library_construction_protocol: FACS isolated cells were pooled and loaded into 3 different lanes on a Chromium Next GEM Chip. Lane 1 was loaded with Mtb-infected cells from all 3 B6 and 3 Sp140–/– lungs. Lane 2 was loaded with bystander myeloid cells from the 3 infected B6 lungs as well as the myeloid cell mixture from the 2 naïve B6 lungs. Lane 3 was loaded with bystander myeloid cells from the 3 infected Sp140–/– lungs as well as the myeloid cell mixture from the 2 naïve Sp140–/– lungs. All 3 lanes of the Chromium Next GEM Chip were super-loaded with 29000 cells with a target of 14800 single cells per lane, The scRNA-sequencing libraries were generated using the v3.1 chemistry Chromium Single Cell 3' Reagent Kit (10X Genomics) largely following this kits protocol and the CITE-seq protocol. 0.5 U/µL RNaseOUT Recombinant Ribonuclease Inhibitor (Invitrogen) was added to single cell RT master mix during the loading step and 1 µL of ADT and HTO additive primers (0.2 µM stock) were added during the cDNA amplification. Following cDNA, ADT, and HTO purification, samples were decontaminated by 2 rounds of centrifugation through 0.2 µM filter microcentrifuge tubes and then removed from the BSL3. Library preparations were completed outside of the BSL3 following the 10X Genomics protocol for the cDNA and the CITE-seq and Cell Hashing Protocol for the ADT and HTO libraries. Quality control of the libraries was performed with a Fragment Analyzer (Agilent). The mRNA, ADT, and HTO libraries were pooled at the following proportions: 85% mRNA, 9% ADT, and 6% HTO. Libraries were sequenced on a NovaSeq 6000 (Illumina) using two lanes of a S1 flow cell and the following cycles read 1 (28 cycles), i7 index (10 cycles), i5 index (10 cycles), read 2 (90 cycles).