Extended Data Fig. 3: Spatial resolution measurements in the mouse hippocampus and Slide-tags snRNA-seq enables characterization of the deep and superficial sublayers in the mouse hippocampal CA1 field.

a, A 10 um nissl-stained section (left) was taken adjacently to the Slide-tags profiled section (right). b, The CA1 nuclei were subsetted in each case and a line was fitted to measure the midpoint of this structure. For Slide-tags, nuclei were selected based on their cell type assignment in Figure S1, with 2 spatial outliers removed. For Nissl, nuclei were computationally segmented. Orthogonal distances from this midpoint were then calculated and points are coloured by this distance. c, Violin plots showing the distribution of distances from the fitted line in b. d, PCA plot showing cells from the CA1 cluster after subsetting, reprojection, and reclustering. Cells are coloured according to their new sub-cluster assignment. e, Cells from a are plotted according to their spatial location (top). The spatial density of nuclei from each population is plotted (bottom). f, Volcano plot showing differentially expressed genes between sps and spd. g, Violin plots showing gene expression differences between each subcluster (top) and the expression of these genes spatially (middle), as well as in situ hybridization data (bottom) from Allen Mouse Brain Atlas²³. Genes were selected based on being discovered as differentially expressed between these two sub-clusters in our dataset and also identified in previous studies as defining these two sub-layers^68,69. Boxplots show: centre line, median; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range; points, outliers. All scale bars denote 500 μm. For Slide-tags CA1, n = 155 nuclei. For imaging data, n = 898 segmented nuclei.