Table 1.

List of key materials, reagents, animal strains, and software.

Reagent or resourceSourceIdentifier
Antibodies
Mouse mAb anti-vinculin (SPM227)AbcamCat. no. ab18058; RRID:AB_444215
Total OXPHOS Rodent WB antibody cocktailAbcamCat. no. ab110413; RRID:AB_2629281
Goat polyAb anti-mouse IgG (H+L)-HRPBio-RadCat. no. 1721011; RRID:AB_11125936
Goat polyAb anti-rabbit IgG (H+L)-HRPBio-RadCat. 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)CSTCat. no. 8814; RRID:AB_11127203
Rabbit mAb anti-PKM2 (D78A4) XPCSTCat. no. 4053; RRID:AB_1904096
Rabbit mAb anti-PPARγ (81B8)CSTCat. no. 2243; RRID:AB_823598
Rabbit polyAb anti-perilipin1 (D418)CSTCat. no. 3470; RRID:AB_2167268
MYH1E antibody (MF 20)Developmental Studies Hybridoma BankCat. no. MF 20; RRID:AB_2147781
PAX7 antibodyDevelopmental Studies Hybridoma BankCat. no. PAX7; RRID:AB_2299243
F(ab′)2-goat anti-mouse IgG (H+L) cross-adsorbed secondary antibody, Alexa Fluor 555InvitrogenCat. no. A-21425; RRID:AB_2535846
Goat anti-mouse IgG (H+L) cross-adsorbed secondary antibody, Alexa Fluor 488InvitrogenCat. no. A-11001; RRID:AB_2534069
Alexa Fluor 488 phalloidinInvitrogenCat. no. A12379
a7-Integrin MicroBeads, mouseMiltenyi BiotecCat. no. 130-104-261
CD31 MicroBeads, mouseMiltenyi BiotecCat. no. 130-097-418
CD45 MicroBeads, mouseMiltenyi BiotecCat. no. 130-052-301
Sca1 MicroBeads, mouseMiltenyi BiotecCat. no. 130-106-641
Goat polyAb anti-PDGFRaR&D SystemsCat. no. AF1062; RRID:AB_2236897
Rabbit polyAb MyoD (M-318)Santa Cruz BiotechnologyCat. no. sc-760; RRID:AB_2148870
Rabbit polyAb GFP antibody (FL)Santa Cruz BiotechnologyCat. no. sc-8334; RRID:AB_641123
Rabbit polyAb anti-LaminSigma-AldrichCat. no. L9393; RRID:AB_477163
Donkey anti-goat IgG(H+L), multi-species SP ads-Alexa Fluor 488SouthernBiotechCat. no. 6425-30
Goat anti-mouse IgG(H+L), human ads-Alexa Fluor 555SouthernBiotechCat. no. 1031-32
Goat anti-rabbit IgG(H+L), mouse/human ads-Alexa Fluor 488SouthernBiotechCat. no. 4050-30
Goat F(ab′)2 anti-mouse Ig, human ads-Alexa Fluor 647SouthernBiotechCat. no. 1012-31
CD140a (PDGFRA) monoclonal antibody (APA5), APCThermo Fisher ScientificCat. no. 17-1401-81; RRID:AB_529482
ITGA7 monoclonal antibody (334908), APCThermo Fisher ScientificCat. no. MA5-23555; RRID:AB_2607368
Pax7 antibody (SPM613) (FITC)Novus BiologicalsCat. no. NBP2-47923F
Chemicals, peptides and recombinant proteins
pLenti CMV GFP Hygro (656-4)AddgeneCat. no. 17446-LVC
Seahorse XF Base MediumAgilent TechnologiesCat. no. 102353-100
Seahorse XF96 Flux PackAgilent TechnologiesCat. no. 102416-100
Bovin Serum Albumin (BSA) Fraction VAppliChemCat. no. A1391
EDTAApplichemCat. no. A5097
Killik, embedding medium for criostate blueBio-OpticaCat. no. 059801
