single-cell RNA-seq profile of adult microglia under acute Csf1r inhibition and early repopulation

Microglia are the resident myeloid cell in the central nervous system (CNS). Like other terminally differentiated myeloid cells, microglia rely on Csf1r signaling for survival and maintenance. Surprisingly, a small subset of microglia in the murine brain can survive without Csf1r signaling, as shown in Csf1r KO mice as well as in mice that have been treated with Csf1r inhibitor PLX5622. The nature of such Csf1r independent microglial population has not been fully characterized. Here we applied single-cell RNA-seq to examine the remaining microglia in C57/BL6J mice that were treated with PLX5622 diet (1200 mg/kg, 14 days), which results >90% microglial removal. Overall design: Mice were placed on PLX diet (1200 mg/kg) for 14 days to deplete microglia (D0). The early stage microglia repopulation (D2) group was switched to control diet (CD) for 2 days. Adult microgia from ctrl (untreated) and the treated mice were isolated by FACS using Cd11b antibody.