Figure 2.

scRNA-seq reveals three concomitant splenic macrophage populations during ELID of S.Tm

(A) Naive mice or mice infected i.v. with WT or ΔSPI-2 S.Tm were harvested 24 hpi and analyzed by flow cytometry using CD11b and F4/80 antibodies.

(B) Single cells from gated populations in (A) were sorted by flow cytometry and analyzed by scRNA-seq. Shown is a forced layout map of single cells (dots) and MCs (large circles), with infection conditions indicated (naive mice [white, n = 631 cells], mice infected with WT [black, n = 643 cells], or a ΔSPI-2 mutant [gray, n = 658 cells]). Cell-type annotations are indicated by outline color of the MC; infection status of the MC by fill color and similarity between MCs are indicated by connecting nodes.

(C) Marker gene annotations presented as the percentage of cells expressing the indicated genes in each MC (shown as the size of the circle) and the relative log₂ fold change of the gene expression in each MC (shown as the color of the circle).

(D) Expression analysis across all MCs of genes used as markers for iNOS Macs (Ly6c2, Nos2) and CD9 Macs (Cd9, Ly6i).

(E) kNN classification of cell types presented as percentage of infected cells classified to cell types in the naive sample. The color bar indicates percentage of cells of each cell type in the infected mice classified to cell types from the naive mice.

See also Figure S2.