Table 1.
List of key materials, reagents, animal strains, and software.
| Reagent or resource | Source | Identifier |
| Antibodies | ||
| Mouse mAb anti-vinculin (SPM227) | Abcam | Cat. no. ab18058; RRID:AB_444215 |
| Total OXPHOS Rodent WB antibody cocktail | Abcam | Cat. no. ab110413; RRID:AB_2629281 |
| Goat polyAb anti-mouse IgG (H+L)-HRP | Bio-Rad | Cat. no. 1721011; RRID:AB_11125936 |
| Goat polyAb anti-rabbit IgG (H+L)-HRP | Bio-Rad | Cat. no. 1706515; RRID:AB_11125142 |
| Rabbit mAb Ki67 (D3B5) | Cell Signaling Technology (CST) | Cat. no. 9129; RRID:AB_2687446 |
| Rabbit mAb anti-non-phospho active β-catenin (Ser33/37/Thr41) (D13A1) | CST | Cat. no. 8814; RRID:AB_11127203 |
| Rabbit mAb anti-PKM2 (D78A4) XP | CST | Cat. no. 4053; RRID:AB_1904096 |
| Rabbit mAb anti-PPARγ (81B8) | CST | Cat. no. 2243; RRID:AB_823598 |
| Rabbit polyAb anti-perilipin1 (D418) | CST | Cat. no. 3470; RRID:AB_2167268 |
| MYH1E antibody (MF 20) | Developmental Studies Hybridoma Bank | Cat. no. MF 20; RRID:AB_2147781 |
| PAX7 antibody | Developmental Studies Hybridoma Bank | Cat. no. PAX7; RRID:AB_2299243 |
| F(ab′)2-goat anti-mouse IgG (H+L) cross-adsorbed secondary antibody, Alexa Fluor 555 | Invitrogen | Cat. no. A-21425; RRID:AB_2535846 |
| Goat anti-mouse IgG (H+L) cross-adsorbed secondary antibody, Alexa Fluor 488 | Invitrogen | Cat. no. A-11001; RRID:AB_2534069 |
| Alexa Fluor 488 phalloidin | Invitrogen | Cat. no. A12379 |
| a7-Integrin MicroBeads, mouse | Miltenyi Biotec | Cat. no. 130-104-261 |
| CD31 MicroBeads, mouse | Miltenyi Biotec | Cat. no. 130-097-418 |
| CD45 MicroBeads, mouse | Miltenyi Biotec | Cat. no. 130-052-301 |
| Sca1 MicroBeads, mouse | Miltenyi Biotec | Cat. no. 130-106-641 |
| Goat polyAb anti-PDGFRa | R&D Systems | Cat. no. AF1062; RRID:AB_2236897 |
| Rabbit polyAb MyoD (M-318) | Santa Cruz Biotechnology | Cat. no. sc-760; RRID:AB_2148870 |
| Rabbit polyAb GFP antibody (FL) | Santa Cruz Biotechnology | Cat. no. sc-8334; RRID:AB_641123 |
| Rabbit polyAb anti-Lamin | Sigma-Aldrich | Cat. no. L9393; RRID:AB_477163 |
| Donkey anti-goat IgG(H+L), multi-species SP ads-Alexa Fluor 488 | SouthernBiotech | Cat. no. 6425-30 |
| Goat anti-mouse IgG(H+L), human ads-Alexa Fluor 555 | SouthernBiotech | Cat. no. 1031-32 |
| Goat anti-rabbit IgG(H+L), mouse/human ads-Alexa Fluor 488 | SouthernBiotech | Cat. no. 4050-30 |
| Goat F(ab′)2 anti-mouse Ig, human ads-Alexa Fluor 647 | SouthernBiotech | Cat. no. 1012-31 |
| CD140a (PDGFRA) monoclonal antibody (APA5), APC | Thermo Fisher Scientific | Cat. no. 17-1401-81; RRID:AB_529482 |
| ITGA7 monoclonal antibody (334908), APC | Thermo Fisher Scientific | Cat. no. MA5-23555; RRID:AB_2607368 |
| Pax7 antibody (SPM613) (FITC) | Novus Biologicals | Cat. no. NBP2-47923F |
| Chemicals, peptides and recombinant proteins | ||
| pLenti CMV GFP Hygro (656-4) | Addgene | Cat. no. 17446-LVC |
| Seahorse XF Base Medium | Agilent Technologies | Cat. no. 102353-100 |
| Seahorse XF96 Flux Pack | Agilent Technologies | Cat. no. 102416-100 |
| Bovin Serum Albumin (BSA) Fraction V | AppliChem | Cat. no. A1391 |
| EDTA | Applichem | Cat. no. A5097 |
| Killik, embedding medium for criostate blue | Bio-Optica | Cat. no. 059801 |
