other:
Lysis:Article Title:
Article Snippet: HiFi Cas9 Nuclease V3 IDT Cat# 1081060 .. EP enhancer IDT Cat# 1075916 CloneR Stemcell Technologies Cat# 05888 Pierce IP lysis buffer ThermoFisher Scientific Cat# 87787 HaltTM Protease Inhibitor Cocktail ThermoFisher Scientific Cat# 87786 HaltTM Protease Inhibitor Cocktail ThermoFisher Scientific Cat# 78420 BSA ThermoFisher Scientific Cat# 23209 Sample Buffer, Laemmli 2× Concentrate Sigma Cat# S3401-10VL 10x Tris/Glycine/SDS Bio-Rad Cat# 1610732 10x Tris Buffered Saline Bio-Rad Cat# 1706435 Dried Skimmed Milk Powder Marvel N/A ECL detection reagent Amersham Cat# RPN2236 Protein G Sepharose®, Fast Flow Sigma Cat# P3296 Paraformaldehyde, 4% in PBS Alfa Aesar Cat# J61899 Live/DeadTM Fixable Near-IR Dead Cell Stain Invitrogen Cat# L34976 Normal donkey serum Jackson ImmunoResearch Cat# 017-000-121 DAPI Sigma Cat# D9564 Vectashield Antifade Mounting Medium Vector Laboratories Cat# H-1000-10 di(N-succimidyl) glutarate Sigma-Aldrich Cat# 80424 PierceTM 16% Formaldehyde (w/v), Methanol-free ThermoFisher Scientific Cat# 28908 Glycine Sigma-Aldrich Cat# 50046 Tris-HCl, pH 7.5 In house1 N/A Tris, pH 8.0 In house1 N/A EDTA ThermoFisher Scientific Cat# 87788 EDTA Sigma Cat# E7889 SDS ThermoFisher Scientific Cat# AM9820 Triton X-100 Sigma Cat# T8787 HEPES, pH 7.9 Sigma Cat# H3375 Sodium deoxycholate Sigma Cat# 30970 LiCl Sigma Cat# L7026 NP-40 Alternative Sigma Cat# 18896 RNase A ThermoFisher Scientific Cat# E0531 Proteinase K ThermoFisher Scientific Cat# 78437 Tris-HCl, pH 7.4 In house1 N/A MgCl2 In house1 N/A NaCl Sigma Cat# S5150 Water ThermoFisher Scientific Cat# AM9937 .. P3 Primary Cell 4D-NucleofectorTM X Kit L Lonza Cat# V4XP-3024 RNeasy Micro Kit Qiagen Cat# 74004 Maxima First Strand cDNA Synthesis kit with dsDNase ThermoFisher Scientific Cat# K1671 Taqman Universal qRT-PCR Master Mix ThermoFisher Scientific Cat# 4304437 Pierce BCA Protein Assay Kit ThermoFisher Scientific Cat# 23225 REAGENT or RESOURCE SOURCE IDENTIFIER 4–15% Mini-PROTEAN® TGXTM Precast Protein Gels Bio-Rad Cat# 4561085 Trans-Blot Turbo Mini 0.2 μm PVDF Transfer Packs Bio-Rad Cat# 1704156 HyperfilmTM ECLTM Amersham Cat# 28-9068-36 Duoluk In Situ Red Started Kit Mouse/Rabbit Sigma-Aldrich Cat# DUO92101-1KT KAPA mRNA polyA HyperPrep Kit Illumina Cat# KR1352 Dynabeads Protein G ThermoFisher Scientific Cat# 10003D Dynabeads Protein A ThermoFisher Scientific Cat# 10008D KAPA pure beads Roche Cat# 07893271001 Zymo Clean & Concetrator-5 Kit Zymo Research Cat# D4014 NEB Ultra II DNA Library Prep Kit for Illumina New England BioLabs Cat# E7103 Illumina Tagment DNA TDE1 Enzyme and Buffer Small Kit Illumina Cat# 20034197 NEBNext HiFi 2X PCR Master Mix New England BioLabs Cat# M0541S QubitTM dsDNA HS assay ThermoFisher Scientific Cat# Q32851
Article Title: The interplay between CB 2 and NMDA receptors in Parkinson’s disease
Article Snippet: .. Then, cells were washed twice with cold PBS and lysed by the addition of ice-cold lysis buffer (50 mM Tris-HCl pH 7.4, 50 mM NaF, 150 mM NaCl, 45 mM glycerol-3-phosphate, 1% Triton X-100, 20 μM phenyl-arsine oxide, 0.4 mM NaVO4 and protease inhibitor mixture (MERK, St. Louis, MO, USA)) Cellular debris were removed by centrifugation at 13,000 g for 10 min at 4 °C, and protein concentration was adjusted to 1 mg/mL by the bicinchoninic acid method (ThermoFisher Scientific, Waltham, MA, USA) using a commercial bovine serum albumin dilution (BSA) (ThermoFisher Scientific) for standardization. ..
