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PROVIDER: PRJNA291917 | ENA |
REPOSITORIES: ENA
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Project description:DNA methylation and hydroxymethylation assessment through Illumina EPIC array analysis of paired bisulfite and oxidative-bisulfite conversion
| PRJNA602861 | ENA
Project description:Background Alzheimer’s disease is a progressive neurodegenerative disorder that is hypothesized to involve epigenetic dysfunction. Previous studies of DNA modifications in Alzheimer’s disease have been unable to distinguish between DNA methylation and DNA hydroxymethylation. DNA hydroxymethylation has been shown to be enriched in the human brain, although its role in Alzheimer’s disease has not yet been fully explored. Here we utilize oxidative bisulfite conversion, in conjunction with the Illumina Infinium Human Methylation 450K microarray, to identify neuropathology-associated differential DNA methylation and DNA hydroxymethylation in the entorhinal cortex. Results We identified one experiment-wide significant differentially methylated position residing in the WNT5B gene. Next, we investigated pathology-associated regions consisting of multiple adjacent loci. We identified one significant differentially hydroxymethylated region consisting of four probes spanning 104 bases in the FBXL16 gene. We also identified two significant differentially methylated regions: one consisting of two probes in a 93 base-pair region in the ANK1 gene and the other consisting of six probes in a 99 base-pair region in the ARID5B gene. We also highlighted three regions that show alterations in unmodified cytosine: two probes in a 39 base-pair region of ALLC, two probes in a 69 base-pair region in JAG2, in addition to the same six probes in ARID5B that were differentially methylated. Finally we replicated significant ANK1 disease-associated hypermethylation and hypohydroxymethylation patterns across eight CpG sites in an extended 118 base-pair region in an independent cohort using oxidative-bisulfite pyrosequencing. Conclusions Our study represents the first epigenome-wide association study of both DNA methylation and hydroxymethylation in Alzheimer’s disease entorhinal cortex. We demonstrate that previous estimates of DNA hypermethylation in ANK1 in Alzheimer’s disease were underestimates as it is confounded by hypohydroxymethylation.
2019-03-05 | GSE105109 | GEO
Project description:Analysis of genome-wide hydroxymethylation within infant placental tissue collected at term. These samples have been collected from the RhodeIsland Child Health Study (RICHS) cohort. Bisulfite and oxidative biulfite converted DNA was hybridized to the 450k platform and processed at the University of Minnesota Genomic Core
2016-07-01 | E-GEOD-71719 | biostudies-arrayexpress
Project description:Genome wide DNA methylation profiling of paired parental and therapy resistant cancer cell lines. Parental cell lines are mostly established cell lines. Resistant cell lines were obtained through long term exposure of the parental cells to gradually increasing doses of cancer therapies. Followig the published TAB-sequencing protocol, the Illumina Infinium 450K or EPIC Human DNA methylation Beadchips were used to obtain DNA hydroxymethylation profiles across approximately 450,000 or 850,000 CpGs from the cells. Samples include 5 parental and 6 derived resistant cell lines.
2020-02-20 | GSE128685 | GEO
Project description:Through parallel processing of genomic DNA with oxidative bisulfite treatments on Illumina 450K arrays we resolved both 5mC in human breast tissues.
2017-12-01 | GSE100653 | GEO
Project description:The most widely utilized approaches for quantifying DNA methylation involve the treatment of genomic DNA with sodium bisulfite, although this method cannot distinguish between DNA methylation (5mC) and DNA hydroxymethylation (5hmC). Previous studies have shown that 5hmC is enriched in the brain, although little is known about its genomic distribution and how it differs between anatomical regions and individuals. In this study, we combined oxidative bisulfite (oxBS) treatment with the Illumina Infinium 450K BeadArray to quantify genome-wide patterns of 5hmC in two distinct anatomical regions of the brain (prefrontal cortex and cerebellum) dissected from multiple individuals. We identified 37,145 and 65,563 sites passing our threshold for detectable 5hmC in the prefrontal cortex and cerebellumm, respectively, with 23,445 loci common across both brain regions. Distinct patterns of 5hmC were identified in each brain region, with notable differences in the genomic location of the most hydroxymethylated loci between these brain regions. Tissue-specific patterns of 5hmC were subsequently confirmed in an independent set of prefrontal cortex and cerebellum samples. Our data are available as downloadable UCSC genome browser tracks (http://epigenetics.iop.kcl.ac.uk/HMC/) as a resource to the community. Our study represents the first systematic analysis of 5hmC in the human brain, identifying tissue-specific hydroxymethylated positions and genomic regions characterized by inter-individual variation in DNA hydroxymethylation. This study demonstrates the utility of combining oxBS-treatment with the Illumina 450k methylation array to systematically quantify 5hmC across the genome and the potential utility of this approach for epigenomic studies of brain disorders.
2015-11-30 | GSE74368 | GEO
Project description:Through parallel processing of genomic DNA with bisulfite and oxidative bisulfite treatments on Illumina 450K arrays we resolved both 5mC and 5hmC in glioblastoma tissues. We developed and applied a novel technique for estimating 5mC, 5hmC, and unmethylated proportions from array data to glioblastoma tissues and compare with normal brain tissue. Genomic distribution of 5hmC was associated with features of transcription despite the glioblastoma genome being relatively depleted of 5hmC. When integrating 5mC and 5hmC data using a Gaussian finite mixture model approach, we observed significant associations between 5hmC levels and gene-sets involved in immune and RNA regulatory processes. We also observed an enrichment of 5hmC in introns, enhancer regions, and genes that are actively transcribed in glioblastomas from TCGA. Significant differences in patient survival were observed among classes of 5hmC obtained from a recursively partitioned mixture model. Glioblastoma dervied (n=30) DNA was subjected to tandem bisulfite and oxidative bisulfite conversion with an input of 4ug per sample using the TrueMethyl® kit v.1.1 (Cambridge Epigenetix) protocol optimized for Illumina HumanMethylation450 arrays.
2016-08-22 | E-GEOD-73895 | biostudies-arrayexpress
Project description:DNA methylation profiling of NeuN+sorted neuronal nuclei from post-mortem brain tissue of Multiple Sclerosis (MS) patients (n=10) (MS) and non-neurological controls (n=7) (non-MS). Genomic DNA was subjected to conventional BS-treatment as well as oxidative BS (oxBS)-conversion using TrueMethylTM 96 kit of CEGXTM (Cambridge Epigenetix Limited) to allow for subsequent detection of hydroxymethylation (5hmC = BS - oxBS).
2019-06-21 | GSE119532 | GEO
Project description:Aim: Tandem bisulfite (BS) and oxidative bisulfite (oxBS) conversion on DNA followed by hybridization to Infinium HumanMethylation BeadChips allows nucleotide resolution of 5-hydroxymethylcytosine genome-wide. Here, the authors compared data quality acquired from BS-treated and oxBS-treated samples. Materials & methods: Raw BeadArray data from 417 pairs of samples across 12 independent datasets were included in the study. Probe call rates were compared between paired BS and oxBS treatments controlling for technical variables. Results: oxBS-treated samples had a significantly lower call-rate. Among technical variables, DNA-specific extraction kits performed better with higher call rates after oxBS conversion. Conclusion: The authors emphasize the importance of quality control during oxBS conversion to minimize information loss and recommend using a DNA-specific extraction kit for DNA extraction and an oxBSQC package for data preprocessing.
2022-01-14 | GSE182919 | GEO
Project description:Genome wide DNA methylation profiling of 12 paired monozygotic twin samples. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs in 12 paired monozygotic twin samples.
2017-10-10 | GSE100940 | GEO