Genomic DNA extraction was performed manually using a QIAamp DNA mini QIAcube Kit (Qiagen, Venlo, Netherlands), according to the manufacturer’s protocol.
DNA was treated with bisulfite using an EZ-96 DNA Methylation Kit on a Zymo Spin I-96 column (Zymo Research, Irvine, CA, U.S.A.). Bisulfite-converted DNA was amplified, fragmented, and hybridized to Illumina Human Methylation 450k microarrays using an Illumina Hybridization Oven (Illumina, San Diego, CA, U.S.A.), according to the manufacturer’s protocol. Slides were analyzed by an Illumina I-Scan (Illumina, San Diego, CA, U.S.A.).
Raw iDAT files were directly imported in R software (R Development Core Team, 2008 ) and processed using the R minfi package (Aryee et al., 2014 (link)). Raw data were normalized using functional normalization (Fortin et al., 2014 (link)) before constructing the beta matrix for all 36 samples and 485,512 CpG sites (methylomics dataset).
DNA was treated with bisulfite using an EZ-96 DNA Methylation Kit on a Zymo Spin I-96 column (Zymo Research, Irvine, CA, U.S.A.). Bisulfite-converted DNA was amplified, fragmented, and hybridized to Illumina Human Methylation 450k microarrays using an Illumina Hybridization Oven (Illumina, San Diego, CA, U.S.A.), according to the manufacturer’s protocol. Slides were analyzed by an Illumina I-Scan (Illumina, San Diego, CA, U.S.A.).
Raw iDAT files were directly imported in R software (R Development Core Team, 2008 ) and processed using the R minfi package (Aryee et al., 2014 (link)). Raw data were normalized using functional normalization (Fortin et al., 2014 (link)) before constructing the beta matrix for all 36 samples and 485,512 CpG sites (methylomics dataset).
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