Clarity Western ECL Blotting SubstratesBio-RadCat. no. 10070-5061
Criterion TGX Gradient gel 4–15%Bio-RadCat. no. 5671085
Criterion TGX Gradient gel 4–20%Bio-RadCat. no. 5671095
Mini-PROTEAN TGX gel 4–15%Bio-RadCat. no. 4561086
Mini-PROTEAN TGX gel 4–20%Bio-RadCat. no. 4561096
Trans-Blot Turbo Midi Nitrocellulose MembraneBio-RadCat. no. 1704157
Trans-Blot Turbo Mini Nitrocellulose MembraneBio-RadCat. no. 1704156
DPBS 1× w/Ca2+, Mg2+BioWestCat. no. L0625-500
DPBS 1× w/o Ca2+, Mg2+BioWestCat. no. L0615-500
Cell-Tak Cell and Tissue adhesiveCorningCat. no. 354240
Falcon 100-μm cell strainerCorningCat. no. 352360
Falcon 40-μm cell strainerCorningCat. no. 352340
Falcon 70-μm cell strainerCorningCat. no. 352350
Matrigel basement membrane mixCorningCat. no. 356234
Eukitt mounting mediumElectron Microscopy SciencesCat. no. 15320
Donor horse serumEurocloneCat. no. ECS0090D
Fetal bovin serum (FBS)EurocloneCat. no. ECS0180L
Goat serumEurocloneCat. no. ECS0200D
Non-fat dried milkEurocloneCat. no. EMR180500
Trypsin–EDTA 0.05% w/phenol redEurocloneCat. no. ECM0920D
Dulbecco’s Modified Eagle’s Medium (DMEM) GlutaMAXGIBCOCat. no. 61965-026
Dulbecco’s Modified Eagle’s Medium (DMEM) no glucose, no glutamine, phenol redGIBCOCat. no. A1443001
GlutaMAX SupplementGIBCOCat. no. 35050038
HBSS w/o Ca2+, Mg2+GIBCOCat. no. 14170112
Penicillin–streptomycin (P/S) 10,000 U/mlGIBCOCat. no. 15140122
RPMI 1640GIBCOCat. no. 21875-091
Cell culture microplate, blackGreiner Bio OneCat. no. 655090
Hoecsth 33342InvitrogenCat. no. H3570
MitoTracker Green FMInvitrogenCat. no. M7514
MitoTracker Red CMXRosInvitrogenCat. no. M7512
Novex NuPAGE Sample Reducing Agent (10×)InvitrogenCat. no. NP0009
NuPAGE LDS Sample Buffer (4×)InvitrogenCat. no. NP0007
TRIzolInvitrogenCat. no. 15596026
Sodium fluoride (NaF)MilliporeCat. no. 67414
MS columnsMiltenyi BiotecCat. no. 130-042-201
Pre-separation filters (30 μm)Miltenyi BiotecCat. no. 130-041-407
Histo-Clear SolutionNational diagnosticsCat. no. HS-200
OrtovanadateNew England BiolabsCat. no. P0758S
11 kcal% fat w/sucrose Surwit Diet (LFD)Research diet
58 kcal% fat w/sucrose Surwit Diet (HFD)Research diet
Cyto-GrowResnovaCat. no. TGM-9001-A
Collagenase ARocheCat. no. 11088793001
Dispase IIRocheCat. no. 04942078001
DNase IRocheCat. no. 11284932001
Paraformaldehyde solution (PFA) 4% in PBSSanta CruzCat. no. sc-281692
RBC Lysis buffer 10×Santa Cruz BiotechnologyCat. no. sc-296258
LY2090314SelleckchemCat. no. S7063
Chicken embryo extractSeralabCat. no. CE-650-J
2-deoxyglucose (2-DG)Sigma-AldrichCat. no. D6134
3-Isobutyl-1-methylxanthine (IBMX)Sigma-AldrichCat. no. I5879
AntimycinSigma-AldrichCat. no. A8674
