Fig. 4. Joint analysis and validation of molecular cell types in molecular tissue regions.

a,b, From top to bottom: molecular tissue region maps, anatomical tissue maps registered to Allen CCFv3 (ref. ²⁰), marker cell-type distribution maps (cells within the specified region marked in dots, otherwise in ‘×’), marker gene STARmap PLUS measurements, marker gene Allen Mouse Brain ISH expression²³ and smFISH–HCR validation of molecular cortical superficial laminar structure (CTX_A_3-[L2/3]) within the anatomical cortical L2/3 (a) and anterior–posterior (i–v) distribution of molecular RSP tissue regions (b). Cortical areas adjacent to RSP are labelled in the anatomical tissue maps. ACAd, anterior cingulate area, dorsal part; ILA, infralimbic area; MOp, primary motor area; MOs, secondary motor area; PL, prelimbic area; POST, postsubiculum; PRE, presubiculum; SUB, subiculum. c, Epha7 and Atp2b4 expression plotted in the single-cell gene expression UMAP of DGGRCs (top) and the spatial niche gene expression UMAP of molecular DG regions (middle), and spatial niche gene expression UMAP coloured by molecular cell types and molecular DG sublevel tissue regions (bottom). DGd-sg, dentate gyrus granule cell layer, dorsal part; DGv-sg, dentate gyrus granule cell layer, ventral part. d, Molecular tissue region map, molecular cell-type map and anatomical region map of dentate gyrus granule cell layer (DGsg) (top), STARmap PLUS measurements and Allen ISH expression (middle)²³, and smFISH–HCR validation (bottom) of Epha7 and Atp2b4. smFISH–HCR images are representative of two (a,d) and three (b) experiments. The ISH data were obtained from the Allen Mouse Brain Atlas²³.