Extended Data Fig. 1: Summary and quality control analyses for nuclei sampling.

a, Bar graph showing the number of cells contributed by each individual per region across the dataset of 611,034 cerebellar nuclei (post-quality control, 6 total individuals, 16 regions). b, Violin plot showing distribution of log₁₀(nUMI) across the regions profiled. Cell numbers: n = 23,364 for region I, n = 29,513 for region II, n = 24,344 for region III, n = 27,680 for region CUL, n = 80,166 for region VI, n = 35,622 for region VII, n = 21,299 for region VIII, n = 47,118 for region IX, n = 20,423 for region X, n = 38,227 for region AN1, n = 72,135 for region AN2, n = 58,142 for region PRM, n = 42,518 for region SIM, n = 14,816 for region COP, n = 20,836 for region F, n = 54,831 for region PF. Box plots centred on median and bounded by interquartile range. c, Violin plot of log₁₀(nUMI) per profile across the 18 cell types identified. The relative median values here are consistent with known differences in cell size; for example, Purkinje cells have the highest median number of UMIs. Cell numbers: n = 16,717 for astrocytes, n = 17,498 for Bergmann glia, n = 591 for choroid, n = 5,333 for fibroblasts, n = 2,271 for mural cells, n = 6,142 for stalk cells, n = 243 for ependymal cells, n = 3,989 for Golgi cells, n = 477,176 for granule cells, n = 280 for macrophages, n = 1,296 for microglia, n = 32,716 for MLI1, n = 10,608 for MLI2, n = 13,363 for oligodendrocytes, n = 2,443 for PLIs, n = 2,121 for polydendrocytes, n = 16,634 for Purkinje cells, n = 1,613 for UBCs. Box plots centred on median and bounded by interquartile range. d, Bar graph of alignment scores (Methods) calculated across replicates for each lobule, after performing LIGER integration (across sex) (Methods) for each regional subset. Subsets sampled from the final set of 611,034 high-quality nuclei profiles. These analyses represent examples of expected replicate alignment when using the described pipeline. Note that lobule COP is excluded as it did not include representation from male and female replicates. e, Visualizations of representative cell type analyses, indicating high alignment across replicate sets (granule is UMAP, all others t-SNE). Replicate sets were designated as in Methods (cluster regional composition test and lobule enrichment). f, Plot indicating probability of sufficiently sampling 10 very rare populations (prevalence 0.15%) as a function of total number of cells profiled in experiment (probability estimated as in Methods). Number of high-quality nuclei profiled here (611,034) and corresponding probability are indicated.