other:Article Title: Erythroid mitochondrial retention triggers myeloid-dependent type I interferon in human SLE.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Fiji/ImageJ Coloc2 plugin https://imagej.net/plugins/coloc-2 N/A FastQC https://www.bioinformatics. babraham.ac.uk/projects/fastqc/ RRID:SCR_014583 HISAT2 http://ccb.jhu.edu/software/hisat2/ index.shtml RRID:SCR_015530 Cutadapt https://cutadapt.readthedocs.io/ en/stable/ RRID:SCR_011841 Samtools https://www.htslib.org/ RRID:SCR_002105 HTSeq-count https://www.huber.embl.de/users/ anders/HTSeq/doc/count.html RRID:SCR_011867 DESeq2 https://bioconductor.org/packages/ release/bioc/html/DESeq2.html RRID:SCR_015687 Image Lab Software BioRad RRID:SCR_014210 Module transcript content http://websle.com/ N/A Proteome Discoverer Software Thermo Fisher RRID:SCR_014477 MaxQuant Software MaxQuant RRID:SCR_014485 Biorender https://biorender.com RRID:SCR_018361 Other Lymphoprep StemCell Technologies, Inc. Cat#07851 StemSpan Serum-Free Expansion Medium StemCell Technologies, Inc. Cat#09650 Human Peripheral Blood Plasma StemCell Technologies, Inc. Cat#70039 Lipids Cholesterol Rich Sigma–Aldrich Cat#L4646-100ML Human Serum Sigma–Aldrich Cat#H4522-100ML Macrophage-SFM Thermo Fisher Cat#12065074 HiPerFect Transfection Reagent QIAGEN Cat#301704 Alexa Fluor 647 Phalloidin Thermo Fisher Cat#A22287 Hoechst 33342 Solution Thermo Fisher Cat#62249 Human BD Fc Block BD Biosciences Cat#564219 MitoTracker Deep Red FM Thermo Fisher Cat#M22426 BD Cytofix/Cytoperm Fixation/Permeablization Kit BD Biosciences Cat#554714 ProLong Gold Antifade Mountant Thermo Fisher Cat#P10144 DNAzol Reagent Thermo Fisher Cat#10503027 Power SYBR Green PCR Master Mix Thermo Fisher Cat#4367659 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 Halt Protease and Phosphatase Inhibitor Cocktail Thermo Fisher Cat#78440 Lane Marker Reducing Sample Buffer Thermo Fisher Cat#39000 Corning Cell-Tak Cell and Tissue Adhesive Corning Cat#354240 ECL Western Blotting Detection Reagent Sigma–Aldrich Cat#iGERPN2209 Seahorse XF Base Medium Agilent Cat#102353-100 Clean-Blot IP Detection Reagent (HRP) Thermo Fisher Cat#21230 Tetramethylrhodamine Methyl Ester (TMRM) Thermo Fisher Cat#T668 ll
Article Title: Local hyperthermia therapy induces browning of white fat and treats obesity.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit-anti-HSF1 antibody CST Cat# 4356S; RRID: AB_10695463 Mouse-anti-PGC1a antibody Santa Cruz Cat# sc-517380; RRID: AB_2755043 Rabbit-anti-UCP1 antibody Abcam Cat# ab10983; RRID: AB_2241462 Mouse-anti-b-ACTIN antibody Sigma-Aldrich Cat# A3854; RRID: AB_262011 Rabbit-anti-HNRNPA2B1 antibody Abcam Cat# ab31645; RRID: AB_732978 Normal Rabbit IgG Antibody CST Cat# 2729; RRID: AB_1031062 IRDye 680RD Goat anti-Rabbit IgG (H +L) Secondary Antibody LI-COR Cat# 926-68071; RRID: AB_10956166 IRDye 800CW goat anti-mouse IgG (H+L) Secondary Antibody LI-COR Cat# 926-32210; RRID: AB_621842 Mouse anti-HSF1 antibody Santa Cruz Cat# sc-17757; RRID: AB_627753 Goat anti-rabbit Alexa 488 Thermo Fisher Cat# A11034; RRID: AB_2576217 Goat anti-mouse Alexa 594 Thermo Fisher Cat# A11032; RRID: AB_2534091 Bacterial and virus