Protease Inhibitor:Article Title:
Article Snippet: HiFi Cas9 Nuclease V3 IDT Cat# 1081060 .. EP enhancer IDT Cat# 1075916 CloneR Stemcell Technologies Cat# 05888 Pierce IP lysis buffer ThermoFisher Scientific Cat# 87787 HaltTM Protease Inhibitor Cocktail ThermoFisher Scientific Cat# 87786 HaltTM Protease Inhibitor Cocktail ThermoFisher Scientific Cat# 78420 BSA ThermoFisher Scientific Cat# 23209 Sample Buffer, Laemmli 2× Concentrate Sigma Cat# S3401-10VL 10x Tris/Glycine/SDS Bio-Rad Cat# 1610732 10x Tris Buffered Saline Bio-Rad Cat# 1706435 Dried Skimmed Milk Powder Marvel N/A ECL detection reagent Amersham Cat# RPN2236 Protein G Sepharose®, Fast Flow Sigma Cat# P3296 Paraformaldehyde, 4% in PBS Alfa Aesar Cat# J61899 Live/DeadTM Fixable Near-IR Dead Cell Stain Invitrogen Cat# L34976 Normal donkey serum Jackson ImmunoResearch Cat# 017-000-121 DAPI Sigma Cat# D9564 Vectashield Antifade Mounting Medium Vector Laboratories Cat# H-1000-10 di(N-succimidyl) glutarate Sigma-Aldrich Cat# 80424 PierceTM 16% Formaldehyde (w/v), Methanol-free ThermoFisher Scientific Cat# 28908 Glycine Sigma-Aldrich Cat# 50046 Tris-HCl, pH 7.5 In house1 N/A Tris, pH 8.0 In house1 N/A EDTA ThermoFisher Scientific Cat# 87788 EDTA Sigma Cat# E7889 SDS ThermoFisher Scientific Cat# AM9820 Triton X-100 Sigma Cat# T8787 HEPES, pH 7.9 Sigma Cat# H3375 Sodium deoxycholate Sigma Cat# 30970 LiCl Sigma Cat# L7026 NP-40 Alternative Sigma Cat# 18896 RNase A ThermoFisher Scientific Cat# E0531 Proteinase K ThermoFisher Scientific Cat# 78437 Tris-HCl, pH 7.4 In house1 N/A MgCl2 In house1 N/A NaCl Sigma Cat# S5150 Water ThermoFisher Scientific Cat# AM9937 .. P3 Primary Cell 4D-NucleofectorTM X Kit L Lonza Cat# V4XP-3024 RNeasy Micro Kit Qiagen Cat# 74004 Maxima First Strand cDNA Synthesis kit with dsDNase ThermoFisher Scientific Cat# K1671 Taqman Universal qRT-PCR Master Mix ThermoFisher Scientific Cat# 4304437 Pierce BCA Protein Assay Kit ThermoFisher Scientific Cat# 23225 REAGENT or RESOURCE SOURCE IDENTIFIER 4–15% Mini-PROTEAN® TGXTM Precast Protein Gels Bio-Rad Cat# 4561085 Trans-Blot Turbo Mini 0.2 μm PVDF Transfer Packs Bio-Rad Cat# 1704156 HyperfilmTM ECLTM Amersham Cat# 28-9068-36 Duoluk In Situ Red Started Kit Mouse/Rabbit Sigma-Aldrich Cat# DUO92101-1KT KAPA mRNA polyA HyperPrep Kit Illumina Cat# KR1352 Dynabeads Protein G ThermoFisher Scientific Cat# 10003D Dynabeads Protein A ThermoFisher Scientific Cat# 10008D KAPA pure beads Roche Cat# 07893271001 Zymo Clean & Concetrator-5 Kit Zymo Research Cat# D4014 NEB Ultra II DNA Library Prep Kit for Illumina New England BioLabs Cat# E7103 Illumina Tagment DNA TDE1 Enzyme and Buffer Small Kit Illumina Cat# 20034197 NEBNext HiFi 2X PCR Master Mix New England BioLabs Cat# M0541S QubitTM dsDNA HS assay ThermoFisher Scientific Cat# Q32851
Article Title: The interplay between CB 2 and NMDA receptors in Parkinson’s disease
Article Snippet: .. Then, cells were washed twice with cold PBS and lysed by the addition of ice-cold lysis buffer (50 mM Tris-HCl pH 7.4, 50 mM NaF, 150 mM NaCl, 45 mM glycerol-3-phosphate, 1% Triton X-100, 20 μM phenyl-arsine oxide, 0.4 mM NaVO4 and protease inhibitor mixture (MERK, St. Louis, MO, USA)) Cellular debris were removed by centrifugation at 13,000 g for 10 min at 4 °C, and protein concentration was adjusted to 1 mg/mL by the bicinchoninic acid method (ThermoFisher Scientific, Waltham, MA, USA) using a commercial bovine serum albumin dilution (BSA) (ThermoFisher Scientific) for standardization. ..
Article Title: Rhodoquinone carries electrons in the mammalian electron transport chain.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies COX4 Cell Signaling Technology Cat# 4850S; RRID:AB_2085424 FLAG Cell Signaling Technology Cat# 14793S; RRID AB_2572291 Total OXPHOS Rodent WB Antibody Cocktail Abcam Cat# ab110413; RRID: AB_2629281 HIF1a Cell Signaling Technology Cat# 36169S; RRID:AB_2799095 SDHA ProteinTech Cat# 14865-1-AP; RRID: 2881948 TOMM20 Santa Cruz Biotechnology Cat# sc-17764; RRID:AB_628381 GLUT1 Abcam Cat# ab115730; RRID:AB_10903230 NDUFS1 Cell Signaling Technology Cat#60153S CYC1 ProteinTech Cat#10242-1-AP ATP5A1 Cell Signaling Technology Cat#18023S ACTIN Cell Singaling Technology Cat# 4967S; RRID:AB_330288 Alexa Fluor 488 goat-anti-rabbit Abcam Cat# ab150077; RRID:AB_2630356 Alexa Fluor 647 goat-anti-mouse Abcam Cat# ab150113; RRID:AB_2576208 Secondary antibody- mouse Cell Signaling Technology Cat#7076S; RRID:AB_330924 Secondary antibody rabbit Cell Signaling Technology Cat#7074S; RRID:AB_2099233 Bacterial and virus strains AAV9.Tre3G-mCherry SV40 CB6 Tet-on 3G RBG University of Massachusetts Medical School Viral Vector Core https://www.umassmed.edu/ research/cores/viralvectorcore/ AAV9.Tre3G-RquA SV40 CB6 Tet-on 3G RBG University of Massachusetts Medical School Viral Vector Core https://www.umassmed.edu/ research/cores/viralvectorcore/ Biological samples Healthy Human Kidney Tissue UMCCTS Biorepository and Tissue Bank https://www.umassmed.edu/ tissue-and-tumor-bank/ Healthy Human Brain Tissue UMCCTS Biorepository and Tissue Bank https://www.umassmed.edu/ tissue-and-tumor-bank/ Healthy Human Muscle Tissue UMCCTS Biorepository and Tissue Bank https://www.umassmed.edu/ tissue-and-tumor-bank/ Ascaris suum worms A gift from Dr. Catherine Clark N/A Rhodospirillum rubrum ATCC 11170 Chemicals, peptides, and recombinant proteins CellROX orange dye Invitrogen Cat# C10443 N-Acetyl Cysteine Sigma Cat# A9165 Tert-butyl hydroperoxide Sigma Cat# 458139 Tetramethylrhodamine, Ethyl Ester Invitrogen Cat# T669 MitoSox Red Thermo Scientific Cat# M36008 13C5 15N2-glutamine Cambridge Isotope Labs Cat# CNLM-1275-H-0.5 13C4-aspartate Sigma Cat# 604852-250mg HBSS with Ca2+, Mg2+ Gibco Cat#14025092 HBSS without Ca2+, Mg2+ Gibco Cat#14175095 EDTA (0.5 M) Invitrogen Cat#15575020 DMEM low glucose Gibco Cat# 11885084 Dulbecco’s Phosphate Buffered Saline (DPBS) without calcium and magnesium Gibco Cat# 70011044 Penicillin-Streptomycin Solution Gibco Cat# 15070063 (Continued on next page) Cell 188, 1–16.e1–e11, February 20, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Trypsin Thermo Fisher Scientific Cat# 25200114 DMEM MEDIA Fisher Scientific Cat# 11-995-073 DMEM No Glutamine Media Fisher Scientific Cat# 10-313-039 cOmplete EDTA-free protease inhibitor Sigma-Aldrich Cat# 11836170001 RIPA Buffer EMD-Millipore Cat# 20-188 Isotone Buffer Beckman Coulter Cat# 8546719 BSA ThermoFisher Scientific Cat# 23227 TritonX-100 Sigma-Aldrich Cat# T9284 ProLong Gold Glass + NucBlue Invitrogen Cat# P36981 Mannitol Sigma-Aldrich Cat# M4125 Sucrose Sigma-Aldrich Cat# S0389 HEPES Fisher Scientific Cat# BP310-100 Fumaric Acid Sigma-Aldrich Cat# 47910 K-ADP Sigma-Aldrich Cat# A5285-100MG Succinic Acid Sigma-Aldrich Cat# S3674 KH2PO4 Sigma-Aldrich Cat# P0662-500G NADH Sigma-Aldrich Cat# N8129-500MG Medium 199 Gibco Cat#11150067 Liberase TM Research Grade Sigma-Aldrich Cat#05401127001 NativePAGE 1x sample buffer ThermoFisher Cat#BN2008 NativePAGE G-250 sample additive ThermoFisher Cat#BN2004 NativePAGE 3-12 %, Bis-Tris gels ThermoFisher Cat#BN1001 NuPAGE transfer buffer ThermoFisher Cat#NP0006 4-20% Tris-Glycine Novex Gels Invitrogen Cat#XP04205BOX PVDF Transfer Membranes, 0.45 mm ThermoFisher Cat#88518 Seahorse XF RPMI Media Seahorse Bioscience Cat# 103336 LCMS-grade Methanol Fisher Scientific Cat#A452SK-4 LCMS-grade Ethanol Sigma-Aldrich Cat#459828-1L LCMS-grade Hexane Honeywell Cat#34986-4X2.5L LCMS-grade Isopropanol Sigma-Aldrich Cat#34863 LCMS-grade Ammonium Hydroxide Sigma-Aldrich Cat#09859-250ML LCMS-grade Formic Acid Sigma-Aldrich Cat#F0507-1L LCMS-grade Water Sigma-Aldrich Cat#270733-4X4L LCMS-grade Chloroform Sigma-Aldrich Cat#366927 Deposited data RNA Sequencing SUB14409949 https://dataview.ncbi.nlm.nih.gov/object/ PRJNA1105324?reviewer= 8hnish5r1lsc23scrnjgi2tftv Metabolomics Workbench StudyID=ST003192 http://dev.metabolomicsworkbench. org:22222/data/DRCCMetadata.php?Mode= Study&StudyID=ST003192 Experimental models: Cell lines Human: 143B ATCC CRL-8303 Human: Caki-1 ATCC HTB-46 Human: DLD1 ATCC CCL-221 Human: HCT116 ATCC CCL-247 Human: HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Mouse: Wildtype- C57BL/6J The Jackson Laboratory RRID:IMSR_JAX:000664 (Continued on next page) ll OPEN ACCESS e2 Cell 188, 1–16.e1–e11, February 20, 2025 Please cite this article in press as: Valeros et al., Rhodoquinone carries electrons in the mammalian electron transport chain, Cell (2025), https://doi.org/10.1016/j.cell.2024.12.007 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Caenorhabditis elegans – Bristol, N2 strain Caenorhabditis Genetics Center N2 (wild type) Recombinant DNA Plasmid: pCW57.1-Luciferase backbone Shadle et al. Addgene Plasmid #99283 Plasmid: SDHB KO Spinelli et al. Addgene Plasmid #177981 Plasmid: RquA This paper Addgene Plasmid #229685 Software and algorithms TraceFinder 5.1 ThermoFisher https://www.thermofisher.com/us/en/home/ industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lcms/lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html BCL convert (version 3.8.2) Illumina https://emea.support.illumina.com/ sequencing/sequencing_software/ bcl-convert.html Samtools (version 1.16.1) Li et al.2 http://samtools.sourceforge.net/ IsoCorrectoR Bioconductor https://www.bioconductor.org/ packages/release/bioc/html/ IsoCorrectoR.html Other Seahorse XFe-96 Analyzer Seahorse Bioscience N/A Q-Exactive orbitrap mass spectrometer with an Ion Max source and HESI II probe ThermoFisher N/A Vanquish Horizon UHLPC system ThermoFisher N/A CentriVap Benchtop Vacuum Concentrator Labconco N/A CentriVap-105 Cold Trap Labconco N/A Supelco Ascentis Express C18 2.7 mm 15 cm x 2.1 mm Sigma Cat# 53825-U Luna 3 mm PFP(2) 100 Å, LC Column 100 x 2 mm Phenomenex Cat# 00D-4447-BB0 SeQuant ZIC-pHILIC 5um 150 x 2.1 mm analytical column Sigma Cat# 1504600001 Invivo2 1000 Hypoxia Chamber Baker N/A Cell strainer, 100 mm Corning CLS431752 Peristaltic pump Gilson Miniplus 3PVC tubing 2.06 mm diameter Sterile 50ml Conical tubes Corning 430829 BD Angiocath 20GA x1.16 in IV catheter BD 381134 moorLDI2-IR laser Doppler imaging system Moor Instruments N/A LSR-II sorter BD Biosciences N/A NEBNext Ultra II Directional RNA Library Prep Kit New England Biolabs Cat# E7765L NEBNext Multiplex Oligos for Illumina New England Biolabs cat# E6440S NEBNext Library Quant Kit for Illumina New England Biolabs Cat# E7630S P2 100 cycle kit Illumina Cat# 20046811 Pierce BCA Protein Assay Kits Life Technologies Cat# 23225 ll OPEN ACCESS Please cite this article in press as: Valeros et al., Rhodoquinone carries electrons in the mammalian electron transport chain, Cell (2025), https://doi.org/10.1016/j.cell.2024.12.007
