Table 3: Comparison of transcriptional alterations in mice infected with WT Y. pestis CO92 (this study) and a strain that is avirulent in humans (Y. pestis strain 201, previous study reported by Liu et al. [21]).

This study Liu et al. Gene FC Tissue Gene FC Tissue CD34 3.7 Liver CD34 2.2 Liver Ifitm1 3.3 All Ifitm3 2.7 Liver Ifitm6 4.4 Lung Tgfbr2 2.3 Liver Tgfb3 2.5 Liver −3 Lung Tnfsf10 2.3 Liver Tnfrsf1a 2.3 Liver Tnfrsf13b 2.3 Lung Ccl20 2.4 Lung Ccl20 7.5 Lung Cd14 12.5 All Cd14 14.1 Lung & Liver Csf3 6.6 All Csf3 5 Lung Cxcl2 39.8 Lung & Liver Cxcl2 14.2 Lung & Liver Cxcl5/6 9.5 All Cxcl5/6 2.6 Lung IL-1b 5.6 All IL-1b 4.8 Lung IL2rg 2.9 Liver IL2rb 2.5 Lung Tnfaip8 2 Liver Tnfaip8 2.3 Lung Cd9 2.8 Liver Cd9 2.4 Liver −2.6 Lung Icam2 2.8 Liver Icam2 1.9 Liver −3.1 Lung IFN- 4.6 All IFN- −2.2 Lung Igfbp1 3.7 Liver Igfbp1 3.2 Liver Igfbp4 2.1 Lbp 4.2 Liver Lbp 4.2 Liver Ndrg −2 Liver Ndrg1 Up ? Gadd45g 8.3 Liver Gadd45g Up ? MT1 5.1 Lung & Liver MT1 Up Lung & Liver MT2 9.2 Lung & Liver MT2 Up Lung & Liver

For this study, fold changes (FCs) shown are averages across affected tissues. Only alterations that were determined to be statistically significant (i.e., Benjamini and Hochberg corrected value and absolute consistency across all replicate experiments) are included. A negative sign before values indicates downregulation.