Fig. 2: Summary of single-nucleus RNA-seq and ATAC-seq data from rat amygdala. | Nature Neuroscience

Fig. 2: Summary of single-nucleus RNA-seq and ATAC-seq data from rat amygdala.

From: Single-nucleus genomics in outbred rats with divergent cocaine addiction-like behaviors reveals changes in amygdala GABAergic inhibition

Fig. 2

a, UMAP plot of snRNA-seq data from rat amygdala. Data are combined across 19 samples, with high, low and naive AI labels. Cells are colored by cluster assignments performed with KNN analysis. We assigned cell-type labels to clusters based on the expression of known marker genes. b, UMAP plot of snATAC-seq data from 12 rat amygdala samples. snATAC-seq data were integrated with snRNA-seq data, and cluster labels were transferred to snATAC-seq cells. c, Feature plot showing expression of marker genes used to label main subsets of cells: Gja1 (astrocytes), Ctss (microglia), Cnp (oligodendrocytes), Pdgfra (OPCs), Slc17a7 (excitatory neurons), Gad1/Gad2 (inhibitory neurons) and Cldn5 (endothelial cells). d, Feature plot showing imputed gene expression of cell-type-specific marker genes in snATAC-seq dataset. e, Expression of marker genes in cell clusters corresponding to highly specific subsets of inhibitory neurons. The shading and diameter of each circle indicate the estimated mean expression and the percentage of cells in the cluster in which the marker gene was detected. f, The number of nuclei assigned to each cell-type cluster for the snATAC-seq and snRNA-seq datasets.

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