Fig. 4: Spatiotemporal transcriptomic atlas of mouse organogenesis.

a, Unsupervised spatially constrained clustering (top left) and tSNE visualization (bottom left) of spots from the developing mouse of E17.5, P0 and P4 based on the gene expression. Spatial distribution of the captured UMI counts (top right) was also plotted. Spots are colored by their annotation or UMI count. Scale bar, 3 mm. b, Heatmap showing the expression patterns of tissue-specific marker genes for the P4 mouse. c, Spatial visualization of tissue-specific marker genes across E17.5, P0 and P4 mouse sections. d, Stacked violin plot showing the expression levels of the differentially expressed genes in the lungs of E17.5, P0 and P4 mice. e, Unsupervised spatially constrained clustering and H&E images of the developing brain from E17.5, P0 and P4 mice. Spots are colored by brain region annotations. The red squares indicate the cerebellum region in the brain. Scale bar, 1 mm. f, Dot plot showing the expression levels of differentially expressed genes in the cerebellum of E17.5, P0 and P4 mice. g, RNA velocity streamline (left) and latent time analysis (right) of the cerebellum from E17.5, P0 and P4 brain. Spots are colored by the cerebellum annotations (left) or latent time (right). h, Heatmap displaying scaled expression pattern of top 300 likelihood genes along the latent time of cerebellum. i, Spatial expression of the dynamically changed genes across E17.5, P0 and P4 cerebellums. j, GO functional enrichment based on the top 300 dynamically changed genes across E17.5, P0 and P4 cerebellums. The significant P values of GO terms were calculated by Fisher’s exact test and adjusted by false discovery rate. CbN, cerebellar nuclei; CbWM, white matter of the cerebellum; CbXigr, internal granular layer of the cerebellum cortex; CbXpu, Purkinje cell layer of cerebellum cortex; CbXegr, external granular layer of cerebellum cortex; Cere, cerebellum; Chp, choroid plexus; EGZ, external germinal zone; PCC, Purkinje cell clusters; VZ, ventricular zone; Die, diencephalon; FMN, facial motor nucleus; Hb, hindbrain; Hy, hypothalamus; Mb, midbrain; IC, inferior colliculus; OB, olfactory bulb; OLF, olfactory areas; ORB, orbital area; PAL, pallidum; PG, pontine gray; STRd, striatum dorsal region; STRv, striatum ventral region.