Fig. 3

FIPRESCI enables analysis of E10.5 whole mouse embryo. a Label transfer from a scRNA-seq profiled mouse organogenesis atlas to FIPRESCI data. UMAP embedding colored by transferred cell types. b A high correlation between cell type proportion was detected by Fipresci-Seq and the public atlas. c Differential usages of TSS for gene Specc1. IGV (Integrative Genomics Viewer) Track plot shows cluster 7 and cluster 9 use the same TSSs of gene Specc1, while other clusters used different ones. The tracks are group scaled and the range is shown on the right margin. d De novo constructing inhibitory neuron trajectory. e Trajectory graph-correlated genes. UMAP plots colored by gene expression (left), those genes are highly correlated with the brain trajectory graph. Heatmap (right) showing genes dynamic changes along with pseudo time within inhibitory neuron trajectory. f Top, heatmap showing TSS usage proportion over 3 stages of inhibitory neuron trajectory. Row names of the heatmap are stages (early, medium, and later pseudo time), the column represents TSSs, and colors indicate TSS reads proportion of all TSS reads in the corresponding gene within one stage (early, medium, or later cells). Track plot (bottom) showing gene Rbfox2 TSS usage changes along the inhibitory trajectory