Single-cell RNA sequencing of Ms4a3-lineage myeloid cells in mouse brain after transient middle cerebral artery occlusion

Ischemic stroke triggers a robust neuroinflammatory response characterized by the activation and infiltration of myeloid cells, including resident microglia and monocyte-derived macrophages. However, the lineage origin and temporal transcriptional dynamics of these myeloid populations remain incompletely understood.In this study, we performed single-cell RNA sequencing (scRNA-seq) on brain immune cells isolated from Ms4a3creERT2-Ai14 reporter mice, in which circulating monocyte-derived cells are permanently labeled following tamoxifen induction. Transient middle cerebral artery occlusion (tMCAO) or sham surgery was performed, and brain tissues were collected at 1 day and 3 days post-ischemia.Using single-cell analysis platform, we generated high-resolution transcriptomic profiles of brain-resident and infiltrating immune populations. Unsupervised clustering revealed distinct immune and non-immune cell types, including microglia, monocyte-derived macrophages, neutrophils, astrocytes, endothelial cells, and neurons. Comparative analysis across time points identified dynamic transcriptional changes in myeloid cell states following ischemic injury.This dataset provides a comprehensive single-cell resource to investigate the lineage tracing, heterogeneity, and temporal remodeling of brain myeloid cells in ischemic stroke.