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. 2022 Jun 24;11:e77490. doi: 10.7554/eLife.77490

Figure 1. Single-cell sequencing characterization of leukocytes in the mouse tongue.

(a) UMAP representation of 6773 sequenced tongue leukocytes from adult, female Bl6 mice (pool of n=8 mice). Data from a biologically and technically independent experiment is shown in Figure 1—figure supplement 1a+b. Cluster annotation was performed with SingleR (Figure 1—figure supplement 1c). See Figure 1—source data 1+2 for complete gene lists and marker genes for all clusters. Abbreviations: ILCs (innate lymphoid cells); NK cells (natural killer cells); int. MF (intermediate macrophages); tFOLR2-MFs (tongue Folr2 +macrophages); cDCs (classical dendritic cells); tCX3CR1-MF (tongue Cx3cr1+macrophages); Fn1+ cells (Fn1-expressing mononuclear phagocytes); LC (Langerhans cells); preDC (pre-dendritic cells). (b) Separate UMAP representation of cells within cluster 4, 9, and 14. Additional abbreviations: pDC (plasmacytoid dendritic cells); nILC (natural ILC); iILC (induced ILC). (c) Gene Set Variation Analysis (GSVA) analysis was used for the discrimination of macrophages and dendritic cells. One signature gene list for macrophages (derived from Gautier et al., 2012) and one for cDC (derived from Schlitzer et al., 2015) were used to evaluate the enrichment score of each list in the 20 identified clusters. See also Figure 1—figure supplement 1d for cDC1 and cDC2 gene signatures and Figure 1—source data 3 for full gene lists. Cells with the highest similarity to each respective signature are labeled red. (d) Heatmap of top marker genes for the main mononuclear phagocyte clusters. See Figure 1—figure supplement 1b for a heatmap of marker genes for all clusters. (e) Expression pattern of example genes laid over the UMAP from a for dimension reduction. (f) Differentially expressed genes in tCX3CR1-MF vs. tFOLR2-MF (left) and tCX3CR1-MF vs. tongue Langerhans cells (right). Indicated genes show an increased expression of >1.5 with an adjusted p-value <0.05. (g) Gene ontology analysis of the differentially expressed genes of the main mononuclear phagocyte clusters. Only GO annotations involved in biological processes are shown and redundant pathways were excluded from this representation. See Figure 1—source data 4 for full list of GO terms per cluster.

Figure 1—source data 1. Marker genes for the 19 identified clusters.
Listed are the marker genes for each cluster of the scRNA-seq experiments 1–4 together with the respective test statistics. Each cluster can be found in separated tabs. As test method we used MAST, the log2fc threshold was set to 0.25 and a Bonferroni mutiple testing correction was applied. We only considered genes that were expressed in at least 20% of the cells in at least one of the groups. Note that cluster 11 is not represented due to low cell numbers and cluster 16 could only be detected in experiment 3 (LPS). These data sets belong to Figures 1, 4 and 6.
elife-77490-fig1-data1.xlsx (679.6KB, xlsx)
Figure 1—source data 2. Average expression matrix of scRNA-seq data.
The file contains the average expression value for each cluster based on the normalized counts of the cells in the respective sample. Additionally, a column for each cluster indicates, whether a gene is a conserved marker for this cluster (see Figure 1—source data 1).
Figure 1—source data 3. Core gene signatures.
Listed are the core gene signatures of cDC (tab 1), macrophages (tab 2), cDC1 (tab 3), and cDC2 (tab 4). The gene lists were derived from Gautier et al., 2012; Schlitzer et al., 2015.
Figure 1—source data 4. GO enrichment of myeloid clusters.
Represented are the full GO lists for the myeloid clusters 0, 1, 3, 5, 6, 7, and 10.
elife-77490-fig1-data4.xlsx (300.1KB, xlsx)

Figure 1.

Figure 1—figure supplement 1. Characterization of adult tongue leukocytes.

Figure 1—figure supplement 1.

(a) Biological and technical replication (experiment 2, right graph) of the scRNA-seq experiment depicted in Figure 1 (experiment 1, left graph). For experiment 2, CD45+ tongue leukocytes were isolated from female mouse tongues (pool of n=10) and 8151 cells were sequenced using the Chromium Single Cell 3’ Reagent Kits v2. Experiment 2 data was integrated with the existing adult data of experiment 1 to allow population comparison. (b) Heatmap representing the top 10 marker genes for all detected clusters. Data is derived from experiment 1 shown in Figure 1. (c) SingleR results for the annotation of cell clusters. Note that cluster 6 cells showed similarities to CD11b+ DCs from Immgen (http://immgen.org/). (d) GSVA analysis of the cDC1 and cDC2 signature genes as defined in Schlitzer et al., 2015. Red indicates cells with higher enrichment scores for the signature genes compared to blue. (e) Heatmap of genes involved in axon guidance. Shown are the normalized read counts in tFOLR2-MF (cluster 0) and tCX3CR1-MF (cluster 5).