SRX17914793 GSM6644983_r1 SRP402989 PRJNA891222 SRS15430519 GSM6644983 GSM6644983 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA All samples subjected to scRNA-seq were prepared and FACS-enriched using the following procedures. STm infected spleens were harvested and digested in buffer containing HBSS + Ca2+ + Mg2+ + 50 μg/mL DNase (Roche) + 25 μg/mL Liberase TL (Sigma) at 37 °C for 25 min, mixing at 200 rpm. EDTA was added to 5 mM final concentration to stop digestion reaction and cells were washed with RPMI containing 10% FCS. Following RBC lysis, splenocytes were washed twice RPMI containing 10% FCS. Splenocytes were stained with an antibody mixture for surface markers (CD11b Alexa fluor 647, CD11c PECy7, Ly6C PerCP Cy5.5, Ly6G FITC, CD3 APC efluor 780, CD19 APC efluor 780, and NK1.1 APC efluor 780) for 25 minutes on ice, washed twice with RPMI containing 10% FCS, then resuspended in the same buffer with 1:2000 DAPI. Splenocytes were then FACS-enriched on a BD FACSAria cell sorter. A permissive gating strategy was utilized to simultaneously enrich CD11b+CD11c+Ly6C+ macrophages and capture other splenocytes for sequencing. Sorting gates were set tightly for size/scatter, singlet, and living cells but more loosely for CD3/CD19/NK1.1-, CD11b+, Ly6G-, Ly6C+, and CD11c+ cells. The viability of sorted cells were checked using Trypan blue staining and hemocytometer inspection under a light microscope. Samples had viability greater than 90%. Cells were resuspended to a concentration to 500-1200 cells/uL, partitioned, and captured for sequencing on a 10x Chromium Controller. Libraries were prepared by the Stanford Functional Genomics Facility (SFGF) using 10X Genomics 3' GEX v3.1 kit and sequenced on the Illumina HiSeq4000 platform to a depth of ~40,000 - 50,000 reads/cell. 10X Genomics 3' GEX v3.1 kit. Illumina HiSeq 4000 SRX17914794 GSM6644984_r1 SRP402989 PRJNA891222 SRS15430521 GSM6644984 GSM6644984 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA All samples subjected to scRNA-seq were prepared and FACS-enriched using the following procedures. STm infected spleens were harvested and digested in buffer containing HBSS + Ca2+ + Mg2+ + 50 μg/mL DNase (Roche) + 25 μg/mL Liberase TL (Sigma) at 37 °C for 25 min, mixing at 200 rpm. EDTA was added to 5 mM final concentration to stop digestion reaction and cells were washed with RPMI containing 10% FCS. Following RBC lysis, splenocytes were washed twice RPMI containing 10% FCS. Splenocytes were stained with an antibody mixture for surface markers (CD11b Alexa fluor 647, CD11c PECy7, Ly6C PerCP Cy5.5, Ly6G FITC, CD3 APC efluor 780, CD19 APC efluor 780, and NK1.1 APC efluor 780) for 25 minutes on ice, washed twice with RPMI containing 10% FCS, then resuspended in the same buffer with 1:2000 DAPI. Splenocytes were then FACS-enriched on a BD FACSAria cell sorter. A permissive gating strategy was utilized to simultaneously enrich CD11b+CD11c+Ly6C+ macrophages and capture other splenocytes for sequencing. Sorting gates were set tightly for size/scatter, singlet, and living cells but more loosely for CD3/CD19/NK1.1-, CD11b+, Ly6G-, Ly6C+, and CD11c+ cells. The viability of sorted cells were checked using Trypan blue staining and hemocytometer inspection under a light microscope. Samples had viability greater than 90%. Cells were resuspended to a concentration to 500-1200 cells/uL, partitioned, and captured for sequencing on a 10x Chromium Controller. Libraries were prepared by the Stanford Functional Genomics Facility (SFGF) using 10X Genomics 3' GEX v3.1 kit and sequenced on the Illumina HiSeq4000 platform to a depth of ~40,000 - 50,000 reads/cell. 10X Genomics 3' GEX v3.1 kit. Illumina HiSeq 