StrokeTime: A comprehensive longitudinal scRNA-seq atlas of the ischemic mouse brain
Abstract
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.
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BibTeX
@article{anrather2026stroketime,
title = {{StrokeTime: A comprehensive longitudinal scRNA-seq atlas of the ischemic mouse brain}},
author = {Josef Anrather and Lidia Garcia-Bonilla},
journal = {iScience},
year = {2026},
month = oct,
doi = {10.1016/j.isci.2026.117938},
url = {https://www.cell.com/iscience/fulltext/S2589-0042(26)03321-3},
note = {CC BY-NC 4.0},
}
RIS
TY - JOUR
TI - StrokeTime: A comprehensive longitudinal scRNA-seq atlas of the ischemic mouse brain
AU - Josef Anrather
AU - Lidia Garcia-Bonilla
PY - 2026
DA - 2026/10/19
JO - iScience
DO - 10.1016/j.isci.2026.117938
UR - https://www.cell.com/iscience/fulltext/S2589-0042(26)03321-3
AB - 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.
SN - 2589-0042
ER -