Fig. 2

Cortex-specific snRNA-seq datasets of sham/BCAS mice contaminated by ambient RNAs. Neun, neuron; MG/Immu, microglia and other immune cell; Ast, astrocyte; Ol, oligodendrocyte; OPC, oligodendrocyte precursor cell; FB, fibroblast; EndoOther, endothelial cell and other cell. A T-distributed stochastic neighbor embedding (t-SNE) plot shows single-nuclei in all combined samples (combined, sham and BCAS groups). B Stacked column plots show the cell proportions of in different groups between the sham and BCAS groups. C t-SNE plots show all single-nuclei in the sham and BCAS groups, respectively. D Dot plots show the average expression of specific genes in different groups. E Violin plots show the expression of Syt1 and Grin2b in different groups between the sham and BCAS groups. F, G t-SNE plots show the expression of Syt1 and Grin2b in different groups between the sham and BCAS groups. H Stacked column plots show nuclear and non-clear ambient RNAs in four samples (sham1, sham2, BCAS1 and BCAS2). I Venn plot shows the overlap of nuclear ambient RNA markers between BCAS1 and BCAS2. J Volcano plot shows DEGs of microglia between the sham and BCAS groups. K Bar plots show the pathway enrichment of the overlap ambient RNA markers in I. L Bar plots show the pathway enrichment of up-regulated genes of microglia in Panel J