Spatial transcriptomic profiling of intact and spinal cord–injured mouse spinal cords using CosMx SMI

This study investigates the temporal remodeling of the immune microenvironment after spinal cord injury (SCI) using Nanostring CosMx SMI high-plex spatial molecular imaging. Spinal cord tissues were collected from female C57BL/6J mice (8 weeks old) subjected to T10 hemi-transection SCI and from uninjured controls. Samples were obtained at intact, 14 days, 21 days, and 56 days post-injury (dpi). A total of seven samples were profiled, and all samples were processed with the Nanostring CosMx SMI platform to obtain single-cell and subcellular-resolution spatial transcriptomic data.The dataset includes the raw CosMx SMI output files (expression matrix, transcript coordinates, FOV positions, metadata, and polygon segmentation files). These files enable the reconstruction of cell segmentation, spatial transcript expression, and downstream analyses of microglia activation, immune-cell interactions, and scar-associated cellular niches during SCI progression.This submission provides a resource for studying immune-microenvironment remodeling and microglia-mediated repair processes following spinal cord injury.