Spatiotemporal transcriptomic map of glial cell response in a mouse model of acute brain ischemia

Hello,

Welcome to the repository for the processed data objects for our manuscript titled "Spatiotemporal transcriptomic map of glial cell response in mouse model of acute brain ischemia" published in PNAS (doi: 10.1073/pnas.2404203121). In this study, we used spatial and single-cell transcriptomics to map out processes governing the response to ischemic stroke during the first week after the injury. Focusing on glial cells, we documented their activation, formation of glial scar and changes in cell-cell communication patterns. Here, we list seurat objects of the spatial and single-cell experiments.

List of files:
- seurat_1stSpatial.rds. A seurat object with Visium ST generated data (gene expression matrix, metadata and image). Clean, suitable for starting-anew analysis.
- seurat_2ndSpatial.rds. A complementary seurat object to the seurat_1stSpatial.rds.
- spatial_seurat_1DP_13_nygen.rds. A complete seurat object of the final Visium spatial dataset (modules scores, deconvolution, ligand-receptor pair values...)
- Seurat_sn_MCAO_Zucha2023_QCFiltered.Rds. Seurat object of pre-processed single-nucleus data.
- Seurat_OLs_integrated_annotated.Rds. Seurat object of processed oligodendrocyte data integrating the single-nucleus and single-cell experiment.

Corresponding author contact: [e-mail]