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. 2022 Sep 29;11:e63296. doi: 10.7554/eLife.63296

Figure 4. Comparison of transcriptional profiles of AMs, IMs, and DCs by scRNA-seq.

(A) UMAP plot depicting automated graph-based clustering of CD11c-enriched cells aggregated from lungs of four naïve wild-type mice. The abundance of Siglecf and Ptprc (CD45) transcripts are shown in middle and right plots. (B) Transcriptional profile of IMs identified as the cluster of cells most highly expressing Mafb and Cx3cr1. Genes of interest that were previously reported to be expressed in IMs are shown in the bottom panels. (C) Transcriptional profile of DCs identified as the clusters of cells most highly expressing Flt3 and Zbtb46. Specific transcripts for each of the sub-clusters are shown in the bottom panels. (D) Heat map showing the top 25 most upregulated, differentially-expressed genes from each of the AMs, IMs, and DCs populations gated according to Figure 4—figure supplement 1.

Figure 4.

Figure 4—figure supplement 1. Gating for AMs, IMs, and DCs for scRNA-seq.

Figure 4—figure supplement 1.

Based on the expression levels of the cell type specific genes: Siglecf, Mafb, Cx3cr1, Flt3 and Zbtb46, clusters containing AMs (green), IMs (blue) and DCs (orange) were gated using polygonal selection in Loupe Browser. These gated populations were analyzed for differentially expressed genes to define the upregulated genes in Figure 4D.