Extended Data Fig. 10: Transcriptional and inflammatory profiles of the lungs in B6.Sst1^S and B6.Sst1^SBach1^-/- mice.

(A-E) B6.Sst1^S and B6.Sst1^SBach1^-/- mice were infected at low-dose with Mtb. Mice were euthanized at 17 days p.i. and single-cell suspensions from lungs were isolated from Mtb-infected and uninfected animals for RNAseq analysis (n = 3-4, each group; samples from one experiment). (A) Heatmap displaying the DEGs identified for each group analyzed. (B) Venn diagram plot from the identified DEGs with the corresponding comparisons. (C) Molecular degree of perturbation (MDP) plot displaying values as bars for each group. Boxplots shows median (centre line), upper and lower quartiles (box limits) and the interquartile range (whiskers). Each symbol represents an individual animal within the group (n = 3-4, each group) and data shown are from one experiment performed. (D) Bacterial loads in the lungs from B6.Sst1^S and B6.Sst1^SBach1^-/- mice at 17 days p.i. (E) Correlation between MDP values and bacterial counts in the lung from Scatter plot summarizing the MDP and CFU values from B6.Sst1^S and B6.Sst1^SBach1^-/- mice at 17 days p.i. (F) Summary data of cytokine/chemokine levels in lung homogenates from B6.Sst1^S and B6.Sst1^SBach1^-/- mice at 35 days p.i. shown in the Fig. 5G. (B6.Sst1^S n = 15 vs B6.Sst1^SBach1^-/- n = 17, pooled from three independent experiments). (G) tSNE analysis of the myeloid cells in the lungs of Mtb infected mice at 17 and 35 days p.i. Proportional events from each animal were concatenated (n = 4-5 each group; samples from one experiment). AM (dark blue gate), IM (green gate), neutrophils (red gate), parenchymal neutrophils (orange gate), DCs (purple and light blue gate) and inflammatory monocytes (yellow gate) are indicated in the tSNE plot and the proportion of each cell population cells is shown (bottom). The data shown in D-F are presented as mean values ± SEM of the pooled samples for each group. Statistical significance was assessed by two-tailed, Mann–Whitney test for the indicated experimental conditions. (ns, not significant).

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