4000 SRX17914795 GSM6644985_r1 SRP402989 PRJNA891222 SRS15430520 GSM6644985 GSM6644985 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA All samples subjected to scRNA-seq were prepared and FACS-enriched using the following procedures. STm infected spleens were harvested and digested in buffer containing HBSS + Ca2+ + Mg2+ + 50 μg/mL DNase (Roche) + 25 μg/mL Liberase TL (Sigma) at 37 °C for 25 min, mixing at 200 rpm. EDTA was added to 5 mM final concentration to stop digestion reaction and cells were washed with RPMI containing 10% FCS. Following RBC lysis, splenocytes were washed twice RPMI containing 10% FCS. Splenocytes were stained with an antibody mixture for surface markers (CD11b Alexa fluor 647, CD11c PECy7, Ly6C PerCP Cy5.5, Ly6G FITC, CD3 APC efluor 780, CD19 APC efluor 780, and NK1.1 APC efluor 780) for 25 minutes on ice, washed twice with RPMI containing 10% FCS, then resuspended in the same buffer with 1:2000 DAPI. Splenocytes were then FACS-enriched on a BD FACSAria cell sorter. A permissive gating strategy was utilized to simultaneously enrich CD11b+CD11c+Ly6C+ macrophages and capture other splenocytes for sequencing. Sorting gates were set tightly for size/scatter, singlet, and living cells but more loosely for CD3/CD19/NK1.1-, CD11b+, Ly6G-, Ly6C+, and CD11c+ cells. The viability of sorted cells were checked using Trypan blue staining and hemocytometer inspection under a light microscope. Samples had viability greater than 90%. Cells were resuspended to a concentration to 500-1200 cells/uL, partitioned, and captured for sequencing on a 10x Chromium Controller. Libraries were prepared by the Stanford Functional Genomics Facility (SFGF) using 10X Genomics 3' GEX v3.1 kit and sequenced on the Illumina HiSeq4000 platform to a depth of ~40,000 - 50,000 reads/cell. 10X Genomics 3' GEX v3.1 kit. Illumina HiSeq 4000 SRX17914796 GSM6644986_r1 SRP402989 PRJNA891222 SRS15430522 GSM6644986 GSM6644986 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA All samples subjected to scRNA-seq were prepared and FACS-enriched using the following procedures. STm infected spleens were harvested and digested in buffer containing HBSS + Ca2+ + Mg2+ + 50 μg/mL DNase (Roche) + 25 μg/mL Liberase TL (Sigma) at 37 °C for 25 min, mixing at 200 rpm. EDTA was added to 5 mM final concentration to stop digestion reaction and cells were washed with RPMI containing 10% FCS. Following RBC lysis, splenocytes were washed twice RPMI containing 10% FCS. Splenocytes were stained with an antibody mixture for surface markers (CD11b Alexa fluor 647, CD11c PECy7, Ly6C PerCP Cy5.5, Ly6G FITC, CD3 APC efluor 780, CD19 APC efluor 780, and NK1.1 APC efluor 780) for 25 minutes on ice, washed twice with RPMI containing 10% FCS, then resuspended in the same buffer with 1:2000 DAPI. Splenocytes were then FACS-enriched on a BD FACSAria cell sorter. A permissive gating strategy was utilized to simultaneously enrich CD11b+CD11c+Ly6C+ macrophages and capture other splenocytes for sequencing. Sorting gates were set tightly for size/scatter, singlet, and living cells but more loosely for CD3/CD19/NK1.1-, CD11b+, Ly6G-, Ly6C+, and CD11c+ cells. The viability of sorted cells were checked using Trypan blue staining and hemocytometer inspection under a light microscope. Samples had viability greater than 90%. Cells were resuspended to a concentration to 500-1200 cells/uL, partitioned, and captured for sequencing on a 10x Chromium Controller. Libraries were prepared by the Stanford Functional Genomics Facility (SFGF) using 10X Genomics 3' GEX v3.1 kit and sequenced on the Illumina HiSeq4000 platform to a depth of ~40,000 - 50,000 reads/cell. 10X Genomics 3' GEX v3.1 kit. Illumina HiSeq 