Schematic of the infections and treatment conditions used in this study. A. The infection and STS treatment conditions were modified to analyze a time course of STS exposure and adapted from the apoptosis assay previously described . Briefly, S. flexneri was applied to a monolayer of HeLa cells and incubated at 37°C for 1 hour in Dulbecco's modified Eagle's medium (DMEM). Afterwards, the cells were washed and DMEM plus 50 μg/ml gentamicin was added to kill the extracellular bacteria and allow the intracellular bacteria to replicate. Uninfected cells received the same treatments and washes. Finally, infected and uninfected cells were washed and received DMEM plus gentamicin or DMEM plus gentamicin and 4 μM STS for 0.5, 1.0, 2.0, or 2.75 hours. After the treatments, the RNA was harvested from the cells. Two biological replicates were performed: one set for the microarray studies and one set for in situ hybridization (ISH) studies to confirm the microarray results. A single time point was analyzed for the ISH (see Methods). B. The individual time points were grouped together and then utilized as a single group in the pairwise comparisons for the microarray analysis. The four pairwise comparisons performed are indicated.