File S1 - Dynamic Cross Talk Model of the Epithelial Innate Immune Response to Double-Stranded RNA Stimulation: Coordinated Dynamics Emerging from Cell-Level Noise

File S1 includes 5 Supplemental Tables and 2 Supplemental Figures. Supplemental Tables are: ST1. System of Ordinary Differential Equations defining the model. ST2. Reaction constants. These reaction constants are the same as in Table ST1 (they are numbered identically). Their dimensions are : 1/(# molecules s) for second-order and 1/s for first-order reactions. ST3. Pseudocode. ST4. TFBS analysis. Table presents counts of TFBS corresponding to IRF family and NF-κB family transcription factors found in promoters of presented genes in four species: cattle (bosTau), mouse (mm), chimpanzee (panTro) and human (hg). Yellow rows correspond to promoter sequences with at least one IRF3 binding site, bright orange rows correspond to sequences containing motifs for all 3 members of IRF family, red cells correspond to sequences with more than 2 binding sites for IRF3. For genes: IRF7, MAVS, IKK1, IKBKB and DDX58 only human and murine promoters were analyzed. ST5. Effect of siRNA knockdown on dsRNA-induced NF-κB/IRF3 gene expressions in A549 cells. Statistical significance of the difference recorded in the knockdown experiment, carried out using the 2-sample, 2-sided t-test (Welch test), corresponding to the bar charts in Figure 3. (A) Comparison of the mRNA-specific siRNA knockdown versus control (nonspecific siRNA), in dsRNA-nonstimulated and dsRNA-stimulated experiment (at 6 hr). (B) Comparison of dsRNAinduced versus dsRNA-noniduced under siRNA knockdown (at 6 hr). Rows: Different knockdowns. Columns: Genes expressed. Supplemental Figures are SF1. Wiring diagram corresponding to the pseudocode and differential equation system. SF2. Snapshots of RelA-specific and IRF3-specific labeling in A549 cells at different times in non dsRNA-induced experiment.
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