4000 SRX17914797 GSM6644987_r1 SRP402989 PRJNA891222 SRS15430523 GSM6644987 GSM6644987 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA All samples subjected to scRNA-seq were prepared and FACS-enriched using the following procedures. STm infected spleens were harvested and digested in buffer containing HBSS + Ca2+ + Mg2+ + 50 μg/mL DNase (Roche) + 25 μg/mL Liberase TL (Sigma) at 37 °C for 25 min, mixing at 200 rpm. EDTA was added to 5 mM final concentration to stop digestion reaction and cells were washed with RPMI containing 10% FCS. Following RBC lysis, splenocytes were washed twice RPMI containing 10% FCS. Splenocytes were stained with an antibody mixture for surface markers (CD11b Alexa fluor 647, CD11c PECy7, Ly6C PerCP Cy5.5, Ly6G FITC, CD3 APC efluor 780, CD19 APC efluor 780, and NK1.1 APC efluor 780) for 25 minutes on ice, washed twice with RPMI containing 10% FCS, then resuspended in the same buffer with 1:2000 DAPI. Splenocytes were then FACS-enriched on a BD FACSAria cell sorter. A permissive gating strategy was utilized to simultaneously enrich CD11b+CD11c+Ly6C+ macrophages and capture other splenocytes for sequencing. Sorting gates were set tightly for size/scatter, singlet, and living cells but more loosely for CD3/CD19/NK1.1-, CD11b+, Ly6G-, Ly6C+, and CD11c+ cells. The viability of sorted cells were checked using Trypan blue staining and hemocytometer inspection under a light microscope. Samples had viability greater than 90%. Cells were resuspended to a concentration to 500-1200 cells/uL, partitioned, and captured for sequencing on a 10x Chromium Controller. Libraries were prepared by the Stanford Functional Genomics Facility (SFGF) using 10X Genomics 3' GEX v3.1 kit and sequenced on the Illumina HiSeq4000 platform to a depth of ~40,000 - 50,000 reads/cell. 10X Genomics 3' GEX v3.1 kit. Illumina HiSeq 4000 SRX17914798 GSM6644988_r1 SRP402989 PRJNA891222 SRS15430524 GSM6644988 GSM6644988 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA All samples subjected to scRNA-seq were prepared and FACS-enriched using the following procedures. STm infected spleens were harvested and digested in buffer containing HBSS + Ca2+ + Mg2+ + 50 μg/mL DNase (Roche) + 25 μg/mL Liberase TL (Sigma) at 37 °C for 25 min, mixing at 200 rpm. EDTA was added to 5 mM final concentration to stop digestion reaction and cells were washed with RPMI containing 10% FCS. Following RBC lysis, splenocytes were washed twice RPMI containing 10% FCS. Splenocytes were stained with an antibody mixture for surface markers (CD11b Alexa fluor 647, CD11c PECy7, Ly6C PerCP Cy5.5, Ly6G FITC, CD3 APC efluor 780, CD19 APC efluor 780, and NK1.1 APC efluor 780) for 25 minutes on ice, washed twice with RPMI containing 10% FCS, then resuspended in the same buffer with 1:2000 DAPI. Splenocytes were then FACS-enriched on a BD FACSAria cell sorter. A permissive gating strategy was utilized to simultaneously enrich CD11b+CD11c+Ly6C+ macrophages and capture other splenocytes for sequencing. Sorting gates were set tightly for size/scatter, singlet, and living cells but more loosely for CD3/CD19/NK1.1-, CD11b+, Ly6G-, Ly6C+, and CD11c+ cells. The viability of sorted cells were checked using Trypan blue staining and hemocytometer inspection under a light microscope. Samples had viability greater than 90%. Cells were resuspended to a concentration to 500-1200 cells/uL, partitioned, and captured for sequencing on a 10x Chromium Controller. Libraries were prepared by the Stanford Functional Genomics Facility (SFGF) using 10X Genomics 3' GEX v3.1 kit and sequenced on the Illumina HiSeq4000 platform to a depth of ~40,000 - 50,000 reads/cell. 10X Genomics 3' GEX v3.1 kit. Illumina