7 protocols | |
|---|---|
| Accession | Type |
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 | |