Gene expression profile at sorted microglia and border-associated macrophage with Ms4a3-Cre: R26-TdTomato: Cx3cr1-gfp bone marrow transplantation

After irradiation and bone-marrow transplantation, most of microglia and boarder-associated macrophages in the central nervous system is replaced by engranft cells. Taking advantages of Ms4a3-Cre: R26-TdTomato: Cx3cr1-gfp mice, we discriminated cells from monocyte precursors and hematopoietic stem cells with colors at 32 weeks following irradiation and bone-marrow transplantation. We sorted HSC-derived, monocyte-derived, and endogenouse microglia and leptomeningeal macrophages, and analyzed gene expression level between different cell populations using a bulk RNAseq method. Overall design: Wild type C57BL6/C mice were lethally irradiated, and took Ms4a3-Cre: R26-TdTomato: Cx3cr1-gfp bone marrow transplantation. After 32 weeks of irradiation and bone morrow transplantation, host cells (no color), HSC-derived cells (GFP+), and monocyte-derived cells (GFP+ and TdTomato+) were sorted, and used for bulk RNAseq transcriptome analysis.