RNA was extracted from cells as described before and quality was assessed on Agilent 2100 Bioanalyzer device (Agilent Technologies, Palo Alto, CA) from the indicated cell lines and clones. If MAB treatment is indicated, cells were exposed for 1:40 SWA11 MAB for 72h. RNA was labeled and hybridized as described before (8), only this time, using the human (HG-U133A) Genechip® (Affymetrix Inc., Santa Clara, CA).
Label
biotin
Label protocol
standard Affymetrix protocol
Hybridization protocol
standard Affymetrix protocol
Scan protocol
standard Affymetrix protocol
Description
none
Data processing
The algorithm, implanted in Affymetrix Suite Version 5.0 (MAS5) generates signal value (which designates a relative measure of the abundance of the transcript), a detection p-value (which indicates the reliability of the transcript’s detection call) and detection call (present, absent or marginal). For interarray comparisons, the data from each array was scaled using MAS5. The bioinformatics analysis was carried out using GeneSpring® version7 software (Silicon Genetics, Redwood City, CA, USA). Normalization procedure: Values below 0.01 were set to 0.01. Each measurement was divided by the 50.0th percentile of all measurements in that sample (per chip normalization). Each gene was divided by the median of its measurements in all samples (per gene normalization). Genes were filtered out if appearing present in only none or 1 of the 8 samples.