strains Adenovirus:Hnrnpa2b1 This paper N/A Adeno-associated virus: HSF1 active form This paper N/A Lentivirus: HSF1 wild-type (CC) This paper N/A Lentivirus: HSF1 Pro365Thr variant (AA) This paper N/A Adeno-associated virus: Hnrnpa2b1 This paper N/A Adeno-associated virus: HSF1 shRNA This paper N/A Adeno-associated virus: Hnrnpa2b1 shRNA This paper N/A Chemicals, peptides, and recombinant proteins PDA-PEG hydrogel (Wang et al., 2017) N/A RNAiso Plus Takara Cat# 9108 PrimeScript RT Master Mix Takara Cat# RR036A Hieff qPCR SYBR Green Master Mix (Low Rox Plus) Yeasen Cat# 11202ES03 DMEM, high glucose, with L-glutamine Gibco Cat# 11995065 Fetal Bovine Serum Gibco Cat# 10270 Forskolin Sigma-Aldrich Cat# F6886 CL 316,243 Sigma-Aldrich Cat# 5976 Dexamethasone Sigma-Aldrich Cat# D4902 Insulin solution Sigma-Aldrich Cat# I9278 Indomethacin Sigma-Aldrich Cat# I8280 3-Isobutyl-1-methylxanthine (IBMX) Sigma-Aldrich Cat# I5879 Lipofectamine2000 Transfection Reagent Thermo Fisher Cat# 11668030 Oil Red O Sigma-Aldrich Cat# O0625 Formalin solution, neutral buffered, 10% Sigma-Aldrich Cat# HT501128-4L RIPA Lysis and Extraction Buffer Thermo Fisher Cat# 89900 Phenyl methane sulfonyl fluoride (PMSF) Thermo Fisher Cat# 36978 Protease inhibitors Thermo Fisher Cat# A32963 Rosiglitazone Sigma-Aldrich Cat# R2408 T3 (3,3’,5-Triiodo-L-thyronine) Sigma-Aldrich Cat# T2877 D-glucose Sigma-Aldrich Cat# GT528 (Continued on next page) Cell 185, 949–966.e1–e8, March 17, 2022 e1
Article Title: 1-deoxysphingolipids bind to COUP-TF to modulate lymphatic and cardiac cell development.
Article Snippet: Reagent or resource Source Identifier Express Five SFM media Gibco Cat#10486025 Expi293 medium Thermo Fisher Cat#A1435101 FreeStyle F17 expression medium Thermo Fisher Cat#A1383502 KSR medium Thermo Fisher Cat#10828010 mTeSR1 media Stem Cell Technologies Cat#85850 OptiMEM media Thermo Fisher Cat#31985088 RPMI-1640 Gibco Cat#11875-093 StemFlex medium Thermo Fisher Cat#A3349401 B-27 Thermo Fisher Cat#17504044 BSA fatty acid free Sigma-Aldrich Cat#A6003 Fetal Bovine Serum Sigma-Aldrich Cat#F2442 glutamax Thermo Fisher Cat#35050061 L-Glutamine Gibco Cat#25030-081 Insulin-Transferrin-Selenium (ITS-A) Thermo Fisher Cat#51300044 Insulin-free B-27 Thermo Fisher Cat#A1895601 N2 supplement Thermo Fisher Cat#17502001 Pen/strep Gibco Cat#15140-122 Matrigel BD Biosciences Cat#354277 Doxycycline Sigma-Aldrich Cat#D9891 4-hydroxytamoxifen Sigma Cat#H6278 Geneticin (G418) Thermo Fisher Cat#10131035 Hygromycin Invitrogen Cat#10687-010 Puromycin Sigma-Aldrich Cat#P8833 Blastocydin Thermo Fisher Cat#A1113902 Myriocin Sigma-Aldrich Cat#476300 4-Methoxy-1-Naphthol Sigma-Aldrich Cat#174556 Rock inhibitor Y-27632 Tocris Cat#1254 IWP2 Tocris Cat#3533 CHIR99021 Tocris Cat#4423 Accutase Stem Cell Technologies Cat # 07920 Collagenase D Sigma-Aldrich Cat#11088882001 DNase I Sigma-Aldrich Cat#D4263 Dispase Stem Cell Technologies Cat#07913 TripLE-Express Gibco Cat#12605-010 lipofectamine 3000 Thermo Fisher Cat#L3000015 Cellfectin II reagent Invitrogen Cat#10362100 Polyethyleneimine (PEI) Polyscience Cat#24765 4*Laemmli sample buffer Bio-Rad Cat#161-0747 Ca++ MgCl2 ++ containing DPBS