Extended Data Fig. 1: Loss of type I IFN signaling in Atg5^fl/fl-LysM-Cre mice alters lesion architecture and neutrophil distribution in the lung without affecting bacterial burdens or neutrophil accumulation.

(A) Median fluorescence intensity of IFNAR1 on neutrophils in the lung at 14 dpi with Mtb quantified by flow cytometry. (B) The amount of IFNβ in the lungs from GFP-Mtb infected mice at 14 dpi quantified by ELISA. (C-L) Immune cell abundance in the lungs of GFP-Mtb infected mice at 14 or 21 dpi determined by flow cytometry. Each datapoint represents one biological replicate from at least 2 independent experiments. (M) Additional representative H&E-stained lung sections from GFP-Mtb infected mice at 21 dpi. Scale bar is 1 mm. (N) Additional representative merged tiled confocal immunofluorescence images of lung sections from GFP-Mtb infected mice at 21 dpi that were probed with antibodies to detect citrullinated histone H3 (H3Cit; red), Ly6G (neutrophil marker; cyan), and DNA (Hoechst; blue). GFP-Mtb is shown in green. Scale bar is 1 mm. (O) Representative confocal immunofluorescence images of lung sections at 60X magnification from GFP-Mtb infected mice at 14 dpi that were probed with antibodies to detect Ly6G (neutrophil marker; cyan), and DNA (Hoechst; blue). GFP-Mtb is also shown. Scale bar is 50μm. (P) The average size of contiguous Ly6G⁺ regions in lung tissue sections at 14 dpi. Each data point is from one field of view where data from 4 mice from at least two independent infection experiments were compiled. (Q) The proportion of Ly6G⁺ pixel area across complete lung sections (Fig. 1j) determined by Fiji analysis of immunofluorescence histology images of lung sections from mice infected with GFP-Mtb for 21 dpi. Each data point is from one lung section from 3 mice from at least 2 independent experiments. All graphs report the mean ± SD. Statistical differences were determined by an unpaired two-tailed student t-test (A-B, P) or one-way ANOVA and Šídák multiple comparison test (C-L, Q) (only comparing within a single timepoint). * P < 0.05, ** P < 0.01, and **** P < 0.0001. Differences that are not statistically significant are designated as ns. Complete statistical analysis including the number of samples used is in Supplementary Table 4.