Extended Data Fig. 8: Non-negative matrix factorization (NMF) patterns across annotated cell types in mouse neuron electroconvulsive stimulation (ECS) snRNA-seq data.

a, Following label transfer of NMF patterns to mouse snRNA-seq electroconvulsive stimulation (ECS) dataset with retroviral tracing dataset⁸⁵ (n = 15990 nuclei), NMF patterns were removed (red) that mapped to <1000 nuclei (x-axis). b, Dotplot of mouse nuclei-level weights for NMF patterns (x-axis) after filtering, averaged by cluster (y-axis). Dot size indicates the proportion of nuclei in each cluster with non-zero pattern weights and dots are colored by the scaled pattern weight. GC: granule cells, CA2–4: cornu ammonis (CA) regions 2 through 4 (CA2, CA3, CA4), PS/Sub: prosubiculum and subiculum neurons, L5/Po: layer 5 and polymorphic layer. c, Dotplot of nuclei-level weights for NMF patterns (x axis) after further filtering to patterns that were present in >1,050 SRT spots, averaged by cluster and ECS condition (y axis). Dot size indicates the proportion of nuclei in each cluster with non-zero pattern weights and dots are colored by the scaled pattern weight averaged across nuclei in y-axis groups. d, Volcano plot of differential expression results tested on genes with non-zero nmf55 weights. Y-axis of −log₁₀(FDR) values are plotted with a log₁₀ scale. X axis is the log₂ fold change (FC), where negative values indicate greater expression in sham-activated GCs and positive values indicate greater expression in ECS GCs. Points are colored by nmf55 weight. Gene names are shown for genes with nmf55 weight > 0.0025, log₂(FC) > 0.5, and FDR < 0.05. e, Spot plots for example capture area from donor Br3942 are colored by (left) spatial domain and (right) nmf55 weight, demonstrating the ubiquitous presence of nmf55.