Mouse_IR_VisiumHD

Kidneys from two control and two IR mice were collected at 24 hours, formalin-fixed and paraffin-embedded. After 5mm sections were taken, hematoxylin and eosin (H&E) staining and imaging were performed. RNA quality was checked before samples were processed and sequenced. Spaceranger-3.1.1 was used to generate raw expression data at 2mm resolution from the sequencing data. Cell segmentation was performed using Bin2cell (v.0.3.4). After cell segmentation using Bin2cell, cells with fewer than 10 detected genes and fewer than 100 total counts were filtered out. We utilized UCell and a deep generative modeling using scVI for integration and cell annotation. Differential gene expression analysis identified cluster marker genes, enabling manual annotation.