ID_REF = VALUE = RMA Log2 expression value.
Data was extracted and normalized using a custom CDF and Robust Multi-array Average (RMA) in R (r-project.org) with default settings.
Arrays were scanned using the GeneArray Scanner 3000 according to the instructions from the manufacturer.
The resulting labeled samples were hybridized to the Affymetrix Mouse Gene 1.0 ST Array from Affymetrix according the instructions of the manufacturer
The 3’ IVT Express Kit (Affymetrix) using conditions recommended by the manufacturer.
Lymphomas used in this study were maintained in B-cell Media (BCM; 45% DMEM, 45% Iscove’s Media, 55 mM b-mercaptoethanol, 10% Fetal Bovine Serum) on g-irradiated Arf-/- MEF feeder layers. Feeder layers were comprised of ~25% confluent irradiated Arf-/- MEFs pre-incubated with BCM for 3 days prior to addition of lymphoma cells. Lymphomas were routinely split 1:3 every 2-3 days and discarded after >3 weeks in culture.
Cells were transduced with either Rluc.713 or Dhx9.1241shRNA
Total RNA was extracted using trizol.