Fig. 1: Single-nucleus transcriptomic sequencing reveals major cell type composition in zona incerta.

a Schematic diagram showing the workflow for microdissection of zona incerta from brain slices in green fluorescent protein knock-in transporter line Gad67-GFP mice, single nucleus isolation and RNA sequencing by 10x Genomics. UMAP plot of the processed dataset containing 15,375 single nuclei collected from two independent cohorts of 10x Genomics experiments (n = 6 mice for each cohort). The cell clusters were annotated according to canonical cell type-specific marker genes. Scale bar, 1 mm. b UMAP plot showing re-clustering the excitatory and inhibitory neurons into ten glutamatergic neuron clusters (Glu_N1 to Glu_N10) and twelve GABAergic neuron clusters (GABA_N1 to GABA_N12). c Heatmap showing the differentially expressed genes (DEGs) among neuron clusters from snRNA-seq dataset. The regional identity (top) of the neuron clusters were annotated by the expression of region specific DEGs (right). TH, Thalamus; STN, Subthalamus nucleus; PVN, Paraventricular nucleus; Hypo, Hypothalamus; ZI, Zona incerta; PIL, Posterior intralaminar thalamus nucleus; TRN, Thalamic reticular nucleus; UnA, Un-Annotated region. d UMAP plot showing the GABAergic neuron clusters (GABA_N4 to GABA_N9) associated with zona incerta. e Dotplot showed the differential expressed genes (DEGs) of GABAergic neuron clusters associated with zona incerta. Source data are provided as a Source Data file.