Fig. 1
ScRNA-seq analysis of CD64+ mononuclear cells in lungs of naive C57BL/6 WT mice. a Gating strategy used for FACS sorting prior to scRNA-seq experiments. b Experimental pipeline of scRNA-seq experiments. c t-SNE plots depicting the CD64-expressing cells analyzed by scRNA-seq. n indicates the number of cells analyzed after quality control and filtering. d Dot plots showing average expression of the indicated genes and percentages of cells expressing the genes within each cluster. Examples of transcripts significantly differentially regulated (Padj < 10−2) between Cluster 4, 2 or 1 vs. the 2 other clusters are depicted. e Representative contour plot of CD16.2 and CD206 expression within CD64+ IM, whose quantification is shown in (f). f Percentage of each mononuclear phagocyte subset among CD64+ bulk IM, assessed by flow cytometry. Stacked bars represent individual mice, and the % of cells per cluster as identified by scRNA-seq (right bar). g Numbers of each mononuclear phagocyte subset within the steady-state lung. Stacked bars represent individual mice. h Representative contour plot of the indicated markers within CD64+ IM. Numbers indicate the percentage of cells within the respective gates. The plots are representative of one of 6 individual mice analyzed, each of them giving similar results. i Representative histograms of surface MHC-II expression within each mononuclear phagocyte subset, whose quantification is shown in (j). j Quantification of MHC-II MFI. f, g Data show individual mice and are pooled from 3 independent experiments (n = 12). j Data show mean ± s.e.m. and are pooled from 2 independent experiments, each symbol representing individual mice (n = 6). P values were calculated using non-parametric f, g Friedman or j Mann–Whitney tests for pairwise comparisons. *P < 0.05; **P < 10−2; ***P < 10−3; ****P < 10−4. Source data are provided as a Source Data file. AM, alveolar macrophage; Exp, experiment; GEM, gel bead in emulsion; IM, interstitial macrophage (sorted in bulk, as shown in a); MFI, Mean Fluorescence Intensity; Mo, monocyte; RT, reverse transcription
