Cells (wild type) were cultured in DMEM medium (Life Technologies, #31966-021) containing 10% fetal calf serum (FCS, Hyclone) in T75 cm2 flasks to 75-90% confluence.
Extracted molecule
genomic DNA
Extraction protocol
DNA was isolated using the DNeasy kit according to manufacturer’s instructions (QIAGEN, cat nr. 69504).
Label
Cy3/Cy5
Label protocol
Bisulfite conversion was performed using 500 ng genomic DNA input using the EZ DNA Methylation Gold Kit (Zymo Research).
Hybridization protocol
The bisulfite converted DNA was processed and hybridized to the HumanMethylation450 BeadChip (Illumina, Inc.), according to the manufacturer's instructions.
Scan protocol
The BeadChip images were scanned on the iScan system and the data was extracted into GenomeStudio software v2011.1, using default analysis settings.
Data processing
Further processing was carried out in R using the LUMI package [1] following the optimized “lumi: QN+BMIQ” pipeline [2] This includes exclusion of poorly performing probes (p<0.01), color adjustment, quantile normalization and correction for probe type bias (Infinium I vs II) using the BMIQ algorithm [3]. 1. Du, P., W.A. Kibbe, and S.M. Lin, lumi: a pipeline for processing Illumina microarray. Bioinformatics, 2008. 24(13): p. 1547-8. 2. Marabita, F., et al., An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform. Epigenetics, 2013. 8(3): p. 333-46. 3. Teschendorff, A.E., et al., A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics, 2013. 29(2): p. 189-96.
Seminoma and embryonal carcinoma footprints identified by analysis of integrated genome-wide epigenetic and expression profiles of germ cell cancer cell lines (methylation data).
Seminoma and embryonal carcinoma footprints identified by analysis of integrated genome-wide epigenetic and expression profiles of germ cell cancer cell lines
Data table header descriptions
ID_REF
VALUE
Normalized Beta (see data processing for normalization method)
