Extracted DNA from 139 placenta samples was run on Illumina Infinium EPIC Methylation arrays. The quality control pipeline was set up using the R-package minfi 1.36.0 [59 (link)]. Two samples were excluded as they showed artefacts in the beta-value distribution. Methylation beta-values were normalized using the swan normalization [60 (link)]. After normalization, slide was the most significant batch and removed using the Combat function in the R-package sva 3.30.1 [61]. We excluded any probes on chromosome X or Y, probes containing SNPs and cross-hybridizing probes according to [62 (link)–64 (link)]. Furthermore, any CpGs with a detection p value > 0.01 in at least 25% of the samples were excluded. The final dataset contained 793,213 CpGs and 137 participants. For 136 of these (52 BET and 84 controls), genotypes and hence MDS components were available. Using MixUpMapper 1.2.4 [65 (link)] we confirmed that methylation levels and genotypes matched and that no sample mix-ups were present.
Infinium epic methylation array
Manufactured by Illumina
Sourced in United States
The Infinium EPIC methylation array is a laboratory equipment product designed for genome-wide DNA methylation analysis. It provides comprehensive coverage of CpG sites across the human genome, enabling researchers to study the epigenetic landscape of their samples.
Automatically generated - may contain errors
Lab products found in correlation
Nanodrop nd 1000 spectrophotometer, by Thermo Fisher Scientific (3 mentions)
Allprep dna rna mini kit, by Qiagen (2 mentions)
Ez 96 dna methylation kit, by Zymo Research (1 mentions)
Humanmethylation450 array, by Illumina (1 mentions)
Ffpe dna restoration kit, by Illumina (1 mentions)
Iscan system, by Illumina (1 mentions)
8 protocols using infinium epic methylation array
1
DNA Methylation Analysis of Placental Samples
2
Array-Based DNA Methylome Analysis
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For array-based methylome analysis, DNA was extracted from cells by Qiagen Allprep DNA/RNA mini kit (Qiagen, Hilden, Germany). 500 ng of genomic DNA were subjected to hybridization on Infinium EPIC methylation arrays (Illumina, San Diego, CA; USA), and analyzed according to the manufacturer's instructions. Assays were scanned, and idat files were imported in R using the minfi package and processed according to the Illumina BeadStudio workflow.
3
Infinium EPIC Array-Based DNA Methylation Analysis
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Array-based DNA methylation analyses were performed as previously described [7 (link)]. In brief, DNA was extracted by Qiagen Allprep DNA/RNA mini kit (Qiagen), concentration and quality of DNA were assessed with a Nanodrop ND-1000 spectrophotometer (Thermo Scientific), and 500 ng DNA was subjected to hybridization on an Infinium EPIC methylation array (Illumina, San Diego, CA; USA). The arrays were scanned, idat files were imported in R using the minfi package [20 (link)], and processed in accordance to the Illumina BeadStudio data analysis workflow (Illumina). Beta values were used for downstream hierarchical clustering analysis along with the beta values retrieved for glioblastoma samples from TCGA database https://www.cancer.gov/tcga [21 (link), 22 ].
4
Genome-wide Methylation Analysis of Glioma Stem Cells
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We downloaded precomputed genome-wide methylation data for 43 GSCs from Gene Expression Omnibus (GSE119774, RRID:SCR_005012; ref. 29 (link)). These methylation data were generated using the Illumina Infinium Epic Methylation Array. In this assay, DNA methylation levels at CpG sites are represented by β, which is the ratio of the methylated (C) to unmethylated (T) signal. We annotated the CpG probe positions based on GENCODE (v28, RRID:SCR_014966) genes and computed the mean β values for promoter regions (i.e., 1 kb upstream to 500 bp downstream of annotated transcription start sites; βpromoter). To discover ASE genes that may be dysregulated by aberrant DNA methylation, we computed Spearman rank correlation between βpromoter and normalized gene expression. We corrected correlation P values for multiple testing using the Benjamini–Hochberg procedure. For this analysis, we only considered genes with ≥ 3 CpG probes mapping to their promoter regions.
5
Profiling CpG Methylation in Kidney Samples
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Illumina Infinium EPIC methylation array was used to profile CpG methylation in 240 human kidney samples. R package SeSAMe69 (link) was used for quality control and methylation quantification. After filtering out probes with missing values in more than 20% of samples, non-CpGs, low mapping quantity, chromosome X, Y, and M, and methylation overlapping with SNPs, 728,582 CpGs remained for further analysis. CpGs overlapping with TE sequences were extracted using the R package Granges70 (link). β values for each CpG probe represent the methylation level, ranging from 0 to 1, or unmethylated to methylated, respectively. A total of 10,660 CpG probes overlapping TE sequences were identified. 380 CpG probes overlap the 2,711 TE sequences associated with fibrosis from our cohort. Of which, 308 are from unique TE. Pearson’s correlation coefficients between the methylation level of each CpG probe and the expression of the TE it overlaps was calculated.
6
Uncovering Epigenetic Drivers in Glioma Stem Cells
7
Genome-wide DNA Methylation Profiling
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DNA bisulfite conversion was performed utilizing a Zymo EZ-96 DNA Methylation Kit [40 ]. DNA methylation was assessed using an Illumina Infinium EPIC DNA Methylation Array on all 657 samples at the Avera Institute for Human Genetics [40 ]. The samples were fully randomized across arrays and run on an Illumina Infinium EPIC methylation array. Additionally, DNA methylation was assessed earlier on 83 of the same samples using an Illumina Infinium HumanMethylation450 array at the human genomics facility (Huge-F), Rotterdam, the Netherlands. Details including quality control of the HumanMethylation450 array data have been described previously [36 (link)].
8
DNA Methylation Profiling Using EPIC Array
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DNA methylation array analyses were performed at the Translational Genomics Laboratory at the Ontario Institute for Cancer Research (Toronto, ON, Canada). For each sample, 250 ng of bisulfite-converted DNA was treated using the FFPE DNA Restoration Kit, hybridized to the Infinium EPIC methylation array, and scanned using the iScan System (Illumina, San Diego, CA). Methylation data were extracted and normalized using the Bioconductor package minfi version 1.30 (Illumina) . Methylation β values were converted to M values before analyses.
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