Saline:Article Title:
Article Snippet: HiFi Cas9 Nuclease V3 IDT Cat# 1081060 .. EP enhancer IDT Cat# 1075916 CloneR Stemcell Technologies Cat# 05888 Pierce IP lysis buffer ThermoFisher Scientific Cat# 87787 HaltTM Protease Inhibitor Cocktail ThermoFisher Scientific Cat# 87786 HaltTM Protease Inhibitor Cocktail ThermoFisher Scientific Cat# 78420 BSA ThermoFisher Scientific Cat# 23209 Sample Buffer, Laemmli 2× Concentrate Sigma Cat# S3401-10VL 10x Tris/Glycine/SDS Bio-Rad Cat# 1610732 10x Tris Buffered Saline Bio-Rad Cat# 1706435 Dried Skimmed Milk Powder Marvel N/A ECL detection reagent Amersham Cat# RPN2236 Protein G Sepharose®, Fast Flow Sigma Cat# P3296 Paraformaldehyde, 4% in PBS Alfa Aesar Cat# J61899 Live/DeadTM Fixable Near-IR Dead Cell Stain Invitrogen Cat# L34976 Normal donkey serum Jackson ImmunoResearch Cat# 017-000-121 DAPI Sigma Cat# D9564 Vectashield Antifade Mounting Medium Vector Laboratories Cat# H-1000-10 di(N-succimidyl) glutarate Sigma-Aldrich Cat# 80424 PierceTM 16% Formaldehyde (w/v), Methanol-free ThermoFisher Scientific Cat# 28908 Glycine Sigma-Aldrich Cat# 50046 Tris-HCl, pH 7.5 In house1 N/A Tris, pH 8.0 In house1 N/A EDTA ThermoFisher Scientific Cat# 87788 EDTA Sigma Cat# E7889 SDS ThermoFisher Scientific Cat# AM9820 Triton X-100 Sigma Cat# T8787 HEPES, pH 7.9 Sigma Cat# H3375 Sodium deoxycholate Sigma Cat# 30970 LiCl Sigma Cat# L7026 NP-40 Alternative Sigma Cat# 18896 RNase A ThermoFisher Scientific Cat# E0531 Proteinase K ThermoFisher Scientific Cat# 78437 Tris-HCl, pH 7.4 In house1 N/A MgCl2 In house1 N/A NaCl Sigma Cat# S5150 Water ThermoFisher Scientific Cat# AM9937 .. P3 Primary Cell 4D-NucleofectorTM X Kit L Lonza Cat# V4XP-3024 RNeasy Micro Kit Qiagen Cat# 74004 Maxima First Strand cDNA Synthesis kit with dsDNase ThermoFisher Scientific Cat# K1671 Taqman Universal qRT-PCR Master Mix ThermoFisher Scientific Cat# 4304437 Pierce BCA Protein Assay Kit ThermoFisher Scientific Cat# 23225 REAGENT or RESOURCE SOURCE IDENTIFIER 4–15% Mini-PROTEAN® TGXTM Precast Protein Gels Bio-Rad Cat# 4561085 Trans-Blot Turbo Mini 0.2 μm PVDF Transfer Packs Bio-Rad Cat# 1704156 HyperfilmTM ECLTM Amersham Cat# 28-9068-36 Duoluk In Situ Red Started Kit Mouse/Rabbit Sigma-Aldrich Cat# DUO92101-1KT KAPA mRNA polyA HyperPrep Kit Illumina Cat# KR1352 Dynabeads Protein G ThermoFisher Scientific Cat# 10003D Dynabeads Protein A ThermoFisher Scientific Cat# 10008D KAPA pure beads Roche Cat# 07893271001 Zymo Clean & Concetrator-5 Kit Zymo Research Cat# D4014 NEB Ultra II DNA Library Prep Kit for Illumina New England BioLabs Cat# E7103 Illumina Tagment DNA TDE1 Enzyme and Buffer Small Kit Illumina Cat# 20034197 NEBNext HiFi 2X PCR Master Mix New England BioLabs Cat# M0541S QubitTM dsDNA HS assay ThermoFisher Scientific Cat# Q32851
Milk:Article Title:
Article Snippet: HiFi Cas9 Nuclease V3 IDT Cat# 1081060 .. EP enhancer IDT Cat# 1075916 CloneR Stemcell Technologies Cat# 05888 Pierce IP lysis buffer ThermoFisher Scientific Cat# 87787 HaltTM Protease Inhibitor Cocktail ThermoFisher Scientific Cat# 87786 HaltTM Protease Inhibitor Cocktail ThermoFisher Scientific Cat# 78420 BSA ThermoFisher Scientific Cat# 23209 Sample Buffer, Laemmli 2× Concentrate Sigma Cat# S3401-10VL 10x Tris/Glycine/SDS Bio-Rad Cat# 1610732 10x Tris Buffered Saline Bio-Rad Cat# 1706435 Dried Skimmed Milk Powder Marvel N/A ECL detection reagent Amersham Cat# RPN2236 Protein G Sepharose®, Fast Flow Sigma Cat# P3296 Paraformaldehyde, 4% in PBS Alfa Aesar Cat# J61899 Live/DeadTM Fixable Near-IR Dead Cell Stain Invitrogen Cat# L34976 Normal donkey serum Jackson ImmunoResearch Cat# 017-000-121 DAPI Sigma Cat# D9564 Vectashield Antifade Mounting Medium Vector Laboratories Cat# H-1000-10 di(N-succimidyl) glutarate Sigma-Aldrich Cat# 80424 PierceTM 16% Formaldehyde (w/v), Methanol-free ThermoFisher Scientific Cat# 28908 Glycine Sigma-Aldrich Cat# 50046 Tris-HCl, pH 7.5 In house1 N/A Tris, pH 8.0 In house1 N/A EDTA ThermoFisher Scientific Cat# 87788 EDTA Sigma Cat# E7889 SDS ThermoFisher Scientific Cat# AM9820 Triton X-100 Sigma Cat# T8787 HEPES, pH 7.9 Sigma Cat# H3375 Sodium deoxycholate Sigma Cat# 30970 LiCl Sigma Cat# L7026 NP-40 Alternative Sigma Cat# 18896 RNase A ThermoFisher Scientific Cat# E0531 Proteinase K ThermoFisher Scientific Cat# 78437 Tris-HCl, pH 7.4 In house1 N/A MgCl2 In house1 N/A NaCl Sigma Cat# S5150 Water ThermoFisher Scientific Cat# AM9937 .. P3 Primary Cell 4D-NucleofectorTM X Kit L Lonza Cat# V4XP-3024 RNeasy Micro Kit Qiagen Cat# 74004 Maxima First Strand cDNA Synthesis kit with dsDNase ThermoFisher Scientific Cat# K1671 Taqman Universal qRT-PCR Master Mix ThermoFisher Scientific Cat# 4304437 