Dual-color (Cy3-Cy5) hybridization of slides was performed using the RNA MICROMAX TSA labeling and detection kit (PerkinElmer) as described earlier [34] . Messenger RNA levels in both infected pools (12 and 18 hpi) were independently compared to the expression levels in the control (uninfected) pool. For each comparison, a dye swap was performed. In addition, a control hybridization experiment was performed in which a microarray slide was simultaneously hybridized with Cy3labeled control RNA and Cy5-labeled control RNA. Scanning of slides, processing of raw images, creation of data reports, data-normalization and statistical analysis were performed as described by Niewold et al. [34] with minor modifications. Briefly, probes were considered to be differentially expressed when at least four of the six data points (spots) on both dye swap slides hybridized with a ratio of 3.6-fold (M = [log 2 (Cy3/Cy5)] \ -1.85 or [1.85) or more (3.6 is considered significant according to the manufacturer of the TSA kit) and were identified by significant analysis of microarrays (SAM) [43] with a median false discovery rate (FDR or q value) of \5%.