HiSeq 4000 SRX17914799 GSM6644989_r1 SRP402989 PRJNA891222 SRS15430525 GSM6644989 GSM6644989 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA All samples subjected to scRNA-seq were prepared and FACS-enriched using the following procedures. STm infected spleens were harvested and digested in buffer containing HBSS + Ca2+ + Mg2+ + 50 μg/mL DNase (Roche) + 25 μg/mL Liberase TL (Sigma) at 37 °C for 25 min, mixing at 200 rpm. EDTA was added to 5 mM final concentration to stop digestion reaction and cells were washed with RPMI containing 10% FCS. Following RBC lysis, splenocytes were washed twice RPMI containing 10% FCS. Splenocytes were stained with an antibody mixture for surface markers (CD11b Alexa fluor 647, CD11c PECy7, Ly6C PerCP Cy5.5, Ly6G FITC, CD3 APC efluor 780, CD19 APC efluor 780, and NK1.1 APC efluor 780) for 25 minutes on ice, washed twice with RPMI containing 10% FCS, then resuspended in the same buffer with 1:2000 DAPI. Splenocytes were then FACS-enriched on a BD FACSAria cell sorter. A permissive gating strategy was utilized to simultaneously enrich CD11b+CD11c+Ly6C+ macrophages and capture other splenocytes for sequencing. Sorting gates were set tightly for size/scatter, singlet, and living cells but more loosely for CD3/CD19/NK1.1-, CD11b+, Ly6G-, Ly6C+, and CD11c+ cells. The viability of sorted cells were checked using Trypan blue staining and hemocytometer inspection under a light microscope. Samples had viability greater than 90%. Cells were resuspended to a concentration to 500-1200 cells/uL, partitioned, and captured for sequencing on a 10x Chromium Controller. Libraries were prepared by the Stanford Functional Genomics Facility (SFGF) using 10X Genomics 3' GEX v3.1 kit and sequenced on the Illumina HiSeq4000 platform to a depth of ~40,000 - 50,000 reads/cell. 10X Genomics 3' GEX v3.1 kit. Illumina HiSeq 4000 SRX17914800 GSM6644990_r1 SRP402989 PRJNA891222 SRS15430526 GSM6644990 GSM6644990 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA All samples subjected to scRNA-seq were prepared and FACS-enriched using the following procedures. STm infected spleens were harvested and digested in buffer containing HBSS + Ca2+ + Mg2+ + 50 μg/mL DNase (Roche) + 25 μg/mL Liberase TL (Sigma) at 37 °C for 25 min, mixing at 200 rpm. EDTA was added to 5 mM final concentration to stop digestion reaction and cells were washed with RPMI containing 10% FCS. Following RBC lysis, splenocytes were washed twice RPMI containing 10% FCS. Splenocytes were stained with an antibody mixture for surface markers (CD11b Alexa fluor 647, CD11c PECy7, Ly6C PerCP Cy5.5, Ly6G FITC, CD3 APC efluor 780, CD19 APC efluor 780, and NK1.1 APC efluor 780) for 25 minutes on ice, washed twice with RPMI containing 10% FCS, then resuspended in the same buffer with 1:2000 DAPI. Splenocytes were then FACS-enriched on a BD FACSAria cell sorter. A permissive gating strategy was utilized to simultaneously enrich CD11b+CD11c+Ly6C+ macrophages and capture other splenocytes for sequencing. Sorting gates were set tightly for size/scatter, singlet, and living cells but more loosely for CD3/CD19/NK1.1-, CD11b+, Ly6G-, Ly6C+, and CD11c+ cells. The viability of sorted cells were checked using Trypan blue staining and hemocytometer inspection under a light microscope. Samples had viability greater than 90%. Cells were resuspended to a concentration to 500-1200 cells/uL, partitioned, and captured for sequencing on a 10x Chromium Controller. Libraries were prepared by the Stanford Functional Genomics Facility (SFGF) using 10X Genomics 3' GEX v3.1 kit and sequenced on the Illumina HiSeq4000 platform to a depth of ~40,000 - 50,000 reads/cell. 10X Genomics 3' GEX v3.1 kit. Illumina