Pierce BCA Protein Assay Kit ThermoFisher Scientific Cat# 23225 REAGENT or RESOURCE SOURCE IDENTIFIER 4–15% Mini-PROTEAN® TGXTM Precast Protein Gels Bio-Rad Cat# 4561085 Trans-Blot Turbo Mini 0.2 μm PVDF Transfer Packs Bio-Rad Cat# 1704156 HyperfilmTM ECLTM Amersham Cat# 28-9068-36 Duoluk In Situ Red Started Kit Mouse/Rabbit Sigma-Aldrich Cat# DUO92101-1KT KAPA mRNA polyA HyperPrep Kit Illumina Cat# KR1352 Dynabeads Protein G ThermoFisher Scientific Cat# 10003D Dynabeads Protein A ThermoFisher Scientific Cat# 10008D KAPA pure beads Roche Cat# 07893271001 Zymo Clean & Concetrator-5 Kit Zymo Research Cat# D4014 NEB Ultra II DNA Library Prep Kit for Illumina New England BioLabs Cat# E7103 Illumina Tagment DNA TDE1 Enzyme and Buffer Small Kit Illumina Cat# 20034197 NEBNext HiFi 2X PCR Master Mix New England BioLabs Cat# M0541S QubitTM dsDNA HS assay ThermoFisher Scientific Cat# Q32851
Staining:Article Title:
Article Snippet: HiFi Cas9 Nuclease V3 IDT Cat# 1081060 .. EP enhancer IDT Cat# 1075916 CloneR Stemcell Technologies Cat# 05888 Pierce IP lysis buffer ThermoFisher Scientific Cat# 87787 HaltTM Protease Inhibitor Cocktail ThermoFisher Scientific Cat# 87786 HaltTM Protease Inhibitor Cocktail ThermoFisher Scientific Cat# 78420 BSA ThermoFisher Scientific Cat# 23209 Sample Buffer, Laemmli 2× Concentrate Sigma Cat# S3401-10VL 10x Tris/Glycine/SDS Bio-Rad Cat# 1610732 10x Tris Buffered Saline Bio-Rad Cat# 1706435 Dried Skimmed Milk Powder Marvel N/A ECL detection reagent Amersham Cat# RPN2236 Protein G Sepharose®, Fast Flow Sigma Cat# P3296 Paraformaldehyde, 4% in PBS Alfa Aesar Cat# J61899 Live/DeadTM Fixable Near-IR Dead Cell Stain Invitrogen Cat# L34976 Normal donkey serum Jackson ImmunoResearch Cat# 017-000-121 DAPI Sigma Cat# D9564 Vectashield Antifade Mounting Medium Vector Laboratories Cat# H-1000-10 di(N-succimidyl) glutarate Sigma-Aldrich Cat# 80424 PierceTM 16% Formaldehyde (w/v), Methanol-free ThermoFisher Scientific Cat# 28908 Glycine Sigma-Aldrich Cat# 50046 Tris-HCl, pH 7.5 In house1 N/A Tris, pH 8.0 In house1 N/A EDTA ThermoFisher Scientific Cat# 87788 EDTA Sigma Cat# E7889 SDS ThermoFisher Scientific Cat# AM9820 Triton X-100 Sigma Cat# T8787 HEPES, pH 7.9 Sigma Cat# H3375 Sodium deoxycholate Sigma Cat# 30970 LiCl Sigma Cat# L7026 NP-40 Alternative Sigma Cat# 18896 RNase A ThermoFisher Scientific Cat# E0531 Proteinase K ThermoFisher Scientific Cat# 78437 Tris-HCl, pH 7.4 In house1 N/A MgCl2 In house1 N/A NaCl Sigma Cat# S5150 Water ThermoFisher Scientific Cat# AM9937 .. P3 Primary Cell 4D-NucleofectorTM X Kit L Lonza Cat# V4XP-3024 RNeasy Micro Kit Qiagen Cat# 74004 Maxima First Strand cDNA Synthesis kit with dsDNase ThermoFisher Scientific Cat# K1671 Taqman Universal qRT-PCR Master Mix ThermoFisher Scientific Cat# 4304437 Pierce BCA Protein Assay Kit ThermoFisher Scientific Cat# 23225 REAGENT or RESOURCE SOURCE IDENTIFIER 4–15% Mini-PROTEAN® TGXTM Precast Protein Gels Bio-Rad Cat# 4561085 Trans-Blot Turbo Mini 0.2 μm PVDF Transfer Packs Bio-Rad Cat# 1704156 HyperfilmTM ECLTM Amersham Cat# 28-9068-36 Duoluk In Situ Red Started Kit Mouse/Rabbit Sigma-Aldrich Cat# DUO92101-1KT KAPA mRNA polyA HyperPrep Kit Illumina Cat# KR1352 Dynabeads Protein G ThermoFisher Scientific Cat# 10003D Dynabeads Protein A ThermoFisher Scientific Cat# 10008D KAPA pure beads Roche Cat# 07893271001 Zymo Clean & Concetrator-5 Kit Zymo Research Cat# D4014 NEB Ultra II DNA Library Prep Kit for Illumina New England BioLabs Cat# E7103 Illumina Tagment DNA TDE1 Enzyme and Buffer Small Kit Illumina Cat# 20034197 NEBNext HiFi 2X PCR Master Mix New England BioLabs Cat# M0541S QubitTM dsDNA HS assay ThermoFisher Scientific Cat# Q32851
Centrifugation:Article Title: The interplay between CB 2 and NMDA receptors in Parkinson’s disease
Article Snippet: .. Then, cells were washed twice with cold PBS and lysed by the addition of ice-cold lysis buffer (50 mM Tris-HCl pH 7.4, 50 mM NaF, 150 mM NaCl, 45 mM glycerol-3-phosphate, 1% Triton X-100, 20 μM phenyl-arsine oxide, 0.4 mM NaVO4 and protease inhibitor mixture (MERK, St. Louis, MO, USA)) Cellular debris were removed by centrifugation at 13,000 g for 10 min at 4 °C, and protein concentration was adjusted to 1 mg/mL by the bicinchoninic acid method (ThermoFisher Scientific, Waltham, MA, USA) using a commercial bovine serum albumin dilution (BSA) (ThermoFisher Scientific) for standardization. ..
Protein Concentration:Article Title: The interplay between CB 2 and NMDA receptors in Parkinson’s disease
Article Snippet: .. Then, cells were washed twice with cold PBS and lysed by the addition of ice-cold lysis buffer (50 mM Tris-HCl pH 7.4, 50 mM NaF, 150 mM NaCl, 45 mM glycerol-3-phosphate, 1% Triton X-100, 20 μM phenyl-arsine oxide, 0.4 mM NaVO4 and protease inhibitor mixture (MERK, St. Louis, MO, USA)) Cellular debris were removed by centrifugation at 13,000 g for 10 min at 4 °C, and protein concentration was adjusted to 1 mg/mL by the bicinchoninic acid method (ThermoFisher Scientific, Waltham, MA, USA) using a commercial bovine serum albumin dilution (BSA) (ThermoFisher Scientific) for standardization. ..
