KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit monoclonal anti alpha-Tubulin | Cell Signaling Technology | Cat# 2125 |
| Rabbit polyclonal anti Tfam | Abcam | Cat# ab131607, RRID:AB_11154693 |
| Rabbit polyclonal anti HIF-1 alpha | Novus Biologicals | Novus Cat# NB100–479SS, RRID:AB_790147 |
| Rabbit polyclonal anti BNIP3 | Cell Signaling Technology | Cat# 3769, RRID:AB_2259284 |
| Rabbit polyclonal anti LDHA | Cell Signaling Technology | Cat# 2012, RRID:AB_2137173 |
| Rabbit polyclonal anti AMPK | Cell Signaling Technology | Cat# 2532, RRID:AB_330331 |
| Rabbit polyclonal anti pAMPK | Cell Signaling Technology | Cat# 2531, RRID:AB_330330 |
| Rabbit polyclonal anti Caspase-3 | Cell Signaling Technology | Cat# 9662, RRID: AB_331439 |
| Anti-EF5 antibody (ELK3–51) Cy3 | Hypoxia-Imaging.org | N/A |
| Bacterial and Virus Strains | ||
| Luciferase Adenovirus | Vector Biolabs | Cat# 1000 |
| Cre recombinase Adenovirus | Vector Biolabs | Cat# 1045 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Hank’s Balanced Salt Solution | Thermo Fisher Scientific | Cat# 24020 |
| Dulbecco's Phosphate-Buffered Saline | Corning | Cat# 21–030-CV |
| DMEM, high glucose, GlutaMAX | Thermo Fisher Scientific | Cat# 10569 |
| HyClone™ Fetal Bovine Serum, Defined | Thermo Fisher Scientific | Cat# SH3007003HI |
| Trypsin-EDTA (0.25%) | Thermo Fisher Scientific | Cat# 25200056 |
| Trypsin-EDTA (0.05%) | Thermo Fisher Scientific | Cat# 25300 |
| Trypan Blue | Gibco | Cat# 15250–061 |
| Collagenase type 2 | Worthington Biochemical | Cat# 4176 |
| Phenol Chlorofom | Thermo Fisher Scientific | Cat# BP1750I |
| GoTaq Green Master Mix | Promega | Cat# M7122 |
| RNA-Bee (Tel Test Inc) |
Thermo Fisher Scientific | Cat# NC9850755 |
| Chloroform | Thermo Fisher Scientific | Cat# BP1145 |
| Isopropanol | Thermo Fisher Scientific | Cat# BP2618 |
| Ethanol | Thermo Fisher Scientific | Cat# BP2818 |
| DEPC water | Thermo Fisher Scientific | Cat# AM9906 |
| RNeasy Mini Kit | Qiagen | Cat # 74104 |
| RNase-Free DNase Set | Qiagen | Cat# 79254 |
| β-mercaptoethanol | Sigma-Aldrich | Cat# M3148 |
| Omniscript Reverse Transcription kit | Qiagen | Cat# 205111 |
| QuantiTect SYBR® Green PCR Kits | Qiagen | Cat# 204143 |
| NaCl 5M | Thermo Fisher Scientific | Cat# AM760G |
| Tris HCl pH8.0 | Thermo Fisher Scientific | Cat# BP1758 |
| Proteinase K | Roche | Cat# 03115828001 |
| Glycerol | Thermo Fisher Scientific | Cat# BP229 |
| Nonidet P-40 substitute | Sigma-Aldrich | Cat# 74385 |
| EDTA 0.5M | Thermo Fisher Scientific | Cat# BP2482 |
| cOmplete™, Mini, EDTA-free Protease Inhibitor Cocktail | Roche | Cat# 11836170001 |
| Phosphatase Inhibitor Cocktail Tablets | Roche | Cat# 04 906 837 001 |
| Pierce BCA Protein Assay Kit | Thermo Fisher Scientific | Cat# 23227 |
