library_construction_protocol: Anesthetized mice were injected intravenously (i.v.) with anti-CD45 to label and exclude blood-borne immune cells, transcardially perfused, and then each tissue extracted and enzymatically dissociated into a single cell suspension in the presence of transcriptional/translational inhibitors to prevent ex vivo changes in gene expression. Single cell suspensions were labeled with antibodies and purified by fluorescence activated cell sorting. For the dura and bone marrow, CD45 i.v. negative immune cells and non-immune cells were sorted at a ratio of approximately 1:1 immune to non-immune cells. For the brain-leptomeninges, CD45 i.v. negative microglia and non-microglial immune cells were sorted at a ratio of approximately 1:4 microglia to non-microglial immune cells. Sorted cells were captured and processed on the 10x Genomics 5' v1.1 platform. Libraries were constructed as per manufacturers protocol for 10x Genomics 5' v1.1.