ED Fig. 1. Experimental overview of the assembled datasets.

A, All data sets were taken from mice after volumetric muscle loss treatment. After surgical excision of a large portion of the quadriceps, the wound site was filled with a biomaterial or saline control and stapled shut. Mice were then harvested 1 or 6 weeks after surgery. Young (6 week) or aged (104 week) old animals were used. Representative histological images of PCL and ECM treated muscles 6 week after injury are shown stained by Masson’s Trichrome. Muscle fibers are stained red and connective tissue is stained blue. The posterior (P) is labeled and the location of original defects circled. B, At time of harvest, cells were isolated one of three ways after digestions. For macrophages, cells were sorted as CD45+F4/80HiLy6c+, for fibroblasts cells were sorted as CD45-CD19-CD29+, and for the all-cell dataset CD45+ cells were enriched to ~50% using MACS beads. C, Data sets were integrated for analysis using Harmony. A complete summary of available data sets is given in Supplementary Table 2. D, Enrichment of fibroblasts and macrophages due to inclusion of sorted fibroblast and macrophage data sets. The sorted fibroblasts (left) and macrophages (right) are shown in comparison to the CD45+ enriched sample (middle). E, Cells by condition. Cells are colored by condition plotted on UMAP dimensions. Cells were plotted in order of ECM, PCL, Saline, and Naïve.