ID_REF = VALUE = MAS5.0 signal intensity
Scanned using Affymetrix GeneChip Scanner 3000.
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings. We normalized such that the median intensity value was 500. We then set the minimum intensity to be 50.
Followed Affymetrix instructions.
BMDMs were infected with parasite strains at the indicated Multiplicity of Infection (MOI) for 18 hours before RNA harvesting; the actual MOI of viable parasites after plaque assays for this series of experiments was between 1 and 2.
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
BMDMs were plated at 3x10^6 cells per well in 6-well plates. They were generated by incubated bonemarrow cells in 20% L929 medium for 6-7 days before harvesting.