Reagents and tools table
| Reagent/Resource | Reference or Source | Identifier or Catalogue Number |
|---|---|---|
| Experimental Models | ||
| 3T3-L1 (Mus musculus) | David E. James’ Lab (University of Sydney, Australia), originally from Howard Green (Harvard Medical School, Boston, MA) | RRID: CVCL_0A20 |
| C57BL/6 J (Mus musculus) | Wellcome-MRC Institute of Metabolic Science Disease Model Core | |
| Primary subcutaneous adipocytes (Mus musculus) - extracted from male and female C57BL/6 J mice | This study | |
| hMADS (Homo sapiens) | Centre National de la Recherche Scientifique (Ez-Zoubir Amri, iBV, Nice, France) | |
| L6 myoblasts (Rattus norvegicus) | David E. James’ Lab (University of Sydney, Australia), originally from David Yaffe (Weizmann Institute of Science, Israel) | RRID: CVCL_0385 |
| Male 129Ev/Sv (Mus musculus) | Frank Gonzalez (National Institutes of Health, Bethesda, MD) | |
| pBAT (Mus musculus) | Ángela María Martínez Valverde (IIBm Alberto Sols (CSIC-UAM)) | |
| FSPS13B iPSC-hepatocytes (Homo sapiens) | Wellcome Sanger Institute HipSci initiative, UK | |
| FOP iPSC-hepatocytes (Homo sapiens) | Ludovic Vallier’s Lab (Cambridge Stem Cell Institute, UK) | |
| iPSC-i3Neurones (Homo sapiens) | Michael E. Ward (National Institute of Neurological Disorders and Stroke, MD, USA) | io1001 (bit.bio) |
| Bone marrow-derived macrophages (Mus musculus) - extracted from C57BL/6 J mice | This study | |
| HES3 (Homo sapiens) | WiCell | RRID: CVCL_7158 |
| Recombinant DNA | ||
| N/A | ||
| Antibodies | ||
| Mouse anti-α-tubulin, monoclonal, 1:1000 (WB) | Sigma-Aldrich | Cat # T9026 |
| Rabbit anti-β-Actin, monoclonal, 1:1000 (WB) | Cell Signaling Technology | Cat # 8457 |
| Rabbit anti-GLUT1, monoclonal, 1:1000 (WB) | Cell Signaling Technology | Cat # 12939 |
| Rabbit anti-GLUT4, polyclonal, 1:1000 (WB) | Gift from F. Koumanov, University of Bath and affinity-purified in-house | N/A |
| Rabbit anti-HIF1α, monoclonal, 1:1000 (WB) | Cell Signaling Technology | Cat # 14179 |
| Mouse OxPhos Rodent WB Antibody Cocktail, monoclonal, 1:250 (WB) | Invitrogen | Cat # 45-8099 |
| Rabbit anti-PDH, polyclonal, 1:2000 (WB) | Cell Signaling Technology | Cat # 2784 |
| Rabbit anti-pPDH, polyclonal, 1:2000 (WB) | Cell Signaling Technology | Cat # 31866 |
| Goat anti-Rabbit IgG, HRP, polyclonal, 1:2500 (WB) | Invitrogen | Cat # G-21234 |
| Goat anti-Mouse IgG, HRP, polyclonal, 1:2500 (WB) | Invitrogen | Cat # 31430 |
| Human-anti-GLUT4, 2 µg/mL, 1:1000 (IF) | Integral Molecular, PA, USA | Cat # LM048 |
| Goat anti-Human IgG Alexa Fluor 647, polyclonal, 1:500 (IF) | Thermo Fisher | Cat # A48279 |
| Goat anti-albumin, polyclonal, 1:500 (IF) | Bethyl Labs | Cat # A80-229A |
| Donkey anti-Goat IgG Alexa Fluor 488, polyclonal, 1:500 (IF) | Thermo Fisher | Cat # A-11055 |
| Rabbit anti-human albumin, polyclonal (Albumin assay) | Agilent Dako | Cat # F0117 |
| Goat anti-Rabbit SULFO-TAG Labelled, polyclonal (Albumin assay) | Meso Scale Discovery | Cat # R32AB |
