Fig. 3: Clustering and marker gene analysis of GABAergic neurons.

A UMAP plot of 18 clusters of putative GABAergic neurons in the CeA, colored by cluster. 15 clusters were identified as amygdalar GABAergic cells. Two clusters were not readily identifiable as GABAergic cells and contained high levels of glial genes (Unknown 1, Unknown 2). One cluster was identified as cholinergic interneurons. B Heatmap plot of the expression level for the top 10 marker genes in each cluster of putative GABAergic neurons. Marker gene expression in each cluster is distinct, indicating that the clustering analysis effectively identified distinct cell types of interneurons in the CeA (see Table S2 data for the list of genes plotted). C Marker gene analysis. Most of the clusters distinctly expressed genes that are associated with known GABAergic subtypes of CeA cells (navy blue dots). Magenta dots indicate cell types that were not identified based on known CeA gene expression, but were identified based on genes that were revealed de novo by clustering and marker gene analysis. The size of each dot indicates the percentage of cells that contained at least one read of each marker gene; the color depth represents the log-scaled average expression, where the darkest color is the highest expressing cluster. D UMAP plots colored by the expression of known CeA GABAergic neuron marker genes (Calcrl, Prkcd, Drd2, Pdyn).