| Clarity Western ECL Blotting Substrates | Bio-Rad | Cat. no. 10070-5061 |
| Criterion TGX Gradient gel 4–15% | Bio-Rad | Cat. no. 5671085 |
| Criterion TGX Gradient gel 4–20% | Bio-Rad | Cat. no. 5671095 |
| Mini-PROTEAN TGX gel 4–15% | Bio-Rad | Cat. no. 4561086 |
| Mini-PROTEAN TGX gel 4–20% | Bio-Rad | Cat. no. 4561096 |
| Trans-Blot Turbo Midi Nitrocellulose Membrane | Bio-Rad | Cat. no. 1704157 |
| Trans-Blot Turbo Mini Nitrocellulose Membrane | Bio-Rad | Cat. no. 1704156 |
| DPBS 1× w/Ca2+, Mg2+ | BioWest | Cat. no. L0625-500 |
| DPBS 1× w/o Ca2+, Mg2+ | BioWest | Cat. no. L0615-500 |
| Cell-Tak Cell and Tissue adhesive | Corning | Cat. no. 354240 |
| Falcon 100-μm cell strainer | Corning | Cat. no. 352360 |
| Falcon 40-μm cell strainer | Corning | Cat. no. 352340 |
| Falcon 70-μm cell strainer | Corning | Cat. no. 352350 |
| Matrigel basement membrane mix | Corning | Cat. no. 356234 |
| Eukitt mounting medium | Electron Microscopy Sciences | Cat. no. 15320 |
| Donor horse serum | Euroclone | Cat. no. ECS0090D |
| Fetal bovin serum (FBS) | Euroclone | Cat. no. ECS0180L |
| Goat serum | Euroclone | Cat. no. ECS0200D |
| Non-fat dried milk | Euroclone | Cat. no. EMR180500 |
| Trypsin–EDTA 0.05% w/phenol red | Euroclone | Cat. no. ECM0920D |
| Dulbecco’s Modified Eagle’s Medium (DMEM) GlutaMAX | GIBCO | Cat. no. 61965-026 |
| Dulbecco’s Modified Eagle’s Medium (DMEM) no glucose, no glutamine, phenol red | GIBCO | Cat. no. A1443001 |
| GlutaMAX Supplement | GIBCO | Cat. no. 35050038 |
| HBSS w/o Ca2+, Mg2+ | GIBCO | Cat. no. 14170112 |
| Penicillin–streptomycin (P/S) 10,000 U/ml | GIBCO | Cat. no. 15140122 |
| RPMI 1640 | GIBCO | Cat. no. 21875-091 |
| Cell culture microplate, black | Greiner Bio One | Cat. no. 655090 |
| Hoecsth 33342 | Invitrogen | Cat. no. H3570 |
| MitoTracker Green FM | Invitrogen | Cat. no. M7514 |
| MitoTracker Red CMXRos | Invitrogen | Cat. no. M7512 |
| Novex NuPAGE Sample Reducing Agent (10×) | Invitrogen | Cat. no. NP0009 |
| NuPAGE LDS Sample Buffer (4×) | Invitrogen | Cat. no. NP0007 |
| TRIzol | Invitrogen | Cat. no. 15596026 |
| Sodium fluoride (NaF) | Millipore | Cat. no. 67414 |
| MS columns | Miltenyi Biotec | Cat. no. 130-042-201 |
| Pre-separation filters (30 μm) | Miltenyi Biotec | Cat. no. 130-041-407 |
| Histo-Clear Solution | National diagnostics | Cat. no. HS-200 |
| Ortovanadate | New England Biolabs | Cat. no. P0758S |
| 11 kcal% fat w/sucrose Surwit Diet (LFD) | Research diet | |
| 58 kcal% fat w/sucrose Surwit Diet (HFD) | Research diet | |
| Cyto-Grow | Resnova | Cat. no. TGM-9001-A |
| Collagenase A | Roche | Cat. no. 11088793001 |
| Dispase II | Roche | Cat. no. 04942078001 |
| DNase I | Roche | Cat. no. 11284932001 |
| Paraformaldehyde solution (PFA) 4% in PBS | Santa Cruz | Cat. no. sc-281692 |
| RBC Lysis buffer 10× | Santa Cruz Biotechnology | Cat. no. sc-296258 |
| LY2090314 | Selleckchem | Cat. no. S7063 |
| Chicken embryo extract | Seralab | Cat. no. CE-650-J |
| 2-deoxyglucose (2-DG) | Sigma-Aldrich | Cat. no. D6134 |
| 3-Isobutyl-1-methylxanthine (IBMX) | Sigma-Aldrich | Cat. no. I5879 |
| Antimycin | Sigma-Aldrich | Cat. no. A8674 |
