We used 16 brain samples from Alzheimer’s cases and controls. These samples were classified into 4 controls and 4 cases of NHBs and 4 controls and 4 cases of NHWs. To correctly assess the correlations between the Human Imprintome array and WGBS, we combined the 4 samples from each group by averaging the DNA methylation levels in the Human Imprintome array. We collapsed the probes that were targeting the same CpG site in the Human Imprintome array.
Extracted molecule
genomic DNA
Extraction protocol
For the preparation of samples, 200 ng of DNA were bisulfite converted using the EZ DNA Methylation kit (Zymo Research, Irvine, CA) according to the manufacturer’s instructions.
Label
Cy3, Cy5
Label protocol
Bisulfite-converted DNA samples were randomly assigned to a chip well on the Human Imprintome array BeadChip (Illumina, Inc., San Diego, CA), amplified, hybridized onto the array, stained, washed, and imaged with the Illumina iScan SQ instrument (Illumina, Inc., San Diego, CA) to obtain raw image intensities.
Hybridization protocol
Bisulfite-converted DNA samples were randomly assigned to a chip well on the Human Imprintome array BeadChip (Illumina, Inc., San Diego, CA), amplified, hybridized onto the array, stained, washed, and imaged with the Illumina iScan SQ instrument (Illumina, Inc., San Diego, CA) to obtain raw image intensities.
Scan protocol
Bisulfite-converted DNA samples were randomly assigned to a chip well on the Human Imprintome array BeadChip (Illumina, Inc., San Diego, CA), amplified, hybridized onto the array, stained, washed, and imaged with the Illumina iScan SQ instrument (Illumina, Inc., San Diego, CA) to obtain raw image intensities.
Data processing
To preprocess the DNA methylation values, we utilized the sesame package due to its compatibility with custom arrays. Specifically, we employed the readIDATpair followed by the getBetas functions, which require the IDAT file locations and the custom manifest to generate a beta value matrix. To visualize the distribution of beta values we employed the densityPlot function from the minfi package
