Fig. 1

A single cell atlas of brain cells from the cortex and hippocampus from mice infected with RML scrapie or mock infection. A Schematic representation of workflow for single-cell sequencing of cortical and hippocampal cells during prion disease. B UMAP projection of all 147,536 cells sequenced from the cortex and hippocampus of RML and mock infected mice. Cells were clustered using graph based clustering and cell types were assigned to each cluster using SCType (Additional file 4) followed by manual inspection of marker genes (Additional file 2) identified for each cluster. The total number of cells isolated from RML and mock infected mice that were assigned to each cluster is provided in Additional file 3. C Normalized expression level of canonical marker genes for major brain cell types were plotted on the UMAP projection to verify identities of each cell type. These include P2ry12 (microglia), Gfap (astrocytes), Rbfox3 (mature neurons), Cd163 (perivascular macrophages), Pdgfra (oligodendrocyte progenitor cells), Spag17 (ependymal cells), Dcx (immature neurons), Mki67 (neural progenitor cells) and Cldn5 (vascular cells). micro—microglia; endo—vascular endothelial cells; astro—astrocytes; peri—pericytes; g.neu—mature glutamergic neurons; im.neu—immature neurons; opc—oligodendrocyte progenitor cells; smc—vascular smooth muscle cells; pvm—perivascular macrophages; epen—ependymal cells; lymph—lymphocytes; vlmc—vascular leptomeningeal cells