DC TRANSCRIPTIONAL ANALYSIS

Affymetrix and Illumina microarray data is available on 3X106 DCs that were either not stimulated or stimulated with different stimuli. Cells were harvested after 4 hours of stimulation. RNA extraction was done with TRIzol reagent (Invitrogen). microarray hybridization were performed on the basis of technology used. Affymetrix array data files (CEL files) were pre-processed and normalized using the Robust Multichip Average procedure (RMA). Annotations were updated following a procedure devised by Dai and co-workers (Dai et al., 2005). Computation was performed with the RMAExpress program (http://rmaexpress.bmbolstad.com) . Bead-summary data saved from Illumina BeadStudio was pre-processed in several steps. Firstly, the background signal was assessed and corrected using the intensity signal from the control probes present on the array, then quantile normalization was performed. In addition to background correction, Illumina probe identifiers were converted to nucleotide universal IDentifiers (nuIDs) (Du et al., 2007) specific for the nucleotide sequence of each probe. The computation was performed using the lumi package (Du et al., 2008), written in the R programming language.

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