Gene expression profile at single cell level of YS-derived cells and monocyte-derived cells from brain parenchyma and leptomeninges of Ms4a3-Cre: R26-TdTomato: Cx3cr1-gfp mice

Ms4a3-Cre: R26-TdTomato: Cx3cr1-gfp mice allow discrimination between YS-derivd and monocyte-derived macrophages in the brain parenchyma and leptomeninges by color. We used single cell RNAseq for RNA profiling to compare YS-derived micrglia, monocyte-derived microglia, YS-derived leptomeningeal macrophages, and monocyte-derived leptomeningeal macrophages. Brain parenchymal and leptomenigeal cells were isolated seperately from the brain of one-year-old Ms4a3-Cre: R26-TdTomato: Cx3cr1-gfp mice. Cells were sorted by color of reporters with staining to discriminate microglia and macrophages.