Fig. 2 |. Spatial transcriptional analysis of the developing human cerebellum.

a, Principal component analysis indicates that the largest source of variation among RNA-seq samples was spatial location, accounting for 57% of the variance, and verifying LCM successfully captured these regions. b-d, Volcano plots illustrating differential expression of genes for each spatial region versus bulk cerebellum. Colored dots represent genes with significant expression [FDR<0.05; Log2(FC)>1.5]. Selected canonical genes with significant expression are labeled. Significance was determined by the Wald test and adjusted using FDR. Statistics are presented in Supplementary Table 3. e, Heatmap of the top 10 genes with significant expression per spatial region (RL, EGL, PCL) are shown for each sample. Samples are ordered by region [RL (purple), EGL (green), PCL (turquoise), bulk (salmon)], then by ascending age (9 to 19 PCW). High expression is in red and low expression is in blue. f,g, Heatmaps of genes and pathways expressed in RL (f) and EGL (g) identified by gene ontology analysis. High expression is in red and low expression is in blue; Z-score legend as in e. Colored boxes indicate genes represented in enriched pathways: Hippo signaling (green), signaling pathways regulating pluripotency of stem cells (magenta), and Tgfβ signaling (blue) in f; MAPK signaling (orange), Rap1 (green), Ras (pink) in g. Statistics are presented in Supplementary Table 4. h, Heatmap of genes expressed in each WGCNA module enriched in a. High expression is in red and low expression is in blue; Z-score legend as in e. Colored boxes represent the cerebellar region interpretation for each WGCNA module, as in Supplementary Table 5.