normalization data transformation protocol
Expression levels were extracted with Affymetrix GeneChip Command Console (AGCC). Arrays were normalized to DMSO samples using the robust multi-array average method and filtered to remove non-informative probes.
array scanning protocol
Scanning were conducted as per the manufacturer's instructions (Illumina).
nucleic acid hybridization to array protocol
nucleic acid extraction protocol
Total RNA of treated EuM2 cells was extracted using RNeasy kit (Qiagen) according to the manufacturer's instructions. The quality of total RNA was evaluated using Agilent Bioanalyzer (Agilent Technologies, USA); only samples with RNA integrity number >7.5 were analyzed. RNA of four different treatments were hybridized to two microarrays each.
nucleic acid labeling protocol
Labeling was conducted as per the manufacturer's instructions (Illumina).
EuM2 cells were maintained in RPMI 1640 medium containing 20 mM HEPES buffer, 10% heat-inactivated fetal bovine serum (Gibco/Invitrogen), 50 uM 2-mercaptoethanol, 200 uM asparagine, and 100 U/mL penicillin-streptomycin.
EuM2 or BC2 cells (1.6 x 105/ml) were treated with 0.1% DMSO or 1 uM Ara-C (Sigma) for 16 hrs. For the combination treatment, the cells were treated with 1 ug/ml Pam3CSK4 (Invivogen) or endotoxin-free water used for dissolving Pam3CSK4 for 16 hrs followed by 1 uM Ara-C or DMSO for 16 hrs.