Liquid Chromatography with Mass Spectroscopy:Article Title: Rhodoquinone carries electrons in the mammalian electron transport chain.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies COX4 Cell Signaling Technology Cat# 4850S; RRID:AB_2085424 FLAG Cell Signaling Technology Cat# 14793S; RRID AB_2572291 Total OXPHOS Rodent WB Antibody Cocktail Abcam Cat# ab110413; RRID: AB_2629281 HIF1a Cell Signaling Technology Cat# 36169S; RRID:AB_2799095 SDHA ProteinTech Cat# 14865-1-AP; RRID: 2881948 TOMM20 Santa Cruz Biotechnology Cat# sc-17764; RRID:AB_628381 GLUT1 Abcam Cat# ab115730; RRID:AB_10903230 NDUFS1 Cell Signaling Technology Cat#60153S CYC1 ProteinTech Cat#10242-1-AP ATP5A1 Cell Signaling Technology Cat#18023S ACTIN Cell Singaling Technology Cat# 4967S; RRID:AB_330288 Alexa Fluor 488 goat-anti-rabbit Abcam Cat# ab150077; RRID:AB_2630356 Alexa Fluor 647 goat-anti-mouse Abcam Cat# ab150113; RRID:AB_2576208 Secondary antibody- mouse Cell Signaling Technology Cat#7076S; RRID:AB_330924 Secondary antibody rabbit Cell Signaling Technology Cat#7074S; RRID:AB_2099233 Bacterial and virus strains AAV9.Tre3G-mCherry SV40 CB6 Tet-on 3G RBG University of Massachusetts Medical School Viral Vector Core https://www.umassmed.edu/ research/cores/viralvectorcore/ AAV9.Tre3G-RquA SV40 CB6 Tet-on 3G RBG University of Massachusetts Medical School Viral Vector Core https://www.umassmed.edu/ research/cores/viralvectorcore/ Biological samples Healthy Human Kidney Tissue UMCCTS Biorepository and Tissue Bank https://www.umassmed.edu/ tissue-and-tumor-bank/ Healthy Human Brain Tissue UMCCTS Biorepository and Tissue Bank https://www.umassmed.edu/ tissue-and-tumor-bank/ Healthy Human Muscle Tissue UMCCTS Biorepository and Tissue Bank https://www.umassmed.edu/ tissue-and-tumor-bank/ Ascaris suum worms A gift from Dr. Catherine Clark N/A Rhodospirillum rubrum ATCC 11170 Chemicals, peptides, and recombinant proteins CellROX orange dye Invitrogen Cat# C10443 N-Acetyl Cysteine Sigma Cat# A9165 Tert-butyl hydroperoxide Sigma Cat# 458139 Tetramethylrhodamine, Ethyl Ester Invitrogen Cat# T669 MitoSox Red Thermo Scientific Cat# M36008 13C5 15N2-glutamine Cambridge Isotope Labs Cat# CNLM-1275-H-0.5 13C4-aspartate Sigma Cat# 604852-250mg HBSS with Ca2+, Mg2+ Gibco Cat#14025092 HBSS without Ca2+, Mg2+ Gibco Cat#14175095 EDTA (0.5 M) Invitrogen Cat#15575020 DMEM low glucose Gibco Cat# 11885084 Dulbecco’s Phosphate Buffered Saline (DPBS) without calcium and magnesium Gibco Cat# 70011044 Penicillin-Streptomycin Solution Gibco Cat# 15070063 (Continued on next page) Cell 188, 1–16.e1–e11, February 20, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Trypsin Thermo Fisher Scientific Cat# 25200114 DMEM MEDIA Fisher Scientific Cat# 11-995-073 DMEM No Glutamine Media Fisher Scientific Cat# 10-313-039 cOmplete EDTA-free protease inhibitor Sigma-Aldrich Cat# 11836170001 RIPA Buffer EMD-Millipore Cat# 20-188 Isotone Buffer Beckman Coulter Cat# 8546719 BSA ThermoFisher Scientific Cat# 23227 TritonX-100 Sigma-Aldrich Cat# T9284 ProLong Gold Glass + NucBlue Invitrogen Cat# P36981 Mannitol Sigma-Aldrich Cat# M4125 Sucrose Sigma-Aldrich Cat# S0389 HEPES Fisher Scientific Cat# BP310-100 Fumaric Acid Sigma-Aldrich Cat# 47910 K-ADP Sigma-Aldrich Cat# A5285-100MG Succinic Acid Sigma-Aldrich Cat# S3674 KH2PO4 Sigma-Aldrich Cat# P0662-500G NADH Sigma-Aldrich Cat# N8129-500MG Medium 199 Gibco Cat#11150067 Liberase TM Research Grade Sigma-Aldrich Cat#05401127001 NativePAGE 1x sample buffer ThermoFisher Cat#BN2008 NativePAGE G-250 sample additive ThermoFisher Cat#BN2004 NativePAGE 3-12 %, Bis-Tris gels ThermoFisher Cat#BN1001 NuPAGE transfer buffer ThermoFisher Cat#NP0006 4-20% Tris-Glycine Novex Gels Invitrogen Cat#XP04205BOX PVDF Transfer Membranes, 0.45 mm ThermoFisher Cat#88518 Seahorse XF RPMI Media Seahorse Bioscience Cat# 103336 LCMS-grade Methanol Fisher Scientific Cat#A452SK-4 LCMS-grade Ethanol Sigma-Aldrich Cat#459828-1L LCMS-grade Hexane Honeywell Cat#34986-4X2.5L LCMS-grade Isopropanol Sigma-Aldrich Cat#34863 LCMS-grade Ammonium Hydroxide Sigma-Aldrich Cat#09859-250ML LCMS-grade Formic Acid Sigma-Aldrich Cat#F0507-1L LCMS-grade Water Sigma-Aldrich Cat#270733-4X4L LCMS-grade Chloroform Sigma-Aldrich Cat#366927 Deposited data RNA Sequencing SUB14409949 https://dataview.ncbi.nlm.nih.gov/object/ PRJNA1105324?reviewer= 8hnish5r1lsc23scrnjgi2tftv Metabolomics Workbench StudyID=ST003192 http://dev.metabolomicsworkbench. org:22222/data/DRCCMetadata.php?Mode= Study&StudyID=ST003192 Experimental models: Cell lines Human: 143B ATCC CRL-8303 Human: Caki-1 ATCC HTB-46 Human: DLD1 ATCC CCL-221 Human: HCT116 ATCC CCL-247 Human: HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Mouse: Wildtype- C57BL/6J The Jackson Laboratory RRID:IMSR_JAX:000664 (Continued on next page) ll OPEN ACCESS e2 Cell 188, 1–16.e1–e11, February 