RNA sequencing data of dural macrophages isolated from brains of Cx3cr1-GFP mice at different ages.

While macrophages in the meningeal compartments of the central nervous system (CNS) has been comprehensively characterized under steady state, studying their contribution to physiological and pathological processes has been severely hampered by the lack of specific targeting tools in vivo. Recent findings have shown that the dural sinus and its adjacent lymphatic vessels act as a neuroimmune interface. Notably, the cellular and functional heterogeneity of extrasinusoidal dural macrophages outside this immune hub is currently unclear. Therefore, we comprehensively characterized these cells using single-cell transcriptomics, fate mapping, confocal imaging, clonal analysis and transgenic mouse lines. Extrasinusoidal dural macrophages were clearly distinct from leptomeningeal and CNS parenchymal macrophages in terms of their origin, expansion kinetics and transcriptional profiles. Lastly, functional studies demonstrated that during autoimmune neuroinflammation, extrasinusoidal dural macrophages perform efferocytosis of granulocytes. Our results highlight a previously unappreciated myeloid cell diversity and provide insights into the brain's innate immune system. Overall design: Dura macrophages were isolated from 3-5 individual mice per age and used for the generation of bulk transcriptomics data. RNA expression levels between the different and ages were compared. Microglia, meningeal macrophages (mMF) and perivascular macrophages (pvMF) were isolated from the same animals and data has been deposited before (GSE194432).