Five hundred ng of genomic DNA was bisulfite-treated using the EZ DNA methylation kit (Zymo research, Irvine, CA, USA). Although Infinium Mouse Methylation BeadChips have been developed recently to measure the methylation profile of mice, there was no mature mouse methylation array when this study started, and thus, the study was carried out using the Illumina Human Infinium Methylation BeadChips. Bisulfite-converted DNA was hybridized with the Illumina Human Infinium MethylationEPIC BeadChip Kit (Illumina, San Diego, CA, USA) and then scanned with the Illumina iScan System (Illumina, CA, USA) using the manufacturer’s standard protocol. Samples from the two groups were randomly loaded on the arrays.
The Infinium MethylationEPIC BeadChip Kit included >850,000 individual CpG sites genome-wide at single-nucleotide resolution. As the Infinium MethylationEPIC array was not specifically designed for the mouse genome, many primers for each probe in the array do not target or specifically align within the mouse genome, so their location cannot be identified in the mouse genome with certainty.
Hence, 22,569 out of the 850,000 probes that were identified in previous studies [20 (link),21 (link)] to have a unique best alignment score when mapping the probe primers to the mouse genome (GRCm38) were used for the following analysis.
The Infinium MethylationEPIC BeadChip Kit included >850,000 individual CpG sites genome-wide at single-nucleotide resolution. As the Infinium MethylationEPIC array was not specifically designed for the mouse genome, many primers for each probe in the array do not target or specifically align within the mouse genome, so their location cannot be identified in the mouse genome with certainty.
Hence, 22,569 out of the 850,000 probes that were identified in previous studies [20 (link),21 (link)] to have a unique best alignment score when mapping the probe primers to the mouse genome (GRCm38) were used for the following analysis.
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