Single-cell RNA-seq profiling of brain myeloid cells following ischemic stroke in Ms4a3-specific Htr2b conditional knockout mice

Brain myeloid cells, including infiltrating monocyte-derived macrophages (MDMs) and resident microglia, play essential roles in debris clearance and neuroinflammation resolution following ischemic brain injury. However, the molecular mechanisms governing the functional heterogeneity of these populations remain poorly understood. In this study, we performed single-cell RNA sequencing (scRNA-seq) to characterize the cellular and transcriptional landscape of immune and non-immune cells in the ischemic brain using a myeloid-specific Htr2b conditional knockout model. Htr2b^flox/flox mice and Htr2b^ERCre; Ms4a3-Cre mice were treated with tamoxifen to induce myeloid-lineage-specific recombination, followed by transient middle cerebral artery occlusion (tMCAO). Ipsilateral brain hemispheres were collected at 3 days post-stroke, a critical time point for inflammatory evolution and macrophage infiltration. Single-cell suspensions were generated from ischemic hemispheres, and both immune and non-immune cells were captured . This dataset enables detailed analysis of myeloid cell states, fate-mapped monocyte-derived macrophages, and the impact of Htr2b deletion on post-ischemic neuroinflammation, providing a valuable resource for studying immune regulation in ischemic stroke.