Extended Data Fig. 8: H3 types were consistent between the control brains and the enucleated brains.

(A) UMAP plots of the gene expression of neurons from all eight littermate brains. In each plot, neurons from the indicated brain are colored and neurons from all other brains are shown in gray. (B) UMAP plot of all excitatory neurons from the pilot brain with excitatory neurons from the eight littermate brains projected onto the same UMAP coordinate space. Merged data on top left shows neurons from the pilot brain in gray and all eight littermate brains in red. Top right shows only neurons from the pilot brain in gray. Bottom row shows excitatory neurons from one pair of littermates. (C) Correspondence between H3 types from the eight animals to H3 types in the pilot brain. Dot sizes and colors indicate Jaccard index. Dashed boxes indicate the parent H2 types. (D)(E) Fractions of cells belonging to each cortical H1 type (D) and H2 type (E) in all paired littermate brains. (F) Fractions of cells belonging to each cortical H3 type in all paired littermate brains. In all fraction plots, enucleated animals are represented by the darker color. (G) The AUROC scores of a nearest neighbor classifier that predicts the condition (control or enucleated) of a neuron in the indicated cortical areas (N = 4 biologically independent littermate pairs). Only areas with performance over 0.5 for at least 3 out of 4 littermate pairs were shown. Boxes indicate quartiles and medians, and whiskers indicate range. Dots indicate performance for each held-out litter. (H) The AUROC scores of a nearest neighbor classifier that predicts the condition (control or enucleated) of a neuron of the indicated H3 types in the indicated cortical areas (N = 4 biologically independent littermate pairs). Only combinations with moderate performance ( > 0.6) were shown. Boxes indicate quartiles and medians, and whiskers indicate range. Dots indicate performance for each held-out litter. (I) Same representative slices as shown in Fig. 5e color coded by H2 types. The dashed boxes indicate the area shown in Fig. 5e. Enu, enucleated.