Figure 3
Mixed-clustering analysis of Tabula Muris data and isolated GFP-positive cells. (a) ScRNA-seq data of isolated cells (210 cells) was combined with Tabula Muris female data (representing 20,586 cells) and clustered by Seurat using a set of 11 principal components (see Methods). Thirty cell clusters were identified and the overall clustering pattern of the data was illustrated by using uniform manifold approximation and projection (UMAP). (b) In the figure, 191 OkabeGFP-expressing cells (as confirmed by scRNA-seq data; 19 of the isolated cells were GFP-negative) are shown as purple dots on the same UMAP plot as in (a). GFP-positive MMc cells were classified into multiple clusters, indicating that MMc cells represent multiple cell types. Gradation of GFP (0–5) indicates the expression of the OkabeGFP gene. (c) Bar plot representation of GFP-positive cells categorized into UMAP clusters. Majority of cells clustered into either cluster 8 (myeloid cell, 69 cells) or cluster 10 (granulocyte, 51 cells). R (https://cran.r-project.org, ver.3.6.1) with Seura package (ver. 4.0.4, https://satijalab.org/seurat/articles/pbmc3k_tutorial.html), and Microsoft EXCEL (https://www.microsoft.com, EXCEL for Mac ver. 16.62) were used to create the images and the graph.
