Fig. 1: Overview of the spatial transcriptomics workflow and quality control results for fracture healing in mouse femurs.

A Schematic representation of the spatial transcriptomics workflow using the CytAssist platform for formalin-fixed paraffin-embedded (FFPE) tissue sections. The process includes H&E staining for initial tissue imaging, followed by probe ligation, permeabilization, barcoding, and library construction, with data analysis performed via the Seurat, CARD, and Monocle software packages. B Bar graph showing the comparison of RNA quality between samples processed using Morse’s solution and EDTA decalcification methods, as indicated by DV200 percentages (a measure of RNA integrity). The data are presented as the means ± standard deviations (SDs). C Violin plots showing the number of detected genes (nFeature_Spatial) and the number of unique molecular identifiers (nCount_Spatial) per spatial spot on Day 0 before fracture and Days 5 and 15 after fracture. D Histological and spatial transcriptomic analysis of mouse femurs on Day 0 before fracture and at Days 5 and 15 after fracture. Upper panel: H&E staining images. Middle panels: spatial plots showing the number of detected genes (nFeature_Spatial) and the number of unique molecular identifiers (nCount_Spatial) per spatial spot on Day 5 post-fracture. The lower panels: spatial plots showing the number of unique molecular identifiers (UMI, nCount_Spatial) per spatial spot on Day 0 before fracture and Days 5 and 15 after fracture. The fracture lines are labeled with dashed lines, the proximal part of the femur is labeled, gp growth plate, Ca callus.