DNA from fresh frozen tissue was isolated with QIAamp DNA mini kit (Qiagen, Valencia, CA)
Label
Cy3,Cy5
Label protocol
sodium bisulfite modified using the EZ DNA Methylation Kit (Zymo Research, Orange, CA).
Hybridization protocol
Illumina GoldenGate® methylation bead arrays interrogated 1505 CpG loci associated with 803 cancer-related genes processed at the UCSF Institute for Human Genetics, Genomics Core Facility as described in Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93.
Scan protocol
Bibikova et al. High-throughput DNA methylation profiling using universal bead arrays. Genome research 2006;16:383-93.
Description
DNA (bisulfite modified)
Data processing
Illumina BeadStudio Methylation software was used for dataset assembly. Fluorescent signals for methylated (Cy5) and unmethylated (Cy3) alleles give methylation level: (max(Cy5 , 0))/(|Cy3| + |Cy5| + 100) with ~30 replicate bead measurements per locus. Detection P-values determined poor performing samples (n=2) and CpG loci (n=8), which were removed from analysis. X chromosome loci were also removed, leaving 1413 CpG loci associated with 773 genes. Raw average beta values were used and not subjected to normalization as per manufacturer's recommendations.
