included 50 smokers and 61 non-smokers.
Project description:Epidemiological studies in humans suggest that acquired paternal traits, such as obesity, are associated with a higher risk of fathering small for gestational age offspring. Studies in non-human mammals suggest that such associations could be mediated by DNA methylation changes in spermatozoa that influence offspring development in utero. Human obesity is associated with differential DNA methylation in peripheral blood. It is unclear, however, whether this differential DNA methylation is reflected in less readily available tissues such as spermatozoa. In this study, we profiled genome-wide DNA methylation with the Infinium MethylationEPIC array in matched samples of human blood and sperm from lean (discovery n = 47; replication n = 21) and obese (n = 22) healthy males of proven fertility. To characterize sperm-specific DNA methylation signatures, we compared spermatozoal DNA methylation data to that of nearly 6,000 somatic tissue samples available on the Gene Expression Omnibus database. We studied covariation patterns between whole blood and sperm and investigated consistent obesity-associated DNA methylation differences.
Project description:Genome wide DNA methylation profiling of smokers and non-smokers in PBMC samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.1 was used to obtain DNA methylation profiles across 485,577 CpGs in PBMC samples. Samples included 50 smokers and 61 non-smokers. Bisulfite converted DNA from the 111 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip v1.1
Project description:The small airway epithelium (SAE), the first site of smoking-induced lung pathology, exhibits genome-wide changes in gene expression in response to cigarette smoking. Based on the increasing evidence that the epigenome can respond to external stimuli in a rapid manner, we assessed the SAE of smokers for genome-wide DNA methylation changes compared to nonsmokers, and whether changes in SAE DNA methylation were linked to the transcriptional output of these cells. Using genome-wide methylation analysis of SAE DNA of nonsmokers and smokers, the data identified 204 unique genes differentially methylated in SAE DNA of smokers compared to nonsmokers, with 67% of the regions with differential methylation occurring within 2 kb of the transcriptional start site. Among the genes with differential methylation were those related to metabolism, transcription, signal transduction and transport. For the differentially methylated genes, 34 exhibited a correlation with gene expression, 53% with an inverse correlation of DNA methylation with gene expression and 47% a direct correlation. These observations provide evidence that cigarette smoking alters the DNA methylation patterning of the SAE and that, for some genes, these changes are associated with the smoking-related changes in gene expression. Small airway epithelium DNA was assessed for genome-wide methylation using the microarray-based high resolution HpaII tiny fragment enriched by ligation-mediated PCR (HELP) assay. Small airway epithelium transcriptome was also assessed for healthy nonsmokers (n=16) and healthy smokers (n=20) with Affymetirx HG-U133 Plus 2.0 arrays
Project description:The Illumina Infinium 27k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 27,000 CpGs in whole blood DNA samples from 84 women (42 BRCA1 wild-type and healthy, 7 BRCA1 mutants and healthy, 35 BRCA1 mutants with breast cancer) whole blood DNA from women, with and without breast cancer, and with or without BRCA1 mutation Bisulphite converted DNA from the whole blood samples were hybridised to the Illumina Infinium 27k Human Methylation Beadchip v1.2 The BRCA1 mutation status represent 0=healthy-brca1wt, 1=healthy-brca1mt, 2=breastcancer-brca1mt.
Project description:We are investigating the methylation profiles associated with cigarette smoke exposure. We used arrays to compare the DNA methylation profiles in healthy human smokers and nonsmokers.
Project description:Genome wide DNA methylation profiling of normal and ICF blood samples. The Illumina Infinium Human Methylation 450 BeadChip was used to obtain DNA methylation profiles across approximately 485,000 CpGs in whole blood from healthy and ICF subjects. Samples included 10 healthy subjects, 8 ICF1, 4 ICF2, 2 ICF3 and 1 ICF4 patients.
Project description:To better characterize smoking–associated methylation changes in whole blood, we used Illumina HumanMethylation450 BeadChip to assess DNA samples from current (SM, n=172) and never smokers (NS, n=81).
Project description:Genome wide DNA methylation profiling of whole blood in schizophrenia patients and healthy subjects of different ages. The Illumina Infinium 450k Human DNA methylation Beadchip v1.2 was used to obtain DNA methylation profiles across approximately 480,000 CpGs. Dataset included 62 schizophrenia patients and 33 healthy subjects from Dutch descent. Bisulphite converted DNA from the 96 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip. Publication: Steve Horvath, Yafeng Zhang, Peter Langfelder, René S. Kahn, Marco P.M. Boks, Kristel van Eijk, Leonard H. van den Berg, Roel A. Ophoff. Aging effects on DNA methylation modules in human brain and blood tissue. Genome Biology. Special Edition. The raw data (non-normalized Unmethylated and Methylated signal intensities) are not available.
