Extended Data Fig. 4: Subclustering of telencephalon projecting excitatory neurons and telencephalon inhibitory interneurons, and spatial maps of representative subcluster cell types.
From: Spatial atlas of the mouse central nervous system at molecular resolution
a,b, Subcluster spatial maps of telencephalon projecting excitatory neurons (TEGLU, a) and telencephalon inhibitory interneurons (TEINH, b). c-e, Cell-type spatial maps, zoomed-in spatial expression heatmap of cell-type marker genes measured by STARmap PLUS and corresponding In Situ Hybridization (ISH) images of the marker genes from the Allen Mouse Brain ISH database23, for subcluster cell types HA_1 (c), HBGLU_2 and HABGLU_1 (d) and EPEN_1 and EPEN_2 (e). Each dot represents a cell colour-coded by its subcluster cell-type symbol. Scale bars, 250 μm if not indicated. f, Mesh graph of cells shown on the STARmap PLUS molecular cell type map. Each cell is represented by a spot in the colour of its corresponding main cell type. Physically neighboring cells are connected via edges. Zoomed-in views of the top, middle, and bottom squares in the middle are shown on the right. g, First-tier cell-cell adjacency quantified by the normalized number of edges between individual pairs of main cell types (left). For each main cell type, the proportion of edges formed with cells of the same main type over the total number of edges with adjacent cells is shown in the bar plot (right). HA, histaminergic neurons; HBGLU, hindbrain excitatory neurons; HABGLU, habenular excitatory neurons; EPEN, ependymal cells; AC, astrocytes; MGL, microglia; DGGRC, dentate gyrus granule cells; DEGLU, diencephalon excitatory neurons. Also see Methods and Supplementary Table 4. Data are provided in the accompanying Source Data file.
