Project description:This cohort is an extension of our previous dataset (Spiers et al) containing DNA methylation profiled with the EPIC array on an additional 40 human fetal brain samples. Please note that these samples are from the same cohort as GSE58885.
Project description:We aimed to investigate genome wide DNA methylation changes in human colon organoids in which the BRAF-V600E mutation was introduced by means of CRISPR genome editing and in BRAF-wildtype human colon cancer organoids. DNA methylation analysis was performed using the Infinium Methylation EPIC beadchip at the Pathology department of the UMC Utrecht (The Netherlands).
Project description:We aimed to investigate genome wide DNA methylation changes in human colon cancer organoids with the BRAF-V600E mutation and in human colon cancer organoids in which the BRAF-V600E mutation was corrected by means of CRISPR genome editing. DNA methylation analysis was performed using the Infinium Methylation EPIC beadchip at the Pathology department of the UMC Utrecht (The Netherlands).
Project description:Genome-wide patterns of DNA methylation were quantified using the Illumina Infinium EPIC array (“EPIC array”) in DNA samples isolated from buccal swabs collected at ages 5, 10 and 18 and whole blood samples collected at age 18 from 118 Monozygotic twin pairs from the Environmental Risk (E-Risk) Longitudinal Twin Study. Comparison of DNA methylation profiles of 233 age 18 blood samples with data on EPIC and Illumina 450K methylation arrays.
Project description:DNA methylation is the most studied epigenetic modification due to its role in regulating gene expression and aberrations in methylation involved in the pathogenesis of cancer and several diseases. The method of choice to evaluate genome-wide methylation has been the Illumina HumanMethylation450 BeadChip (450K), but it was recently replaced with the MethylationEPIC BeadChip (EPIC). We therefore sought to validate the EPIC array in comparison to the 450K array for both fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) pediatric brain tumors. We also performed analysis on the EPIC array with paired FF and FFPE samples, to adapt to a clinical setting where FFPE is routinely used. Further, we compared two restoration methods, REPLI-g and Infinium, for FFPE-derived DNA on the EPIC array.
Project description:DNA methylation is the most studied epigenetic modification due to its role in regulating gene expression and aberrations in methylation involved in the pathogenesis of cancer and several diseases. The method of choice to evaluate genome-wide methylation has been the Illumina HumanMethylation450 BeadChip (450K), but it was recently replaced with the MethylationEPIC BeadChip (EPIC). We therefore sought to validate the EPIC array in comparison to the 450K array for both fresh-frozen (FF) and formalin-fixed paraffin-embedded (FFPE) pediatric brain tumors. We also performed analysis on the EPIC array with paired FF and FFPE samples, to adapt to a clinical setting where FFPE is routinely used. Further, we compared two restoration methods, REPLI-g and Infinium, for FFPE-derived DNA on the EPIC array.
Project description:DNA methylation microarray analysis was performed on human donor whole blood samples from patients with and without AMD. A total of 30 patient samples including 16 Normal, 3 AREDS grade 2 (early AMD) and 11 AREDS grade 3 (intermediate AMD) (AMD total, n = 14) were selected. Samples were obtained from individuals phenotyped according to the Age-Related Eye Disease Study (AREDS) classification. DNAm levels were measured using the EPIC-array (Illumina Inc., San Diego, CA, USA). Samples run on the EPIC-array were randomized and balanced for disease status and smoking status to minimise chip and row specific effects. The EPIC-array incorporated technical controls into the experimental design. In total, 500 ng (50 ng/μL) total peripheral whole blood-derived gDNA was bisulfite converted using the EZ-96 DNA methylation kit (Zymo Research, Irvine, CA, USA) and hybridised to the EPIC-array according to the manufacturer’s instructions. Quality control analysis was performed using GenomeStudio (v2011.1). Raw IDAT files were then read into R (version 3.31) using the read.metharray.exp function within the minfi package. DNA methylation microarray data was collected in order to assess the estimated DNA methylation age using the Horvath multi-tissue, Hannum and Skin & Blood epigenetic clocks and to identify loci of differential methylation between the experimental groups.