| Oligonucleotides and sequence-based reagents | ||
| qPCR Primers | This study | Table 1 |
| Chemicals, enzymes and other reagents | ||
| DMEM - high glucose | Sigma-Aldrich | Cat # D6546 |
| Foetal bovine serum | Gibco | Cat # 10270106 |
| GlutaMAX | Gibco | Cat # 35050-038 |
| Insulin from bovine pancreas | Sigma-Aldrich | Cat # I5500 |
| 3-isobutyl-1-methylxanthine | Sigma-Aldrich | Cat # I5879 |
| Dexamethasone | Sigma-Aldrich | Cat # D4902 |
| Biotin | Sigma-Aldrich | Cat # B4639 |
| DMEM/F12 | Invitrogen | Cat # 31330-038 |
| Collagenase from Clostridium histolyticum | Sigma-Aldrich | Cat # C0130 |
| Bovine serum albumin | Sigma-Aldrich | Cat # A2153 |
| Phosphate buffered saline | Sigma-Aldrich | Cat # 806552 |
| L-glutamine | Gibco | Cat # 25030081 |
| Penicillin/Streptomycin (10,000 U/mL) | Gibco | Cat # 15140122 |
| DMEM - low glucose | Sigma-Aldrich | Cat # D6046 |
| Human fibroblast growth factor 2 (FGF2) | Abcam | Cat # ab9596 |
| Rosiglitazone | Cayman | Cat # 71740 |
| Glucose-free DMEM | Sigma-Aldrich | Cat # D5030 |
| Sodium pyruvate | Gibco | Cat # 11360070 |
| Sodium bicarbonate | Sigma-Aldrich | Cat # S6014 |
| D-(+)-glucose | Sigma-Aldrich | Cat # G7021 |
| Chloroform, HPLC grade | Merck | Cat # 270636 |
| Methanol, HPLC grade | Merck | Cat # 34860 |
| Boron trifluoride-methanol solution | Sigma-Aldrich | Cat # B1252 |
| n-Hexane, HPLC grade | Fisher Scientific | Cat # 10499170 |
| Food Industry FAME Mix | Restek | Cat # 35077 |
| Pierce Protease and Phosphatase Inhibitor Mini Tablets | Thermo Scientific | Cat # A32959 |
| Pierce BCA Protein Assay Kit | Thermo Scientific | Cat # 23227 |
| 4x Laemmli Sample Buffer | Bio-Rad | Cat # 1610747 |
| Pierce TCEP-HCl | Thermo Scientific | Cat # 20490 |
| SuperSignal™ West Pico PLUS Chemiluminescent Substrate | Thermo Scientific | Cat # 34580 |
| Acetonitrile, LC-MS grade | Fisher Scientific | Cat # 10001334 |
| Valine-d8 | Cambridge Isotope Laboratories, Inc. | Cat # DLM-488-PK |
| Cytochalasin B | Sigma-Aldrich | Cat # C6762 |
| 2-Deoxy-D-glucose | Sigma-Aldrich | Cat # D3179 |
| Triton™ X-100 | Sigma-Aldrich | Cat # X100 |
| RNeasy Mini kit | Qiagen | Cat # 74104 |
| GoScript Reverse Transcriptase kit | Promega | Cat # A2801 |
| SYBR Green Master Mix | Applied Biosystems | Cat # 4309155 |
| RNA STAT-60 | AMSBIO | Cat # CS-110 |
| Lysing Matrix D | MP Biomedicals | Cat # 116913050-CF |
| TruSeq® Stranded mRNA Library Prep | Illumina | Cat # 20020594 |
| Mouse Leptin Kit | Meso Scale Discovery | Cat # K152BYC-2 |
| Mouse Adiponectin Kit | Meso Scale Discovery | Cat # K152BXC |
| 16% Formaldehyde | Thermo Scientific | Cat # 28906 |
| Glycine | Millipore | Cat # 3570 |
| Normal swine serum | Jackson ImmunoResearch | Cat # 014-000-121 |
| Lectin-FITC | Sigma-Aldrich | Cat # L4895 |
| Hoechst 33342 | Invitrogen | Cat # H3570 |
| Glycerol | Sigma-Aldrich | Cat # G2025 |
| DABCO (1,4-Diazabicyclo[2.2.2]octane) | Sigma-Aldrich | Cat # D27802 |
| Free glycerol reagent | Sigma-Aldrich | Cat # F6428 |