Gibco Cat#14040-117 Elution buffer Sigma-Aldrich Cat#G4251 fixation/permeabilization buffer Thermo Fisher Cat#00-5523-00 HBS-P+ 10x Fisher Scientific Cat#50-105-5346 RIPA lysis and extraction buffer Thermo Fisher Cat#89900 TURBO DNA-free kit Thermo Fisher Cat#AM1907 Ribo-Zero Gold Kit (Human/Mouse/Rat probe) Illumina Cat#MRZH11124 NEBNext Ultra RNA Library Prep Kit Illumina Cat# E7770 Qubit 2.0 Fluorometer RNA assay Invitrogen Cat#Q32855 KAPA qPCR assay KAPA Biosystems Cat#KK4601 SuperScript II Reverse Transcriptase Thermo Fisher Cat#18064014 iTaq Universal SYBR Green Supermix Bio-Rad Cat#M7128 (Continued on next page) Developmental Cell 56, 3128–3145.e1–e15, November 22, 2021 e4
Article Title: TAK1 Prevents Endothelial Apoptosis and Maintains Vascular Integrity.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Ammonium Pyrrolidinedithiocarbamate (PDTC) Sigma-Aldrich Cat#P8765 Caffeic Acid Phenethyl Ester (CAPE) Tokyo Chemical Industry Cat#P2088 (5Z)-7-Oxozeaenol Enzo Life Science Cat# ALX-380-267-M005 Z-VAD-FMK MBL Cat#4800-520 Necrostatin-1 Focus Biomolecules Cat#10-1162 4% Paraformaldehyde Phosphate Buffer Solution Wako Cat#161-20141 OCT compound Sakura Finetek Japn Cat#18921 Sodium Citrate Buffer (0.1M Citric Acid Monohydrate: 0.1M Trisodium Citrate Dihydrate:DW=9:41:450) Wako Cat#035-03495 Cat#191-01785 3,3’-Diaminobenzidine, Tetrahydrochloride (DAB) Wako Cat#349-00903 Nickel (II) Chloride Hexahydrate (NiCl2$6H2O) Wako Cat#147-01042 Fluorescein Isothiocyanate–Dextran Mol Wt 70,000 Sigma-Aldrich Cat#FD70S Fluorescein Isothiocyanate–Dextran Mol Wt 2,000,000 Sigma-Aldrich Cat#FD2000S Paraformaldehyde Powder Nacalai Tesque Cat#26126-25 Glutaraldehyde Electron Microscopy Science Cat#16300 Sucrose Nacalai Tesque Cat#30404-45 Osmium Tetroxide Electron Microscopy Science Cat#19152 Potassium Ferrocyanide Trihydrate Nacalai Tesque Cat#28608-42 Epoxy Resin TAAB Laboratories Equipment Cat#T024 Uranyl Acetate Merck Cat#8473 Lead Stain Solution Sigma-Aldrich Japan Cat#18-0875-2-25ML-J Vandetanib LC Laboratories Cat#V-9402 Axitinib Selleck Chemicals Cat#S1005 Dimethyl Sulfoxide (DMSO) Nacalai Tesque Cat#13445 Poly(ethylene glycol) BioUltra, 400 (PEG-400) Sigma-Aldrich Cat#91893 Clodronate Liposome Katayama Chemical Cat#166-0432 RIPA Lysis and Extraction Buffer Thermo Fisher Cat#89900 2-Amino-2-Hydroxymethyl-1,3-Propanediol (Tris) Wako Cat#207-06275 Sodium Lauryl Sulfate (SDS) Nacalai Tesque Cat#31607-65 Glycerol Wako Cat#075-00616 Bromophenol Blue Wako Cat#021-02911 Critical Commercial Assays PrimeScriptTM RT Reagent Kit (Perfect Real Time) Takara Cat#RR037A TB GreenTM Premix Ex TaqTM II Takara Cat#RR820A RNeasy Plus Mini Kit Qiagen Cat#74134 Hemoglobin Assay Kit BioChain Cat#Z5030026 in situ Apoptosis Detection Kit Takara Cat#MK500 Live/Dead Cell Staining Kit II PromoCell Cat#PK-CA707-30002 Vectastain Elite ABC Kit Vector Laboratories Cat#PK-6100 HypoxyprobeTM-1 Kit Hypoxyprobe Cat#HP1-100 Deposited Data RNAseq This paper GEO:GSE115190 Experimental Models: Cell Lines OP9 Riken RCB1124 LLC Riken RCB0558 EL-4 JCRB Cell Bank JCRB1350 bEnd.3 ATCC ATCC CRL-2299
Lysis:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq. ..