| D-Galactose | Sigma-Aldrich | Cat. no. G0750 |
| D-Glucose | Sigma-Aldrich | Cat. no. G8270 |
| Dexamethasone | Sigma-Aldrich | Cat. no. D4902 |
| Dimethyl sulfoxide (DMSO) Hybri-Max | Sigma-Aldrich | Cat. no. D2650 |
| EGTA | Sigma-Aldrich | Cat. no. E3889 |
| Eosin | Sigma-Aldrich | Cat. no. E4009 |
| FCCP | Sigma-Aldrich | Cat. no. C2920 |
| Glutamine 200 mM | Sigma-Aldrich | Cat. no. G7513 |
| Hematoxylin | Sigma-Aldrich | Cat. no. H3136 |
| Hepes 1 M | Sigma-Aldrich | Cat. no. H0887 |
| Inhibitor phosphatase mixture II | Sigma-Aldrich | Cat. no. P5726 |
| Inhibitor phosphatase mixture III | Sigma-Aldrich | Cat. no. P0044 |
| Insulin solution human | Sigma-Aldrich | Cat. no. I9278 |
| Magnesium chloride | Sigma-Aldrich | Cat. no. M8266 |
| Oil Red O | Sigma-Aldrich | Cat. no. O0625 |
| Oleic acid | Sigma-Aldrich | Cat. no. O1008 |
| Oligomycin | Sigma-Aldrich | Cat. no. O4876 |
| Palmitic acid | Sigma-Aldrich | Cat. no. P0500 |
| Phenylmethanesulfonyl fluoride (PMSF) | Sigma-Aldrich | Cat. no. P7626 |
| Protease inhibitor mixture | Sigma-Aldrich | Cat. no. P8340 |
| Rotenone | Sigma-Aldrich | Cat. no. R8875 |
| Sodium chloride | Sigma-Aldrich | Cat. no. S5150 |
| Sodium dodecyl sulfate | Sigma-Aldrich | Cat. no. L3771 |
| Sodium pyruvate 100 mM | Sigma-Aldrich | Cat. no. S8636 |
| TERGITOL Solution NP-40 | Sigma-Aldrich | Cat. no. NP40S |
| Triton X-100 | Sigma-Aldrich | Cat. no. T9284 |
| Trizma base | Sigma-Aldrich | Cat. no. T1503 |
| Tween 20 | Sigma-Aldrich | Cat. no. P1379 |
| Critical commercial assays | ||
| Click-iT EdU Alexa Fluor 488 Imaging Kit | Invitrogen | Cat. no. C10337 |
| CellTiter-Glo luminescent cell viability assay | Promega | Cat. no. G7571 |
| Custom mouse follistatin ELISA | RayBiotech | Cat. no. ELM-FST-1 |
| In situ cell death detection lit, TMR red | Sigma-Aldrich | Cat. no. 12156792910 |
| Deposited data | ||
| Proteome of wt and mdx FAPs from mice fed with LFD and HFD | This paper | N/A |
| Proteome of wt and mdx MuSCs from mice fed with LFD and HFD | This paper | N/A |
| Proteome of wt and mdx FAPs | Marinkovic et al (2019) | N/A |
| Experimental models: organisms/strains | ||
| Mouse C57BL/6J | Jaxmice | Cat. no. JAX:000664; RRID:IMSR_JAX:000664 |
| Mouse C57BL10ScSn-Dmdmdx/J | Jaxmice | Cat. no. JAX:001801; RRID:IMSR_JAX:001801 |
| Software and algorithms | ||
| Illustrator CC 2017 | Adobe; http://www.adobe.com/products/illustrator.html | RRID:SCR_010279 |
| CytExpert software | Beckman Coulter | RRID:SCR_017217 |
| Photoshop CC 2017 | Adobe; https://www.adobe.com/products/photoshop.html | RRID:SCR_014199 |
| GraphPad Prism | GraphPad Software; http://www.graphpad.com/ | RRID:SCR_002798 |
| Cytoscape 3.7.1 | http://cytoscape.org; Shannon et al (2003) | RRID:SCR_003032 |
| Fiji | http://fiji.sc; Schindelin et al (2012) | RRID:SCR_002285 |
| MaxQuant 1.5.3.6 | http://www.biochem.mpg.de/5111795/maxquant; Cox and Mann (2008) | RRID:SCR_014485 |
| Perseus 1.6.2.3 | http://www.perseus-framework.org; Tyanova et al (2016) | RRID:SCR_015753 |
| Seahorse Wave Desktop software | Agilent; http://www.agilent.com/en-us/products/cell-analysis-(seahorse)/software-download-for-wave-desktop | RRID:SCR_014526 |