Humanwg 6 v2

Global gene expression of PBMCs from naturally infected malaria patients was analyzed employing the Illumina HumanWG-6 v2.0 method (~47,000 transcripts/microchip) (Franklin et al., 2009 (link)). Each patient served as his/her own control. Fold increase of gene expression was calculated by using PBMCs from the same patient before and 30–40 days after documented curative treatment. Sample filtering, normalization, and averaging were conducted with BASE (Bio-Array Software Environment) (https://base.thep.lu.se) and log transformed (log2) (Vallon-Christersson et al., 2009 (link)). Genes were filtered to include those with a signal greater than the average from the negative controls in at least one of the samples with a detection p<0.01. For mouse experiments, we used splenocytes from three C57BL/6, three IFNγ^−/− and three RAG^−/− mice at zero (uninfected) and at six days p.i. with Pc. Gene expression was assessed using a gene chip from Affymetrix (23,000 transcripts). The expression value for each gene was determined by calculating the average of differences in intensity (perfect match intensity – mismatch intensity) between its probe pairs.