Fig. 1
scRNA-seq analysis of human PBMCs before and after ex vivo Salmonella infection. a Overview of the scRNA-seq experiment: PBMCs were isolated from a blood sample of a healthy individual and were infected ex vivo with Salmonella (exposed), or remained unexposed (naïve). Overall ~7000 cells were sequenced using 10x genomics Chromium. b Visualization of the scRNA-seq data using forced layout on a two-dimensional space by k-nearest neighbor (KNN)-graph (k = 20; naive cells (gray) and exposed cells (black)). K-means clustering of the cells revealed the seven main cell types: NK cells (red), CD8 T cells (orange), CD4 T cells (yellow), NKT cells (brown), B cells (green), monocytes (purple), and dendritic cells (DC; pink), as inferred using cluster-specific genes and marker genes expression (see Supplementary Data 1 and Supplementary Fig. 3d). Colored contours represent cells which belong to the same cell type in each sample (see also Supplementary Fig. 3a–c for complete KNN-graph with edges and clusters). c Expression levels of representative genes from the infection signature (see methods and Supplementary Fig. 5). Top: general infection genes which are upregulated following Salmonella infection in all exposed cells, and bottom: cell-type specific infection genes. Gene expression is shown using the same layout as in b, with the nodes colored by the indicated gene expression in each cell (see colorbar). d KNN-graph (k = 20) of the scRNA-seq data after removal of the global infection signature eliminated the separation between naïve and exposed cells for all cell types, except for the monocytes, which contain intracellular bacteria. Colors and contours are the same as in b (see also Supplementary Fig. 3e–g)