HiSeq 4000 SRX17914801 GSM6644991_r1 SRP402989 PRJNA891222 SRS15430527 GSM6644991 GSM6644991 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA All samples subjected to scRNA-seq were prepared and FACS-enriched using the following procedures. STm infected spleens were harvested and digested in buffer containing HBSS + Ca2+ + Mg2+ + 50 μg/mL DNase (Roche) + 25 μg/mL Liberase TL (Sigma) at 37 °C for 25 min, mixing at 200 rpm. EDTA was added to 5 mM final concentration to stop digestion reaction and cells were washed with RPMI containing 10% FCS. Following RBC lysis, splenocytes were washed twice RPMI containing 10% FCS. Splenocytes were stained with an antibody mixture for surface markers (CD11b Alexa fluor 647, CD11c PECy7, Ly6C PerCP Cy5.5, Ly6G FITC, CD3 APC efluor 780, CD19 APC efluor 780, and NK1.1 APC efluor 780) for 25 minutes on ice, washed twice with RPMI containing 10% FCS, then resuspended in the same buffer with 1:2000 DAPI. Splenocytes were then FACS-enriched on a BD FACSAria cell sorter. A permissive gating strategy was utilized to simultaneously enrich CD11b+CD11c+Ly6C+ macrophages and capture other splenocytes for sequencing. Sorting gates were set tightly for size/scatter, singlet, and living cells but more loosely for CD3/CD19/NK1.1-, CD11b+, Ly6G-, Ly6C+, and CD11c+ cells. The viability of sorted cells were checked using Trypan blue staining and hemocytometer inspection under a light microscope. Samples had viability greater than 90%. Cells were resuspended to a concentration to 500-1200 cells/uL, partitioned, and captured for sequencing on a 10x Chromium Controller. Libraries were prepared by the Stanford Functional Genomics Facility (SFGF) using 10X Genomics 3' GEX v3.1 kit and sequenced on the Illumina HiSeq4000 platform to a depth of ~40,000 - 50,000 reads/cell. 10X Genomics 3' GEX v3.1 kit. Illumina HiSeq 4000 SRX17914802 GSM6644992_r1 SRP402989 PRJNA891222 SRS15430528 GSM6644992 GSM6644992 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA All samples subjected to scRNA-seq were prepared and FACS-enriched using the following procedures. STm infected spleens were harvested and digested in buffer containing HBSS + Ca2+ + Mg2+ + 50 μg/mL DNase (Roche) + 25 μg/mL Liberase TL (Sigma) at 37 °C for 25 min, mixing at 200 rpm. EDTA was added to 5 mM final concentration to stop digestion reaction and cells were washed with RPMI containing 10% FCS. Following RBC lysis, splenocytes were washed twice RPMI containing 10% FCS. Splenocytes were stained with an antibody mixture for surface markers (CD11b Alexa fluor 647, CD11c PECy7, Ly6C PerCP Cy5.5, Ly6G FITC, CD3 APC efluor 780, CD19 APC efluor 780, and NK1.1 APC efluor 780) for 25 minutes on ice, washed twice with RPMI containing 10% FCS, then resuspended in the same buffer with 1:2000 DAPI. Splenocytes were then FACS-enriched on a BD FACSAria cell sorter. A permissive gating strategy was utilized to simultaneously enrich CD11b+CD11c+Ly6C+ macrophages and capture other splenocytes for sequencing. Sorting gates were set tightly for size/scatter, singlet, and living cells but more loosely for CD3/CD19/NK1.1-, CD11b+, Ly6G-, Ly6C+, and CD11c+ cells. The viability of sorted cells were checked using Trypan blue staining and hemocytometer inspection under a light microscope. Samples had viability greater than 90%. Cells were resuspended to a concentration to 500-1200 cells/uL, partitioned, and captured for sequencing on a 10x Chromium Controller. Libraries were prepared by the Stanford Functional Genomics Facility (SFGF) using 10X Genomics 3' GEX v3.1 kit and sequenced on the Illumina HiSeq4000 platform to a depth of ~40,000 - 50,000 reads/cell. 10X Genomics 3' GEX v3.1 kit. Illumina