| Triiodothyronine (T3) | Sigma-Aldrich | Cat # T6397 |
| Indomethacin | Sigma-Aldrich | Cat # I7378 |
| MEM α, nucleosides | Gibco | Cat # 12571063 |
| Insulin-Transferrin-Selenium | Thermo Fisher | Cat # 41400045 |
| Sodium Bicarbonate Solution 7.5% | Thermo Fisher | Cat # 25080060 |
| L-Ascorbic acid 2-Phosphate | Sigma-Aldrich | Cat # A8960 |
| Zebrafish FGF2 | Qkine | Cat # Qk002 |
| TGFß | R&D | Cat # 240-B-500/CF |
| StemPro™ Accutase™ Cell Dissociation Reagent | Thermo Fisher | Cat # A1110501 |
| DPBS, no calcium, no magnesium | Thermo Fisher | Cat # 14190250 |
| ROCK inhibitor (Y-27632) | Selleckchem | Cat # S1049 |
| IMDM | Thermo Fisher | Cat # 21980 |
| Chemically Defined Lipid Concentrate | Thermo Fisher | Cat # 11905031 |
| 1-Thio Glycerol (MTG) | Sigma-Aldrich | Cat # M6145 |
| Human Apo-Transferrin, CF | R&D | Cat # 3188-AT-001G |
| Insulin solution human | Sigma-Aldrich | Cat # I9278 |
| PVA | Sigma-Aldrich | Cat # P8136 |
| RPMI | Thermo Fisher | Cat # 61870010 |
| MEM Non-Essential Amino Acids Solution | Thermo Fisher | Cat # 11140035 |
| B27+insulin | Thermo Fisher | Cat # 17504044 |
| HepatoZYME-SFM | Thermo Fisher | Cat # 17705021 |
| BMP-4 | Qkine | Cat # Qk038 |
| LY29004 | Promega | Cat # V1201 |
| CHIR99021 | Stratech Scientific | Cat # S1263 |
| Hepatocyte Growth Factor (HGF) | Peprotech | Cat # 100-39 |
| Oncostatin M (OSM) | R&D | Cat # 295-OM-01M |
| Doxycycline | Sigma-Aldrich | Cat # 9891 |
| Vitronectin XF | Stem Cell Technologies | Cat # 07180 |
| 0.5 M EDTA | Invitrogen | Cat # AM9260G |
| Diluent 100 | Meso Scale Discovery | Cat # R50AA |
| P450-Glo™ CYP3A4 Assay kit | Promega | Cat # V9001 |
| IL-4 | PeproTech | Cat # AF-214-14 |
| [1-14C]oleate | PerkinElmer | Cat # NEC317250UC |
| Hionic-Fluor scintillation liquid | PerkinElmer | Cat # 6013311 |
| mTeSR PLUS | Stem Cell Technologies | Cat # 100-0276 |
| ReLeSR | Stem Cell Technologies | Cat # 100-0483 |
| IWP-4 | Stem Cell Technologies | Cat # 72552 |
| L-Ascorbic acid 2-phosphate sesquimagnesium salt hydrate | Sigma-Aldrich | Cat # A8960 |
| Collagenase type I | Sigma-Aldrich | Cat # SCR103 |
| MEM α, GlutaMAX | Thermo Fisher | Cat # 32561037 |
| Antimycin A | Sigma-Aldrich | Cat # A8674 |
| Dichloroacetate | Sigma-Aldrich | Cat # 347795 |
| Cobalt chloride | Sigma-Aldrich | Cat # 255599 |
| CL316,243 | Tocris | Cat # 1499 |
| Indinavir | Sigma-Aldrich | Cat # SML0189 |
| MG132 | Sigma-Aldrich | Cat # 474790 |
| 13C6-glucose | Cambridge Isotope Laboratories, Inc. | Cat # CLM-1396-PK |
| Deuterium oxide | Sigma-Aldrich | Cat # 756822 |
| tridecanoic-d25 acid | Cambridge Isotope Laboratories, Inc. | Cat # DLM-1392-PK |
| Complete Essential 8 Medium (iPSC-neurons) | Thermo Scientific | Cat # A1517001 |
| DMEM/F12 with HEPES (iPSC-neurons) | Gibco | Cat # 11330032 |
| N2 supplement | Gibco | Cat # 17502048 |
| 1% NEAA | Gibco | Cat # 11140050 |
| poly-L-ornithine | Sigma-Aldrich | Cat # P3655 |
| BrainPhys neuronal medium | Stem Cell Technologies | Cat # 05790 |
