RNA sequencing of microglia and monocyte-derived macrophages from mice with experimental autoimmune encephalomyelitis illustrates a changing phenotype with disease course

The role of microglia and monocyte-derived macrophages in experimental autoimmune encephalomyelitis pathogenesis has been controversial. To gain insight into their respective roles, we developed a method for differentiating between microglia and monocyte-derived macrophages in the CNS by flow cytometry utilizing anti-CD44 antibodies. We used this system to monitor changes in cell number, activation status, and gene expression by RNA sequencing over the course of disease. This in vivo characterization and RNA-Seq dataset improves our understanding of macrophage biology in the brain under inflammatory conditions and may lead to strategies to identify therapies for neuroinflammatory diseases.