Fig. 3

Potential applications of spatial transcriptomics. A Regional differences between fast type IIx (MYH1) and slow type I (MYH7) fiber portions in healthy rotator cuff. B Only a few very specific spots showed fiber degeneration/regeneration in healthy rotator cuff as indicated by neonatal myosin (MYH8) and myosin light chain 4 (MYL4) expression. Conversely, in (C) Muscle at 2 weeks after tenotomy presented with an entire area undergoing a degeneration/regeneration cycle. D Manual selection of the regenerating area (blue) based on MYH8 and MYL4 transcript detection and two randomly selected areas (orange and green) which i) did not present with those transcripts and ii) looked healthy based on H&E. These were then used for (E) Differentially expressed gene analysis of those healthy vs. regenerating muscle fibers. MYH8 and MYL4 were biased differentially expressed because they were used as a selection criterion for these areas, but the other differentially expressed genes may give us further transcriptional insights into regeneration or lack thereof in this pre-clinical setting. ENSOCUG sequences could not be annotated because we did not find corresponding gene IDs