HiSeq 4000 SRX17914803 GSM6644993_r1 SRP402989 PRJNA891222 SRS15430529 GSM6644993 GSM6644993 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA All samples subjected to scRNA-seq were prepared and FACS-enriched using the following procedures. STm infected spleens were harvested and digested in buffer containing HBSS + Ca2+ + Mg2+ + 50 μg/mL DNase (Roche) + 25 μg/mL Liberase TL (Sigma) at 37 °C for 25 min, mixing at 200 rpm. EDTA was added to 5 mM final concentration to stop digestion reaction and cells were washed with RPMI containing 10% FCS. Following RBC lysis, splenocytes were washed twice RPMI containing 10% FCS. Splenocytes were stained with an antibody mixture for surface markers (CD11b Alexa fluor 647, CD11c PECy7, Ly6C PerCP Cy5.5, Ly6G FITC, CD3 APC efluor 780, CD19 APC efluor 780, and NK1.1 APC efluor 780) for 25 minutes on ice, washed twice with RPMI containing 10% FCS, then resuspended in the same buffer with 1:2000 DAPI. Splenocytes were then FACS-enriched on a BD FACSAria cell sorter. A permissive gating strategy was utilized to simultaneously enrich CD11b+CD11c+Ly6C+ macrophages and capture other splenocytes for sequencing. Sorting gates were set tightly for size/scatter, singlet, and living cells but more loosely for CD3/CD19/NK1.1-, CD11b+, Ly6G-, Ly6C+, and CD11c+ cells. The viability of sorted cells were checked using Trypan blue staining and hemocytometer inspection under a light microscope. Samples had viability greater than 90%. Cells were resuspended to a concentration to 500-1200 cells/uL, partitioned, and captured for sequencing on a 10x Chromium Controller. Libraries were prepared by the Stanford Functional Genomics Facility (SFGF) using 10X Genomics 3' GEX v3.1 kit and sequenced on the Illumina HiSeq4000 platform to a depth of ~40,000 - 50,000 reads/cell. 10X Genomics 3' GEX v3.1 kit. Illumina HiSeq 4000 SRX17914804 GSM6644994_r1 SRP402989 PRJNA891222 SRS15430530 GSM6644994 GSM6644994 RNA-Seq TRANSCRIPTOMIC SINGLE CELL cDNA All samples subjected to scRNA-seq were prepared and FACS-enriched using the following procedures. STm infected spleens were harvested and digested in buffer containing HBSS + Ca2+ + Mg2+ + 50 μg/mL DNase (Roche) + 25 μg/mL Liberase TL (Sigma) at 37 °C for 25 min, mixing at 200 rpm. EDTA was added to 5 mM final concentration to stop digestion reaction and cells were washed with RPMI containing 10% FCS. Following RBC lysis, splenocytes were washed twice RPMI containing 10% FCS. Splenocytes were stained with an antibody mixture for surface markers (CD11b Alexa fluor 647, CD11c PECy7, Ly6C PerCP Cy5.5, Ly6G FITC, CD3 APC efluor 780, CD19 APC efluor 780, and NK1.1 APC efluor 780) for 25 minutes on ice, washed twice with RPMI containing 10% FCS, then resuspended in the same buffer with 1:2000 DAPI. Splenocytes were then FACS-enriched on a BD FACSAria cell sorter. A permissive gating strategy was utilized to simultaneously enrich CD11b+CD11c+Ly6C+ macrophages and capture other splenocytes for sequencing. Sorting gates were set tightly for size/scatter, singlet, and living cells but more loosely for CD3/CD19/NK1.1-, CD11b+, Ly6G-, Ly6C+, and CD11c+ cells. The viability of sorted cells were checked using Trypan blue staining and hemocytometer inspection under a light microscope. Samples had viability greater than 90%. Cells were resuspended to a concentration to 500-1200 cells/uL, partitioned, and captured for sequencing on a 10x Chromium Controller. Libraries were prepared by the Stanford Functional Genomics Facility (SFGF) using 10X Genomics 3' GEX v3.1 kit and sequenced on the Illumina HiSeq4000 platform to a depth of ~40,000 - 50,000 reads/cell. 10X Genomics 3' GEX v3.1 kit. Illumina HiSeq 4000