Extended Data Fig. 8: Joint analysis and validation of molecular cell clusters in molecular tissue regions.
From: Spatial atlas of the mouse central nervous system at molecular resolution
a, Heatmap showing the distribution of telencephalon inhibitory interneuron (TEINH) cell types across molecular telencephalon (TE) tissue regions. b, Correspondence of interneuron subtypes within the molecular striatal tissue regions to interneuron (IN) cell types annotated in the scRNA-seq dataset of adult mouse ventral striatum (nucleus accumbens)10. c-e, Cell type maps overlaid on molecular tissue regions, spatial expression heatmap of cell-type marker genes measured by STARmap PLUS, corresponding ISH images of the marker genes from the Allen Mouse Brain ISH database23 and independent smFISH-HCR validation of the distribution of the positive cells for TEINH_25 in the striatum (c), TEINH_10 and TEINH_22 in the olfactory bulb outer plexiform layer (OBopl, d) and TEINH_11 in cerebral cortical layer 2/3 (e). smFISH-HCR images are representative of two experiments (c-e). The ISH data were obtained from Allen Mouse Brain Atlas. f, UMAP embedding of OPC and OLG (left) and DC embedding69 coloured by molecular cell types (middle) and DC1 value (right). g,i, Spatial distribution of DC1 values of the OPC-OLG lineage and OPC-OLG molecular cell cluster identities in the cerebral cortical layers (g) and midbrain-pons dorsal-ventral axis (i). h, DC1 values of the OPC-OLG lineage across the molecular cortical layers. Data shown as mean ± s.t.d. j, DC embedding (top) and spatial maps (bottom) coloured by marker gene expression levels indicating oligodendrocyte differentiation and maturation states. Only OPC and OLG cells are plotted (g,i,j). k, STARmap PLUS expression heatmap of Cxcl14, Rxfp1, and Neurod6 in representative coronal slices along the anterior-posterior axis. Data are provided in the accompanying Source Data file.
