disease state: Normal sample type: Self-sampled cervico-vaginal material (self-sample)
Extracted molecule
genomic DNA
Extraction protocol
DNA from self-samples was isolated using the NucleoMag 96 Tissue kit (Macherey-Nagel, Düren, Germany) and a Microlab Star robotic system (Hamilton, Martinsried, Germany) according to the manufacturer’s protocol. Isolated DNA was bisulphite-converted using the EZ DNA Methylation kit (Zymo Research, Orange, CA, USA) according to manufacturer's instructions.
Label
Cy3 en Cy5
Label protocol
Labelling was done as described in the automated protocol of the Infinium HD assay methylation protocol guide.
Hybridization protocol
Hybridisation was done as described in the automated protocol of the Infinium HD assay methylation protocol guide.
Scan protocol
Scanning was done as described in the automated protocol of the Infinium HD assay methylation protocol guide.
Description
Lavage-based self-sample
Data processing
Data were pre-processed, including probe quality control. Probes which, (i) showed a low bead count (<3 in at least 5% of samples), (ii) had a detection p-value of > 0.05 in at least 3% of samples, (iii) contained SNPs at or within 10 bp from the target CpG-site (Chen et al. Epigenetics 2013), (iv) were vulnerable to cross-hybridization (Chen et al. Epigenetics 2013) or (v) were located on allosomes, were removed, leaving 365,620 probes for analysis. Data were normalised using dasen normalisation (Pidsley et al. BMC Genomics 2013), which uses a different background correction and quantile normalisation for type I and type II probes. It returns normalised beta-values, representing methylation percentage at the corresponding CpG-site.