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Evaluating The Infinium Human MethylationEPIC v2 BeadChip

ABSTRACT: Evaluating The Infinium Human MethylationEPIC v2 BeadChip

PROVIDER: PRJNA951687 | ENA |

REPOSITORIES: ENA

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Evaluating The Infinium Human MethylationEPIC v2 BeadChip

Project description:We conducted a comprehensive evaluation of the updated Infinium MethylationEPIC v2 BeadChip (EPICv2). Our evaluation revealed that EPICv2 offers significant improvements over its predecessors, including expanded enhancer coverage, applicability to diverse ancestry groups, support for low-input DNA down to one nanogram, coverage of existing epigenetic clocks, cell type deconvolution panels, and human trait associations, while maintaining accuracy and reproducibility.

2023-07-04 | GSE228820 | GEO

Illumina Infinium MethylationEPIC BeadChip (850k) analysis of growing teratoma tissues

Project description:Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of 12 different growing teratoma tissues. Samples were subgrouped based on growth speed into GTSslow to GTSrapid (see corresponding publication).

2024-04-28 | GSE240091 | GEO

Comprehensive Evaluation of The Infinium Human MethylationEPIC v2 BeadChip.

Project description:Infinium Methylation BeadChips are widely used to profile DNA cytosine modifications in large cohort studies for reasons of cost-effectiveness, accurate quantification, and user-friendly data analysis in characterizing these canonical epigenetic marks. In this work, we conducted a comprehensive evaluation of the updated Infinium MethylationEPIC v2 BeadChip (EPICv2). Our evaluation revealed that EPICv2 offers significant improvements over its predecessors, including expanded enhancer coverage, applicability to diverse ancestry groups, support for low-input DNA down to one nanogram, coverage of existing epigenetic clocks, cell type deconvolution panels, and human trait associations, while maintaining accuracy and reproducibility. Using EPICv2, we were able to identify epigenome and sequence signatures in cell line models of DNMT and SETD2 loss and/or hypomorphism. Furthermore, we provided probe-wise evaluation and annotation to facilitate the use of new features on this array for studying the interplay between somatic mutations and epigenetic landscape in cancer genomics. In conclusion, EPICv2 provides researchers with a valuable tool for studying epigenetic modifications and their role in development and disease.

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Illumina Infinium MethylationEPIC BeadChip (850k) analysis of growing teratoma tissues

Project description:Illumina Infinium MethylationEPIC BeadChip (850k) analysis of growing teratoma tissues

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Project description:Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of germ cell tumor related somati-type malignancies (STM), i. e. adenocarcinomas and rhabdomyosarcomas. As controls, yolk-sac tumors and teratoma without STM population were included.

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Project description:Illumina Infinium MethylationEPIC BeadChip (850k) array analysis of DNA methylation of embryonal carcinoma cell lines NCCIT and 2102EP deficient for CD24 and parental cells. CD24 deficiency was genereted by CRISPR/Cas9 method. Three different NCCIT and 2102EP knock out clones were analyzed.

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Project description:Infinium MethylationEPIC BeadChip array data for HGSOC PH039 PDXs at baseline and treated with cycles of 100 mg/kg niraparib for 21 days for four treatment rounds and murine sample.

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