Fig. 3: Regulatory networks of Purkinje cell development.
From: Single-cell epigenomics and spatiotemporal transcriptomics reveal human cerebellar development
a Cell lineage relationships of progenitors and Purkinje cells analyzed in the developing human cerebellum in ATAC-seq using the same layout as in Fig. 1b (ATAC). Monocle recovered a branched single-cell trajectory beginning with progenitors and terminating at Purkinje cells. Each dot represents a single cell; the color of each cell represents the cell type (left) and pseudotime (right). Cells from other lineages are colored gray. b Smoothed pseudotime-dependent accessibility curves of VZ progenitor and Purkinje cells generated by negative binomial regression and scaled as a percent of the maximum accessibility of each site. The top 10000 highly expressed sites with pseudotime-dependent accessibility are shown. c Regulon PTF1A, FOXP1, BCL11B, RORA, RORB and FOXP4 patterns shown in the UMAP plots using the same layout as in Fig. 1b (RNA), black, no expression; yellow, relative expression. The graphs on the left show the motif sequences of the regulon (left); gene expression of ATAC (blue) across pseudotime for the above genes (middle), the shadow represents the 95% confidence interval around the fitted curve; 10x Genomics Visium data showing the gene spatial expression in the GW12 cerebellum. d Heatmap showing the expression level and identity of marker genes in Purkinje cell subtypes. e The pseudo-time and subtype-specific gene patterns in GW12 spatial data. f Trajectory analysis of nine subtypes of Purkinje cells in the developing human cerebellum using UMAP and FeuturePlots showing PCP4, RORA and RORB expression. Each dot represents a single cell, and cells are laid out to show similarities. Each cell color represents the cell type. g RNAscope images of RORA and RORB in the GW16 cerebellum. Scale bar, 500 μm (top), 100 μm (bottom). The experiments were repeated three times independently with similar results. h Gene ontology analysis of target genes of Regulon RORB showing the predicted function of target genes of Regulon RORB in Purkinje cells in the developing human cerebellum.
