Biotinylated cRNA were prepared according to the Affymetrix protocol from total RNA.
Hybridization protocol
Samples were prepared for and measured on Affymetrix HG-U133-plus2 Chip (Santa Clara/CA).
Scan protocol
GeneChips were scanned using the scanner GCS3000 and GCOS1.2 Software Suite (Affymetrix).
Data processing
After RMA-background correction with 9 further published samples (IMC-1 and KHYG1 from GEO:GSE19067; NK-92 from GEO:GSE53478; SNK6 from GEO:GSE19067 and 5 T-ALL cell lines i.e. ALL-SIL, CCRF-CEM, PEER, JURKAT, LOUCY from GSE87334), quantile normalisation of spot intensities, data were logarithmically transformed. Data processing was done via R/Bioconductor using limma and affy packages.
