SRP126298 PRJNA421379 GSE107791 Mononuclear phagocytes locally specify and adapt their phenotype in the inflamed central nervous system, peak of disease expression data We introduce an in vivo imaging approach that allows us to temporally and spatially resolve the evolution of iNOS and Arginase-positive phagocyte phenotypes in a murine MS model. We show that the polarization of individual phagocytes is established after CNS entry, is dependent on the CNS compartment and can be adapted as inflammatory lesions move from expansion to resolution. Our study thus provides a first real-time analysis of phagocyte specification in the intact CNS. Overall design: Cells were isolated from the CNS of Arginase-YFP X iNOS-Tomato-Cre mice at peak of disease of Experimental Autoimmune Encephalomyelitis. CD11bhigh, CD45high, CD64+ cells were FACS sorted based on their relative expression of the reporter proteins YFP and Tomato, indicative of M2 and M1 macrophage polarization, respectively. Total RNA was extracted from the separated YFP+, Tomato+, YFP+Tomato+ and unpolarized populations. GSE107791 pubmed 30127427 parent_bioproject PRJNA421374