Related to Fig. 3. a, SDS–PAGE gel stained with SYPRO Ruby reveals enrichment of select proteins during fractionation of total cell lysate (T) from C2C12 myotubes, the enriched fraction (EF) and immunoprecipitation of TDP-43. n = 3 biologically independent experiments, each showing similar results. TDP-43 and IgG control immunoprecipitation experiments are representative of the fractions used for mass spectrometry. b, Venn diagram showing significant overlap between the myo-granule proteome and TDP-43 interactome (previously defined22). The P value was determined using a hypergeometric test. c, Gene Ontology of myo-granules reveals enrichment for processes relating to the localization and translation of RNA. n = 356 proteins, P values were determined using hypergeometric tests with Benjamini–Hochberg false-discovery rate corrections. d, Venn diagram showing significant overlap between myo-granules and neuronal RNA granule proteomes (previously defined23). P value was determined using a hypergeometric test. e, VCP, a top hit in the myo-granule proteome, co-localizes with the cytoplasmic TDP-43 and A11 signals in mouse skeletal muscle at 5 DPI. n = 3 mice. f, The RNA-binding protein HNRNPA2B1 is not associated with the myo-granule proteome and remains localized in myonuclei in injured (5 DPI) and uninjured tibialis anterior muscle. n = 3 mice.