Fig. 3: Spatially resolved neuronal atlas of the KF.

a Overlay of Franklin-Paxinos atlas anatomic boundaries on MERFISH image depicting Slc32a1, Chat, Tfap2b, and Calca transcripts. (scale bar: 200 μm). b Voronoi plots depicting KF cells across 3 bregma levels. Glia/non-neuronal cells are in gray. c t-SNE plot of 4554 neurons from the KF. d Donut plot showing the fraction (%) of each neuronal cluster of the KF. e Stacked area chart showing each cluster’s cell frequency (cluster trajectory) across 3 bregma levels. f Dot plot showing the top 3 markers for each cluster. Red boxes indicate the 5 groups. Bold characters indicate KF clusters; other clusters are from neighboring regions. Clusters displayed by the Voronoi, t-SNE, donut plot, and stacked area chart are color-coded according to the legend in (f). g Heatmap depicting the Pearson’s r correlation coefficient of the average expression of 315 genes for all possible combinations of the PB cluster at2_2, KF clusters at1_6, at1_10, and at1_11. h Dot Plot of marker genes specific for PB cluster at2_2, all PB clusters except at2_2, KF clusters at1_6, at1_10, and at1_11. i MERFISH images depicting Calca, Prph, Col11a1, Pou6f2, and Chst9 transcripts in the KF at bregma levels −4.8 and −4.9. Green, red, and orange arrows represent high Calca (Calca+++/Pou6f2, KF cluster at1_10), medium Calca (Calca++/Chst9, KF cluster at1_11), and low Calca (Calca+/Col11a1, KF cluster at1_6) neuronal clusters, respectively. (scale bar: 50 μm). j Donut plot depicting the fraction of Calca+ neuronal clusters (clusters at1_6, at1_10, and at1_11) at bregma level −4.8 and −4.9 of the KF. The cluster percentage in plots refers to the images in (i). All differentially expressed genes in the dot plot have an average log fold-change >0.25 and an adjusted p-value <0.01. Test used: Wilcoxon Rank Sum two-sided Bonferroni-corrected Test. Source Data are provided as Source Data file.