Fig. 6: NMF reveals a continuum of pyramidal cell types across the RHP.

All spot plots are filled by the spot-level weights for the indicated NMF pattern, with scales corresponding to the maximum spot-level weight of any spot in the SRT dataset. Spot border color indicates the spatial domain. See Supplementary Table 2 for abbreviations. a, Spot plots of example areas from donor Br3942 highlight the laminar organization of nmf40 (snRNA-seq cluster Sub.1) and nmf54 (snRNA-seq cluster Sub.2), as well as the clear distinction from the CA1 (nmf15). b, Dot plot of NMF weights (dot color) after transfer to mouse single-cell methylation sequencing (snmC-seq) with retroviral tracing (n = 2004 HPC and RHP nuclei)⁹⁵. Rows indicate nuclei axonal projection target region. Dot size indicates the number of nuclei with non-zero pattern weights. c, Spot plots of example capture area from donor Br2743 show ENT-specific NMF patterns. d, TSNE plots of pyramidal nuclei from the snRNA-seq dataset colored by the NMF patterns in c. e, Spot plots of example capture area from donor Br2743 show RHP NMF patterns that exhibit spot-level weights distributed across the ENT and subicular complex. f, TSNE plots of pyramidal nuclei from the snRNA-seq dataset colored by the NMF patterns in e. g, Spot plots (for example, donor Br3942) exemplify the anatomical location of nmf17 to the PreS, indicated by the asterisk. h, Violin plots show snRNA-seq log₂-normalized counts (y axis) across HPC and RHP clusters (x axis, reflecting spatially-informed annotations; Supplementary Table 2) for traditional cortical layer markers (SATB2, TLE4 and CUX2), canonical subiculum marker FN1, and new subiculum markers (COL24A1, TOX). i, new DEGs distinguish the superficial, middle and deep subiculum (Sub.1, Sub.2, Sub.3, respectively), and the PreS. Dot size indicates the proportion of nuclei in each cluster (column) with non-zero expression for each gene (row). The dot color indicates average log₂-normalized gene counts. TSNE, t-distributed stochastic neighbor embedding; HPF, hippocampal field; MOB, main olfactory bulb; RSP, retrosplenial cortex; PTLp, posterior parietal cortex; ACA, anterior cingulate cortex; PIR, piriform cortex; STR, striatum; TH, thalamus; AMY, amygdala; HY, hypothalamus; MOp, primary motor cortex; PFC, prefrontal cortex.