| 10x Tris/Glycine/SDS | Bio-Rad | Cat# 1610732 |
| Tris | Thermo Fisher Scientific | Cat# BP152 |
| Glycine | Sigma-Aldrich | Cat# G8790 |
| Methanol | Sigma-Aldrich | Cat# 494437 |
| Laemmli sample buffer | Bio-Rad | Cat# 1610737 |
| Kaleidoscope protein marker | Bio-Rad | Cat# 1610324 |
| Tris Buffered Saline 10X | Thermo Fisher Scientific | Cat# BP 2471 |
| Tween-20 | Thermo Fisher Scientific | Cat# BP 337 |
| ECL™ Prime Western Blotting System | GE Healthcare | Cat# RPN2232 |
| Restore™ PLUS Western Blot Stripping Buffer | Thermo Fisher Scientific | Cat# 46430 |
| Acetone | Thermo Fisher Scientific | Cat# A18 |
| Alcian blue 8 GX | Sigma-Aldrich | Cat# A3157 |
| Alizarin Red S | Sigma-Aldrich | Cat# A5533 |
| Weigerťs iron hematoxylin solution PartA | Sigma-Aldrich | Cat# HT107 |
| Weigerťs iron hematoxylin solution Part B | Sigma-Aldrich | Cat# HT108 |
| Fast green FCF | JT Baker | Cat# M377–03 |
| Safranin O | Sigma-Aldrich | Cat# 58884 |
| Acetic Acid, Glacial | Thermo Fisher Scientific | Cat# A38 |
| Potassium hydroxide | Thermo Fisher Scientific | Cat# P250 |
| EF5 | Hypoxia-Imaging.org | N/A |
| Oligomycin | Sigma-Aldrich | Cat# 75351 |
| Carbonyl cyanide-trifluoromethoxyphenylhydrazone (FCCP) | Sigma-Aldrich | Cat# C2920 |
| Antimycin A | Sigma-Aldrich | Cat# A8674 |
| Rotenone | Sigma-Aldrich | Cat# R8875 |
| Ammonium acetate | Sigma-Aldrich | Cat# A1542 |
| Cytoseal Xyl | Thermo Fisher Scientific | Cat # 8312 |
| DAPI, FluoroPure™ grade | Thermo Fisher Scientific | Cat # D21490 |
| Triton X-100 | Sigma-Aldrich | Cat # T8787 |
| Sodium citrate | Thermo Fisher Scientific | Cat # BP327 |
| Paraformaldehyde | Acros organics | Cat# 41678 |
| Ethylenediaminetetraacetic Acid, Disodium Na Salt | Thermo Fisher Scientific | Cat # BP120 |
| Critical Commercial Assays | ||
| In situ Cell Death Detection kit, fluorescein | Roche | Cat # 11684795910 |
| Click-iT EdU Alexa Fluor 488 Imaging Kit | Thermo Fisher Scientific | Cat # C10337 |
| MitoSOX™ Red Mitochondrial Superoxide Indicator, for live-cell imaging | Thermo Fisher Scientific | Cat # M36008 |
| MitoTracker™ Green FM | Thermo Fisher Scientific | Cat # M7514 |
| TMRE-Mitochondrial Membrane Potential Assay Kit | Abcam | Cat # ab113852 |
| ROS Detection Cell-Based Assay Kit | Cayman Chemical | Cat# 601290 |
| Experimental Models: Organisms/Strains | ||
| Mus musculus: B6.Cg-Tg(Prrx1-cre)1Cjt/J | The Jackson Laboratory (Logan, et al., 2002) | Cat# JAX:005584, RRID:IMSR_JAX:005584 |
| Mus musculus: B6.Cg-Tfamtm1.1Ncdl/J | The Jackson Laboratory (Larsson, et al., 1998) | Cat# JAX:026123, RRID:IMSR_JAX:026123 |
| Mus musculus: B6.129-Hif1atm3Rsjo/J | The Jackson Laboratory (Schipani, et al., 2001) | Cat# JAX:005584, RRID:IMSR_JAX:005584 |
