StrokeTime: A comprehensive longitudinal scRNA-seq atlas of the ischemic mouse brain

Ischemic stroke triggers profound, dynamic changes in the brain's cellular landscape. To systematically characterize these dynamics, we integrated single-cell RNA-sequencing data from 21 mouse stroke studies (103 samples; 414,359 cells) spanning multiple models and post-stroke intervals. Using a harmonized computational workflow, we constructed StrokeTime, a single-cell mouse brain atlas covering hyperacute, acute, subacute, and chronic stages post-ischemia. The atlas contains 17 major cell classes and 120 fine-grained transcriptional states within myeloid, lymphoid, vascular, epithelial, neuronal, and glial populations. Myeloid cells showed the greatest plasticity, including disease-associated microglia/macrophage programs shared across resident and infiltrating cells, whereas lymphocytes featured activation and regulatory signatures within lineage constraints. Vascular and mural cells shifted from early inflammatory and barrier-disruptive programs to later fibrotic and angiogenic states. StrokeTime delineates both convergent and cell type-specific injury responses, offering a resource for studying post-ischemic brain immunity, tissue remodeling, and benchmarking future single-cell and single-nucleus studies of cerebrovascular disease.