Strokemap

Strokemap is a data website accompanying our "Integrating spatial and single-cell transcriptomics to characterize the molecular and cellular architecture of the ischemic mouse brain" paper.

Summary

Although complex inflammatory-like mechanisms are observed around the ischemic core, little is known about the cellular and molecular interactions that characterize the stroke response with emphasis of the dysregulated immune cells and post-demyelinating myelin regeneration within ischemia lesions. Here, using spatial transcriptomic (ST) and single-cell RNA sequencing (scRNA-seq) analyses of brain section and peri-infarct area respectively, we have evaluated the correlation between gene expression differences and distance from the infarct core according to the designed algorithm. Integration the single cell and spatial data, the spatial localizations of specific genes and specific cell clusters were analyzed, and further verified by RNAscop experiments. Finally, we explored the new characteristics of cell interaction after stroke by the analysis of receptor-ligand-based cell communication and focused on the initiation factors of peripheral immune cells to the central chemotaxis. Our study depicts a high-resolution transcriptomic landscape of ischemia brain, serving as an resource for further investigation of stroke and other brain diseases.