We analysed DNA methylation with the Infinium Methylation EPIC Bead Chip kit (Illumina, Inc., San Diego, CA). This assay covers over 850,000 methylation sites per sample at single nucleotide resolution. OD and OND controls were placed randomly among the Bead Chips. We performed the Illumina Infinium methylation assay protocol, according to manufacturer’s instructions, and we used iScan to scan the arrays. Methylation data were visualized and analysed with Genome Studio software version 2011.1 (Illumina) and the Methylation Module. Only samples that passed quality control evaluations were used in the analysis. Methylation beta values were estimated as the ratio of the signal intensity of the methylated probe to the sum of methylated and unmethylated probes. The beta values ranged from 0 to 1.
Infinium methylation assay protocol
Manufactured by Illumina
The Infinium methylation assay protocol is a laboratory tool designed to analyze DNA methylation patterns. It provides a high-throughput and comprehensive approach to measure DNA methylation levels across the genome. The core function of this protocol is to enable the detection and quantification of DNA methylation at specific genomic sites.
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Lab products found in correlation
2 protocols using infinium methylation assay protocol
1
Infinium Methylation EPIC Bead Chip Analysis
2
Genome-wide DNA Methylation Profiling
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We used the HumanMethylation27 BeadChip (Illumina, Inc., San Diego, CA, USA), which covered 27,578 CpG sites (CpGs) around 14,495 genes throughout the genome. Cases and controls were randomly located among the BeadChips. Arrays were processed following the Illumina Infinium Methylation assay protocol, and were scanned in an Illumina iScan. The array results were visualized using Illumina GenomeStudio software (V2011.1). We only included samples which passed quality control (QC) of internal control probes. CpGs in sex chromosomes were excluded, and the subsequent quality-filtered analyses included 26,486 CpGs. The methylation value was calculated as Beta, ranging from 0 (unmethylated) to 1 (completely methylated). The Beta value represents the ratio of the methylated probe intensity and the sum of methylated and unmethylated probe intensities.
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