| B27 supplement 50x (iPSC-neurons) | Gibco | Cat # 17504044 |
| BDNF | Peprotech | Cat # 450-02 |
| NT-3 | Peprotech | Cat # 450-03 |
| Laminin | Gibco | Cat # 23017015 |
| Software | ||
| Prism 9 | https://www.graphpad.com/features | |
| Lucid Lab | https://lab.lucidsci.com | |
| Agilent MassHunter Workstation Quantitative Analysis (version B.07.00) | https://www.agilent.com/en/product/software-informatics/mass-spectrometry-software/data-analysis/quantitative-analysis | |
| Agilent MassHunter Workstation Qualitative Analysis (version B.07.00) | https://www.agilent.com/en/product/software-informatics/mass-spectrometry-software/data-analysis/qualitative-analysis | |
| ImageJ2 | https://imagej.net/software/imagej2/ | |
| Image Lab (v 6.1) | https://www.bio-rad.com/en-uk/product/image-lab-software?ID=KRE6P5E8Z | |
| Matlab | https://www.mathworks.com/products/matlab.html | |
| R | https://www.r-project.org | |
| Compound Discoverer (v 3.2) | https://www.thermofisher.com/uk/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/multi-omics-data-analysis/compound-discoverer-software.html | |
| Tracefinder (v 5.0) | https://www.thermofisher.com/uk/en/home/industrial/mass-spectrometry/liquid-chromatography-mass-spectrometry-lc-ms/lc-ms-software/lc-ms-data-acquisition-software/tracefinder-software.html | |
| FastQC (v. 0.11.9) | http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | |
| hisat2 (v2.1.0) | http://daehwankimlab.github.io/hisat2/ | |
| HTseq-count (v 0.11.1) | https://htseq.readthedocs.io/en/release_0.11.1/ | |
| DESeq2 (v 3.15) | https://bioconductor.org/packages/release/bioc/html/DESeq2.html | |
| Harmony High-Content Imaging and Analysis Software | https://www.perkinelmer.com/uk/product/harmony-4-9-office-license-hh17000010 | |
| MSD Discovery Workbench | https://www.mesoscale.com/en/products_and_services/software | |
| Other | ||
| Tecan Spark 10 M Plate Reader | Tecan | |
| Resipher | Lucid Scientific | |
| 24-well Lumox plates | Sarstedt | |
| OxoPlates | PreSens | |
| Agilent 7890B gas chromatography system | Agilent | |
| Agilent 5977 A mass spectrometer | Agilent | |
| Tecan M1000 Pro Plate Reader | Tecan | |
| Oroboros Oxygraph-2K | Oroboros Instruments, Innsbruck, Austria | |
| Chemidoc MP | Bio-Rad | |
| Millipore Sequant ZIC-pHILIC analytical column (5 µm, 2.1 × 150 mm) | Merck Millipore | |
| Vanquish Horizon UHPLC | Thermo Fisher | |
| Orbitrap Exploris 240 mass spectrometer | Thermo Fisher | |
| TriCarb 2900TR | PerkinElmer | |
| ABI QuantStudio 5 | Thermo Fisher | |
| Whitley H35 Hypoxystation | Don Whitley Scientific | |
| Agilent Bioanalyser 2100 | Agilent | |
| Illumina NovaSeq6000 | Illumina | |
| Opera Phenix | PerkinElmer | |
| MSD Meso Sector S600 Plate Reader | Meso Scale Discovery | |
| Zeiss inverted 710 confocal microscope | Zeiss | |
| GloMax plate reader | Promega | |
| Heart-Dyno | Mills et al, 2017 PNAS | |
| Nikon ANDOR WD Revolution Spinning Disk microscope | Nikon | |