| Mus musculus: STOCK Epas1tm1Mcs/J | The Jackson Laboratory (Gruber, et al., 2007) | Cat# JAX:008407, RRID:IMSR_JAX:008407 |
| Mus musculus: Prx1-Cre;TFAM+/fl (mixed FVB/N-C57/B6) | This study | N/A |
| Mus musculus: Prx1-Cre;TFAMfl/fl (mixed FVB/N-C57/B6) | This study | N/A |
| Mus musculus: Prx1-Cre;HIF-1afl/fl (FVB/N) | This study | N/A |
| Mus musculus: Prx1-Cre;TFAMfl/+;HIF-1afl/fl (mixed FVB/N-C57/B6) | This study | N/A |
| Mus musculus: Prx1-Cre;TFAMfl/fl;HIF-1afl/fl (mixed FVB/N-C57/B6) | This study | N/A |
| Mus musculus: Prx1-Cre;HIF-1afl/fl (FVB/N) | This study | N/A |
| Mus musculus: Prx1-Cre; TFAMfl/fl;HIF-1afl/fl;HIF-2afl/fl (mixed FVB/N-C57/B6) | This study | N/A |
| Oligonucleotides | ||
| Prx1-Cre Forward: 5’-CAGGCGCCGCACAAAGGC-3’ Prx1-Cre Reverse: 5’-TGAACGAACCTGGTCGAAATC-3’ | (Logan, et al., 2002) | N/A |
| Tfam Floxed Forward (2-LoxP): 5’-CTGCCTTCCTCTAGCCCGGG-3’ Tfam Floxed Reverse (2-LoxP): 5’-GTAACAGCAGACAACTTGTG-3’ | (Larsson, et al., 1998) | N/A |
| Hif1a Floxed Forward (2-LoxP): 5’-TGATGTGGGTGCTGGTGTC Hif1a Floxed Forward (2-LoxP): TTGTGTTGGGGCAGTACTG-3’ | (Schipani, et al., 2001) | N/A |
| Hif2a Floxed Forward (2-LoxP): 5'-CAGGCAGTATGCCTGGCTAATTCCAGTT-3' Hif2a Floxed Forward (2-LoxP): 5'-CTTCTTCCATCATCTGGGATCTGGGACT-3'(Gruber, et al., 2007) | (Gruber et al PNAS 2007) | N/A |
| TBP Forward: 5’-AGAACAATCCAGACTAGCAGCA-3’ TBP Reverse: 5’-GGGAACTTCACATCACAGCTC-3’ | (Merceron, et al., 2019) | N/A |
| Tfam Forward 5’-CAAAGGATGATTCGGCTCAGG-3’ Tfam Reverse: 5’-TCGACGGATGAGATCACTTCG-3’ | This study | N/A |
| Hif-1a Forward: 5’-TCTCGGCGAAGCAAAGAGTC-3’ Hif-1a Reverse: 5’-AGCCATCTAGGGCTTTCAGATAA-3’ | (Merceron, et al., 2019) | N/A |
| Pgk1 Forward: 5’-ATGTCGCTTTCCAACAAGCTG-3’ Pgk1 Reverse: 5’-GCTCCATTGTCCAAGCAGAAT-3’ | This study | N/A |
| β2-Microglobulin Forward: 5’-TCATTAGGGAGGAGCCAATG-3’ β2-Microglobulin Reverse: 5’-ATCCCCTTTCGTTTTTGCTT-3’ | This study | N/A |
| mt-Cytb Forward: 5’-TGAGGGGGCTTCTCAGTAGA-3’ mt-Cytb Reverse: 5’-TAGGGCCGCGATAATAAATG-3’ | This study | N/A |
| mt-Rnr2 Forward: 5’-GGGATAACAGCGCAATCCTA-3’ mt-Rnr2 Reverse: 5’-ATTGGGATGTCCTGATCCAA-3’ | This study | N/A |
| mt-Co3 Forward: 5’-TAACCCTTGGCCTACTCACC-3’ mt-Co3 Reverse: 5’-ATAGGAGTGTGGTGGCCTTG-3’ | This study | N/A |
| Recombinant DNA | ||
| Sox9 ISH Probe | Mangiavini dev biol 2014 | N/A |
| Col2a1 ISH Probe | Merceron Plos One 2014 | N/A |
| Col10a1 ISH Probe | Merceron Plos One 2014 | N/A |
| Gdf5 ISH Probe | Provot J Cell Biol 2007 | N/A |
| Software and Algorithms | ||
| Bioquant (Bioquant Osteo 17.2.6) | Bioquant Image Analysis Corp. | RRID:SCR_016423 |
| Image J | Image J | RRID:SCR_003070 |
| FlowJo | FlowJo LLC | RRID:SCR_008520 |
| Photoshop CS6 | Adobe | RRID:SCR_014199 |