20, 2025 Please cite this article in press as: Valeros et al., Rhodoquinone carries electrons in the mammalian electron transport chain, Cell (2025), https://doi.org/10.1016/j.cell.2024.12.007 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Caenorhabditis elegans – Bristol, N2 strain Caenorhabditis Genetics Center N2 (wild type) Recombinant DNA Plasmid: pCW57.1-Luciferase backbone Shadle et al. Addgene Plasmid #99283 Plasmid: SDHB KO Spinelli et al. Addgene Plasmid #177981 Plasmid: RquA This paper Addgene Plasmid #229685 Software and algorithms TraceFinder 5.1 ThermoFisher https://www.thermofisher.com/us/en/home/ industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lcms/lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html BCL convert (version 3.8.2) Illumina https://emea.support.illumina.com/ sequencing/sequencing_software/ bcl-convert.html Samtools (version 1.16.1) Li et al.2 http://samtools.sourceforge.net/ IsoCorrectoR Bioconductor https://www.bioconductor.org/ packages/release/bioc/html/ IsoCorrectoR.html Other Seahorse XFe-96 Analyzer Seahorse Bioscience N/A Q-Exactive orbitrap mass spectrometer with an Ion Max source and HESI II probe ThermoFisher N/A Vanquish Horizon UHLPC system ThermoFisher N/A CentriVap Benchtop Vacuum Concentrator Labconco N/A CentriVap-105 Cold Trap Labconco N/A Supelco Ascentis Express C18 2.7 mm 15 cm x 2.1 mm Sigma Cat# 53825-U Luna 3 mm PFP(2) 100 Å, LC Column 100 x 2 mm Phenomenex Cat# 00D-4447-BB0 SeQuant ZIC-pHILIC 5um 150 x 2.1 mm analytical column Sigma Cat# 1504600001 Invivo2 1000 Hypoxia Chamber Baker N/A Cell strainer, 100 mm Corning CLS431752 Peristaltic pump Gilson Miniplus 3PVC tubing 2.06 mm diameter Sterile 50ml Conical tubes Corning 430829 BD Angiocath 20GA x1.16 in IV catheter BD 381134 moorLDI2-IR laser Doppler imaging system Moor Instruments N/A LSR-II sorter BD Biosciences N/A NEBNext Ultra II Directional RNA Library Prep Kit New England Biolabs Cat# E7765L NEBNext Multiplex Oligos for Illumina New England Biolabs cat# E6440S NEBNext Library Quant Kit for Illumina New England Biolabs Cat# E7630S P2 100 cycle kit Illumina Cat# 20046811 Pierce BCA Protein Assay Kits Life Technologies Cat# 23225 ll OPEN ACCESS Please cite this article in press as: Valeros et al., Rhodoquinone carries electrons in the mammalian electron transport chain, Cell (2025), https://doi.org/10.1016/j.cell.2024.12.007
RNA Sequencing:Article Title: Rhodoquinone carries electrons in the mammalian electron transport chain.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies COX4 Cell Signaling Technology Cat# 4850S; RRID:AB_2085424 FLAG Cell Signaling Technology Cat# 14793S; RRID AB_2572291 Total OXPHOS Rodent WB Antibody Cocktail Abcam Cat# ab110413; RRID: AB_2629281 HIF1a Cell Signaling Technology Cat# 36169S; RRID:AB_2799095 SDHA ProteinTech Cat# 14865-1-AP; RRID: 2881948 TOMM20 Santa Cruz Biotechnology Cat# sc-17764; RRID:AB_628381 GLUT1 Abcam Cat# ab115730; RRID:AB_10903230 NDUFS1 Cell Signaling Technology Cat#60153S CYC1 ProteinTech Cat#10242-1-AP ATP5A1 Cell Signaling Technology Cat#18023S ACTIN Cell Singaling Technology Cat# 4967S; RRID:AB_330288 Alexa Fluor 488 goat-anti-rabbit Abcam Cat# ab150077; RRID:AB_2630356 Alexa Fluor 647 goat-anti-mouse Abcam Cat# ab150113; RRID:AB_2576208 Secondary antibody- mouse Cell Signaling Technology Cat#7076S; RRID:AB_330924 Secondary antibody rabbit Cell Signaling Technology Cat#7074S; RRID:AB_2099233 Bacterial and virus strains AAV9.Tre3G-mCherry SV40 CB6 Tet-on 3G RBG University of Massachusetts Medical School Viral Vector Core https://www.umassmed.edu/ research/cores/viralvectorcore/ AAV9.Tre3G-RquA SV40 CB6 Tet-on 3G RBG University of Massachusetts Medical School Viral Vector Core https://www.umassmed.edu/ research/cores/viralvectorcore/ Biological samples Healthy Human Kidney Tissue UMCCTS Biorepository and Tissue Bank https://www.umassmed.edu/ tissue-and-tumor-bank/ Healthy Human Brain Tissue UMCCTS Biorepository and Tissue Bank https://www.umassmed.edu/ tissue-and-tumor-bank/ Healthy Human Muscle Tissue UMCCTS Biorepository and Tissue Bank https://www.umassmed.edu/ tissue-and-tumor-bank/ Ascaris suum worms A gift from Dr. Catherine Clark N/A Rhodospirillum rubrum ATCC 11170 Chemicals, peptides, and recombinant proteins CellROX orange dye Invitrogen Cat# C10443 N-Acetyl Cysteine Sigma Cat# A9165 Tert-butyl hydroperoxide Sigma Cat# 458139 Tetramethylrhodamine, Ethyl Ester Invitrogen Cat# T669 MitoSox Red Thermo Scientific Cat# M36008 13C5 15N2-glutamine Cambridge Isotope Labs Cat# CNLM-1275-H-0.5 13C4-aspartate Sigma Cat# 604852-250mg HBSS with Ca2+, Mg2+ Gibco Cat#14025092 HBSS without Ca2+, Mg2+ Gibco Cat#14175095 EDTA (0.5 M) Invitrogen Cat#15575020 DMEM low glucose Gibco Cat# 11885084 Dulbecco’s Phosphate Buffered Saline (DPBS) without calcium and magnesium Gibco Cat# 