*2.2. Isolation of MPs from Skeletal Muscle*

Fascia of the TA muscles was removed. Muscles were dissociated and digested in RPMI medium containing 0.2% of collagenase B (Roche Diagnostics GmbH 11088815001) at 37 ◦C for 1 h and passed through a 70 μm and a 30 μm cell strainer. CD45<sup>+</sup> cells were isolated using magnetic beads (Miltenyi Biotec 130-052-301) and incubated with FcR blocking reagent (Miltenyi Biotec 130-059-901) for 20 min at 4 ◦C in PBS 2% FBS. Cells were then stained with Ly6C-PE (eBioscience 12-5932) and CD64-APC (BD Pharmingen 558539) antibodies for 30 min at 4 ◦C. MPs were analyzed or sorted using a FACS Aria III cell sorter (BD Biosciences) (gating strategy is shown Figure S1). In some experiments, Ly6C<sup>+</sup> and Ly6C<sup>−</sup> MPs were cytospined on starfrost (Knitterglaser, Bielefeld, Germany) slides and immunostained.

### *2.3. Histology and Immunofluorescence Analyses*

The fascia of TA muscles was removed and the muscles were frozen in liquid nitrogen-cooled isopentane (VWR) and placed at −80 ◦C until cut. Then, 8 μm-thick cryosections were stained for hematoxylin-eosin (H&E) and immunofluorescence. H&E (Sigma-Aldrich, Saint-Louis, MO 63103, USA) staining was processed according to standard protocols. For immunofluorescence analysis, sections or cells were fixed for 15 min with 4% paraformaldehyde (except for F4/80 and eMyHC staining). Then, samples were permeabilized with 0.5% Triton X-100 (Sigma-Aldrich) in PBS for 10 min and blocked with 4% BSA (Sigma-Aldrich) in PBS at RT for 1 h. Primary antibodies were incubated O/N at 4 ◦C in PBS. After three washes of 5 min with PBS, samples were incubated with secondary antibodies (1:500, Jackson Laboratory. Fluorochromes used: 488, 594, 546 and 647) and Hoechst (1:500, Sigma-Aldrich) in PBS for 45 min at RT, then washed four times for 5 min with PBS and mounted with Fluorescence Mounting Medium (Dako). For Nfix-F4/80 double immunolabeling, cryosections were labelled with antibodies against F4/80 (1:400, Novus Biologicals NB300-605) overnight at 4 ◦C and Nfix labelling using (1:200, Novus Biologicals NBP2-15039) the antibody was performed for 2 h at 37 ◦C. For EdU-Pax7-laminin immunolabelling, after fixation and permeabilization of muscle sections, we followed the manufacturer's instructions of the Click-iT EdU Imaging Kits Alexa Fluor 594 (Thermo Fisher A10044) to reveal the DNA integrated EdU. Then, for Pax7 immunostaining, antigen retrieval was performed by incubating muscle sections in boiling 10 mM citrate buffer pH6 for 20 min. Muscle sections were then incubated O/N with Pax7 (1:2, Hybridoma, DSHB, Iowa City, IA 52242, USA) and laminin (1:200, Sigma L9393). The other antibodies used were eMyHC (1:2, Hybridome), MyoD (1:50, Santacruz Biotechnology sc-377460), TNFα (1:50, Abcam ab34839), CCL3 (1:500, Abcam ab32609, Cambridge, UK), iNOS (1:25, Novus Biologicals NB300-605, Centennial, CO 80112, USA), CD163 (1:50, Santacruz Biotechnology sc-33560), CD206 (1:50, Bio-Rad MCA2235GA), TGFβ (1:100, Abcam ab64715), Arginase I (1:100, Santacruz Biotechnology, Cambridge, UK).

#### *2.4. Bone Marrow Derived MPs (BMDM) Culture*

Total mouse bone marrow was obtained by flushing femur and tibiae with DMEM. Cells were cultured in DMEM containing 20% Fetal Bovine Serum (FBS) and 30% of L929 cell line-derived conditioned medium (enriched in CSF-1) for 6 to 7 days. MPs were polarized using 50 ng/mL IFNγ (for M1 polarization) (Peprotech #315-05), 10 ng/mL IL10 (for M2c polarization) (Peprotech #210-10), in DMEM (10% FBS) for 3 days. After washing three times, DMEM serum-free medium was added for 24 h, and supernatants were recovered and centrifuged to obtain macrophage-conditioned medium. For some experiments, cells were directly used for various analyses. In some experiments, DMSO or 10 μM of ROCK inhibitor Y27632 (Santacruz sc-3536) was added on MPs.
