Extended Data Fig. 4: Cell type comparisons across different samples.
a, Comparison of cell compositions in datasets from this study versus previously published datasets33. Heatmaps showing the distribution of the densities of cells sampled at E11.5 in this study (upper left), at E15.5 in this study (lower left), at E11.5 from the published literature (upper right), and at E15.5 from published literature (lower right) mapped in the UMAP space. b, Cell types in panel a are indicated by canonical markers of neural progenitor (Sox2), neuroblast (Neurod1), and GABAergic neuroblast (Otx2+/Gata3+). c, Co-staining of Nkx6-1 and Nkx6-2 using in situ hybridization (RNAscope) in E11.5 vMB. Representative regions are magnified to show NPBL (Nkx6-1+/Nkx6-2+) and NPBM (Nkx6-1+/Nkx6-2−) cells. BL, basal lateral; BM, basal medial; FP, floor plate. Scale bar, left 50 µm, right 10 µm. d, Hierarchical clustering of pairwise correlations between cell types in of E11.5 and E15.5 datasets based on transcriptomic similarities. Neuroblasts captured at both timepoints are highlighted in red. Cell type names are prefixed with ‘E11’ or ‘E15’ to indicate their sources from the E11.5 or E15.5 vMB datasets, respectively. e, Comparison of cell type compositions between En1-Cre-CREST and normally developed (En1-Cre/Ai9) mouse vMB. Two-sided paired t-test was used to examine the correlations between two groups. f, Gene expression correlation of each cell type between En1-Cre-CREST and normally developed (En1-Cre/Ai9) vMB datasets. Each dot represents a gene.