70011044 Penicillin-Streptomycin Solution Gibco Cat# 15070063 (Continued on next page) Cell 188, 1–16.e1–e11, February 20, 2025 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Trypsin Thermo Fisher Scientific Cat# 25200114 DMEM MEDIA Fisher Scientific Cat# 11-995-073 DMEM No Glutamine Media Fisher Scientific Cat# 10-313-039 cOmplete EDTA-free protease inhibitor Sigma-Aldrich Cat# 11836170001 RIPA Buffer EMD-Millipore Cat# 20-188 Isotone Buffer Beckman Coulter Cat# 8546719 BSA ThermoFisher Scientific Cat# 23227 TritonX-100 Sigma-Aldrich Cat# T9284 ProLong Gold Glass + NucBlue Invitrogen Cat# P36981 Mannitol Sigma-Aldrich Cat# M4125 Sucrose Sigma-Aldrich Cat# S0389 HEPES Fisher Scientific Cat# BP310-100 Fumaric Acid Sigma-Aldrich Cat# 47910 K-ADP Sigma-Aldrich Cat# A5285-100MG Succinic Acid Sigma-Aldrich Cat# S3674 KH2PO4 Sigma-Aldrich Cat# P0662-500G NADH Sigma-Aldrich Cat# N8129-500MG Medium 199 Gibco Cat#11150067 Liberase TM Research Grade Sigma-Aldrich Cat#05401127001 NativePAGE 1x sample buffer ThermoFisher Cat#BN2008 NativePAGE G-250 sample additive ThermoFisher Cat#BN2004 NativePAGE 3-12 %, Bis-Tris gels ThermoFisher Cat#BN1001 NuPAGE transfer buffer ThermoFisher Cat#NP0006 4-20% Tris-Glycine Novex Gels Invitrogen Cat#XP04205BOX PVDF Transfer Membranes, 0.45 mm ThermoFisher Cat#88518 Seahorse XF RPMI Media Seahorse Bioscience Cat# 103336 LCMS-grade Methanol Fisher Scientific Cat#A452SK-4 LCMS-grade Ethanol Sigma-Aldrich Cat#459828-1L LCMS-grade Hexane Honeywell Cat#34986-4X2.5L LCMS-grade Isopropanol Sigma-Aldrich Cat#34863 LCMS-grade Ammonium Hydroxide Sigma-Aldrich Cat#09859-250ML LCMS-grade Formic Acid Sigma-Aldrich Cat#F0507-1L LCMS-grade Water Sigma-Aldrich Cat#270733-4X4L LCMS-grade Chloroform Sigma-Aldrich Cat#366927 Deposited data RNA Sequencing SUB14409949 https://dataview.ncbi.nlm.nih.gov/object/ PRJNA1105324?reviewer= 8hnish5r1lsc23scrnjgi2tftv Metabolomics Workbench StudyID=ST003192 http://dev.metabolomicsworkbench. org:22222/data/DRCCMetadata.php?Mode= Study&StudyID=ST003192 Experimental models: Cell lines Human: 143B ATCC CRL-8303 Human: Caki-1 ATCC HTB-46 Human: DLD1 ATCC CCL-221 Human: HCT116 ATCC CCL-247 Human: HEK293T ATCC CRL-3216 Experimental models: Organisms/strains Mouse: Wildtype- C57BL/6J The Jackson Laboratory RRID:IMSR_JAX:000664 (Continued on next page) ll OPEN ACCESS e2 Cell 188, 1–16.e1–e11, February 20, 2025 Please cite this article in press as: Valeros et al., Rhodoquinone carries electrons in the mammalian electron transport chain, Cell (2025), https://doi.org/10.1016/j.cell.2024.12.007 Article .. REAGENT or RESOURCE SOURCE IDENTIFIER Caenorhabditis elegans – Bristol, N2 strain Caenorhabditis Genetics Center N2 (wild type) Recombinant DNA Plasmid: pCW57.1-Luciferase backbone Shadle et al. Addgene Plasmid #99283 Plasmid: SDHB KO Spinelli et al. Addgene Plasmid #177981 Plasmid: RquA This paper Addgene Plasmid #229685 Software and algorithms TraceFinder 5.1 ThermoFisher https://www.thermofisher.com/us/en/home/ industrial/mass-spectrometry/liquidchromatography-mass-spectrometry-lcms/lc-ms-software/lc-ms-data-acquisitionsoftware/tracefinder-software.html BCL convert (version 3.8.2) Illumina https://emea.support.illumina.com/ sequencing/sequencing_software/ bcl-convert.html Samtools (version 1.16.1) Li et al.2 http://samtools.sourceforge.net/ IsoCorrectoR Bioconductor https://www.bioconductor.org/ packages/release/bioc/html/ IsoCorrectoR.html Other Seahorse XFe-96 Analyzer Seahorse Bioscience N/A Q-Exactive orbitrap mass spectrometer with an Ion Max source and HESI II probe ThermoFisher N/A Vanquish Horizon UHLPC system ThermoFisher N/A CentriVap Benchtop Vacuum Concentrator Labconco N/A CentriVap-105 Cold Trap Labconco N/A Supelco Ascentis Express C18 2.7 mm 15 cm x 2.1 mm Sigma Cat# 53825-U Luna 3 mm PFP(2) 100 Å, LC Column 100 x 2 mm Phenomenex Cat# 00D-4447-BB0 SeQuant ZIC-pHILIC 5um 150 x 2.1 mm analytical column Sigma Cat# 1504600001 Invivo2 1000 Hypoxia Chamber Baker N/A Cell strainer, 100 mm Corning CLS431752 Peristaltic pump Gilson Miniplus 3PVC tubing 2.06 mm diameter Sterile 50ml Conical tubes Corning 430829 BD Angiocath 20GA x1.16 in IV catheter BD 381134 moorLDI2-IR laser Doppler imaging system Moor Instruments N/A LSR-II sorter BD Biosciences N/A NEBNext Ultra II Directional RNA Library Prep Kit New England Biolabs Cat# E7765L NEBNext Multiplex Oligos for Illumina New England Biolabs cat# E6440S NEBNext Library Quant Kit for Illumina New England Biolabs Cat# E7630S P2 100 cycle kit Illumina Cat# 20046811 Pierce BCA Protein Assay Kits Life Technologies Cat# 23225 ll OPEN ACCESS Please cite this article in press as: Valeros et al., Rhodoquinone carries electrons in the mammalian electron transport chain, Cell (2025), https://doi.org/10.1016/j.cell.2024.12.007
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