Single cell RNA sequencing data of brain myeloid cells after experimental stroke

Acute stroke triggers extensive changes to myeloid immune cell populations in the brain that may be targets for limiting brain damage and enhancing repair. Immunomodulatory approaches will be most effective with precise manipulation of discrete myeloid cell phenotypes in time and space. Here, we investigate how stroke alters mononuclear myeloid cell composition and phenotypes at single-cell resolution and key spatial patterns. Our results show that multiple reactive microglial states and monocyte-derived populations contribute to an extensive myeloid cell repertoire in post-stroke brains. We identify important overlaps and distinctions among different cell types/states that involve ontogeny- and spatial-related properties. Notably, brain connectivity with infarcted tissue underpins the pattern of local and remote altered cell accumulation and reactivity. Our discoveries suggest a global but anatomically governed brain myeloid cell response to stroke that comprises diverse phenotypes arising through intrinsic cell ontogeny factors interacting with exposure to spatially organized brain damage and neuro-axonal cues. Overall design: Distal middle cerebral artery occlusion was performed on three C57BL/6 mice using electrocoagulation. Mononuclear phagocytes (CD45+CD3-CD19-Ly6G-) were isolated from ipsilateral and contralateral brain regions using FACs at day three. Samples obtained from each mouse were individually barcoded with hash-tag oligonucletide-conjugated CD45 antibodies and then multiplexed for 10x Chromium single cell RNA sequencing with feature barcoding technology.