The study identifies transmembrane protein 119 (Tmem119) as a highly expressed and microglia-specific marker in both mouse and human central nervous system (CNS). The authors developed monoclonal antibodies against the intracellular and extracellular domains of Tmem119, which enable immunostaining of microglia in histological sections and isolation of pure, nonactivated microglia by FACS. Using these antibodies, the authors performed RNA sequencing (RNAseq) on highly pure mouse microglia during development and after an immune challenge, providing the first such profiles. The results show that mouse microglia mature by the second postnatal week and suggest novel microglial functions. The tools and resources developed in this study will facilitate future research on microglial function in health and disease.The study identifies transmembrane protein 119 (Tmem119) as a highly expressed and microglia-specific marker in both mouse and human central nervous system (CNS). The authors developed monoclonal antibodies against the intracellular and extracellular domains of Tmem119, which enable immunostaining of microglia in histological sections and isolation of pure, nonactivated microglia by FACS. Using these antibodies, the authors performed RNA sequencing (RNAseq) on highly pure mouse microglia during development and after an immune challenge, providing the first such profiles. The results show that mouse microglia mature by the second postnatal week and suggest novel microglial functions. The tools and resources developed in this study will facilitate future research on microglial function in health and disease.