Fig. 4

Identifying cell populations in the cerebellum with ST. a Dimensionality reduction and clustering of 473 spots from cerebellum section from WT mice at P7. n = 2 mice. They are sample I and sample II. Each cluster’s annotated anatomical region of sample I is indicated in c. Spots are colored according to clusters. b Dot plot for the expression of representative marker genes in cerebellar cell types corresponding to the anatomical region. Color represents the mean expression in each cluster, and size indicates the fraction of cells expressing the marker genes. c–d Mapping spots to their spatial positions shows that spots defined by marker genes are localized to the expected layers of cerebellum in sample I. Magnified images of the histological structures are shown in F1–F4. Scale bar: 25 μm. e–f Intersection analysis of all scRNA-seq-identified cell types and spatial transcriptomics-defined regions. Each value of the heatmap is computed as described in f. All pairs of cell types and cerebellum region using the same background genes (16,293 genes). The numbers of cell-type-specific and spatial region-specific genes used in the calculation are shown in f. Red indicates enrichment (significantly high overlap; P value < 0.05) and blue indicates depletion (P value > 0.05). The bar on the top indicates the regions defined in a