7 protocols
AccessionType
normalization data transformation protocol
For each interrogated CpG site, methylation status is calculated by dividing the signal from the methylated probe (M) by the sum of signals for both methylated and unmethylated (U) probes (Genome Studio 2008.1, Illumina Inc.). Missing values were imputed by nearest neighbors averaging (impute R package)
array scanning and feature extraction protocol
Illumina HumanMethylation27 kit, as recommended
nucleic acid hybridization to array protocol
Illumina HumanMethylation27 kit, as recommended
nucleic acid labeling protocol
Illumina HumanMethylation27 kit, as recommended
nucleic acid extraction protocol
QIAamp DNA Mini Kit Qiagen, as recommended
sample collection protocol
Biopsies were immediately snap- frozen in liquid nitrogen and kept at –80°C until used
conversion protocol
EZ DNA Methylation Kit Proteigene, as recommended