Extended Data Fig. 4: Cell type gene module expression of mCEL-Seq2 data and validation with mass cytometry.
From: Multiomic spatial landscape of innate immune cells at human central nervous system borders
a. UMAP visualizations color coded for the expression of gene modules enriched in the indicated cell types. The color coding represents module enrichment scores for each cell using the Mann-Whitney U statistic. b. UMAP visualization color coded for the expression of published myeloid (left) and lymphoid cell homing gene modules28. The color coding represents module enrichment scores for each cell using the Mann-Whitney U statistic. c. Spider visualization of 1,999 CD45+ cells analyzed using mass cytometry. The plots are color coded for K-nearest-neighbor density-based X-shift algorithm-based cluster assignment. The indicated cell type assignment is based on the expression of published cell type markers31. The cells labeled as ‘others’ did not show CD45 expression. Numbers indicate the different clusters. d. Spider presentation of the cells from panel f color coded for the compartment the cells were extracted from. The right bottom panel is showing a Marimekko chart of the distribution of compartments per cluster. CP: choroid plexus, LM: Leptomeninges, PV/PC: perivascular space and parenchyma. e. Spider visualization of the cells from panel f color coded for the expression of selected genes. The color scale represents Pearson’s residuals from a regularized negative-binomial regression. f. Single-cell heatmap of the protein expression in each cluster depicted in panel f. The color scale represents Pearson’s residuals from a regularized negative-binomial regression.
