The data archive contains The Cancer Genome Atlas (TCGA) analysis of DNA methylation profilings using the Illumina Golden Gate Methylation Bead Array platform. DNA samples were received, bisulfite converted and the methylation profiling was evaluated using Illumina DNA Methylation Golden Gate technology.

This archive contains data on one DNA methylation bead array for 28 GBM tumor samples (plus the cytogenetically normal TCGA-07-0227 sample) from Batch .

The AVG_beta value represents the final methylation value for each locus, while the Cy3 and Cy5 measurements represent methylated and unmethylated DNA signal intensities for each hybridization. The Detection p-values (Detection PVAL)provide an indication of DNA methylation measurement quality for each locus. Data points labeled "P>0.05" represent beta values with an accompanying detection p-value > 0.05 (non-significant detection of DNA methylation).

OMA003 refers to the GBM custom version of the Illumina GoldenGate DNA methylation Oligonucleotide pool for Methylation Assay (OMA), described by Illumina as DNA Methylation-GBM-OMA-003.

Data package includes full data information for each sample using background subtraction normalization method, i.e., AVG_beta value, cy3 measurement, cy5 measurement, and p-value.

July 29, 2008
