A Spatial and Temporal Transcriptomic Atlas of Mouse Intestinal Regeneration

The highly proliferative intestine is prone to damage, making it an ideal model for studying tissue regeneration. We performed spatial transcriptomics to characterize intestinal healing over a six-day period, revealing shifts in the spatial organization of epithelial and stromal cell populations, as well as changes in gene expression patterns and functional roles across tissue compartments. Furthermore, our analysis recapitulates known features of intestinal regeneration, highlighting the robustness of the dataset and its value as a resource for developing novel therapeutic strategies. 23 C57BL/6J mice were included in the study to generate 4 spatial transcriptomics datasets. Mice were treated with 12Gy whole-body irradiation (IR). Control (non-IR) mice, and mice post-IR days 1 through 6 were analyzed using Visium HD spatial transcriptomics. The platform uses near-genome scale probes to capture transcripts within a 2x2um array. A supplementary file (README_spatial_data_guide.pdf) is provided with instructions for accessing the datasets, and includes a description of the treatment post-IR per mouse, per each dataset.