Cell lines were cultured in Dulbecco’s Modified Eagle Medium (EC, Teratoma and YST) and RPMI-1640 media (Seminoma) (Sigma-Aldrich). containing 10% fetal bovine serum (Sigma-Aldrich). and 1% Penicillin/Streptomycin (Sigma-Aldrich).
Extracted molecule
total RNA
Extraction protocol
RNA extraction was performed using the RNeasy extraction kit (Qiagen) according to the manufacturer protocol. RNA was eluted with RNAse-free water.
Label
biotin
Label protocol
not provided
Hybridization protocol
not provided
Scan protocol
not provided
Data processing
Data was first preprocessed using the statistical software, R with packages provide by www.bioconductor.org. Data was preprocessed using the RMA method [66] and filtered such that probes which gave expression outputs below control background probes (recorded in the GeneChip) for all four cell lines were excluded. Fold changes in expression between each probe of each cell lines relative to Seminoma were calculated, and annotation packages were used to assign gene information to each probe set. The data was exported as a .txt file in order to be read and analysed in Excel. The Excel tool PivotTable was used to assign average expression intensity values to each gene.