D-GalactoseSigma-AldrichCat. no. G0750
D-GlucoseSigma-AldrichCat. no. G8270
DexamethasoneSigma-AldrichCat. no. D4902
Dimethyl sulfoxide (DMSO) Hybri-MaxSigma-AldrichCat. no. D2650
EGTASigma-AldrichCat. no. E3889
EosinSigma-AldrichCat. no. E4009
FCCPSigma-AldrichCat. no. C2920
Glutamine 200 mMSigma-AldrichCat. no. G7513
HematoxylinSigma-AldrichCat. no. H3136
Hepes 1 MSigma-AldrichCat. no. H0887
Inhibitor phosphatase mixture IISigma-AldrichCat. no. P5726
Inhibitor phosphatase mixture IIISigma-AldrichCat. no. P0044
Insulin solution humanSigma-AldrichCat. no. I9278
Magnesium chlorideSigma-AldrichCat. no. M8266
Oil Red OSigma-AldrichCat. no. O0625
Oleic acidSigma-AldrichCat. no. O1008
OligomycinSigma-AldrichCat. no. O4876
Palmitic acidSigma-AldrichCat. no. P0500
Phenylmethanesulfonyl fluoride (PMSF)Sigma-AldrichCat. no. P7626
Protease inhibitor mixtureSigma-AldrichCat. no. P8340
RotenoneSigma-AldrichCat. no. R8875
Sodium chlorideSigma-AldrichCat. no. S5150
Sodium dodecyl sulfateSigma-AldrichCat. no. L3771
Sodium pyruvate 100 mMSigma-AldrichCat. no. S8636
TERGITOL Solution NP-40Sigma-AldrichCat. no. NP40S
Triton X-100Sigma-AldrichCat. no. T9284
Trizma baseSigma-AldrichCat. no. T1503
Tween 20Sigma-AldrichCat. no. P1379
Critical commercial assays
Click-iT EdU Alexa Fluor 488 Imaging KitInvitrogenCat. no. C10337
CellTiter-Glo luminescent cell viability assayPromegaCat. no. G7571
Custom mouse follistatin ELISARayBiotechCat. no. ELM-FST-1
In situ cell death detection lit, TMR redSigma-AldrichCat. no. 12156792910
Deposited data
Proteome of wt and mdx FAPs from mice fed with LFD and HFDThis paperN/A
Proteome of wt and mdx MuSCs from mice fed with LFD and HFDThis paperN/A
Proteome of wt and mdx FAPsMarinkovic et al (2019)N/A
Experimental models: organisms/strains
Mouse C57BL/6JJaxmiceCat. no. JAX:000664; RRID:IMSR_JAX:000664
Mouse C57BL10ScSn-Dmdmdx/JJaxmiceCat. no. JAX:001801; RRID:IMSR_JAX:001801
Software and algorithms
Illustrator CC 2017Adobe; http://www.adobe.com/products/illustrator.htmlRRID:SCR_010279
CytExpert softwareBeckman CoulterRRID:SCR_017217
Photoshop CC 2017Adobe; https://www.adobe.com/products/photoshop.htmlRRID:SCR_014199
GraphPad PrismGraphPad Software; http://www.graphpad.com/RRID:SCR_002798
Cytoscape 3.7.1http://cytoscape.org; Shannon et al (2003)RRID:SCR_003032
Fijihttp://fiji.sc; Schindelin et al (2012)RRID:SCR_002285
MaxQuant 1.5.3.6http://www.biochem.mpg.de/5111795/maxquant; Cox and Mann (2008)RRID:SCR_014485
Perseus 1.6.2.3http://www.perseus-framework.org; Tyanova et al (2016)RRID:SCR_015753
Seahorse Wave Desktop softwareAgilent; http://www.agilent.com/en-us/products/cell-analysis-(seahorse)/software-download-for-wave-desktopRRID:SCR_014526