Article Title: Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads mRNA DIRECT Kit Life Technologies Cat# 61012 Pierce Anti-HA Magnetic Beads ThermoFisher Scientific Cat# 88837 Anti-FLAG M2 Magnetic Beads Sigma Aldrich Cat# M8823 Pierce Anti-c-Myc Magnetic Beads ThermoFisher Scientific Cat# 88842 Dulbecco’s Modified Eagle Medium (DMEM) - high glucose, pyruvate, L-glutamine Thermo Fisher Cat# 11995073 Fetal bovine serum (FBS) Thermo Fisher Cat# 26140079 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher Cat# 13778075 L-Histidinol dihydrochloride Sigma Aldrich Cat# H6647 Anisomycin from Streptomyces griseolus Sigma Aldrich Cat# A9789 RIPA Lysis and Extraction Buffer Thermo Fisher Cat# 89901 Sodium phosphate dibasic Sigma Aldrich Cat# 71640 b-glycerophosphate Sigma Aldrich Cat# G9422 Benzonase nuclease Sigma Aldrich Cat# E1014 TCEP GoldBio Cat# TCEP25 Halt Protease and Phosphatase Inhibitor Cocktail (100X) – EDTA free Thermo Fisher Cat# 78440 10x Tris/Glycine/SDS running buffer Bio-rad Cat# 1610732 Blotto, non-fat dry milk Santa Cruz Biotechnology Cat# sc-2324 Emetine dihydrochloride Sigma Aldrich Cat# 324693 Sodium chloride (NaCl) Sigma Aldrich Cat# S9888 NP-40 Alternative, PROTEIN GRADE Detergent, 10% Solution, Sterile-Filtered Millipore Sigma Cat# 492018 1M Tris-HCl pH 7.0 Thermo Fisher Cat# AM9850G Sucrose Sigma Aldrich Cat# S7903 PBS pH 7.4 Thermo Fisher Cat# 10010049 Triton X-100 Sigma Aldrich Cat# T9284 EDTA (0.5 M), pH 8.0, RNase-free Thermo Fisher Cat# AM9260G TRIzol Reagent Thermo Fisher Cat# 15596026 Chloroform Sigma Cat# C2432 GlycoBlue Coprecipitant (15 mg/mL) Thermo Fisher Cat# AM9515 2-Propanol (HPLC), Fisher Chemical Fisher Scientific Cat# A451SK-4 Ethanol 200 Prf, 24x1 Gl Pint Pharmco Cat# 111000200CSPT Nuclease-Free Water (not DEPC-Treated) Thermo Fisher Cat# 4387936 TURBO DNase (2 U/mL) Thermo Fisher Cat# AM2238 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Thermo Fisher Cat# AM9722 Sodium Acetate (3 M), pH 5.5, RNase-free Thermo Fisher Cat# AM9740 iScript cDNA Synthesis Kit Bio-rad Cat# 1708891 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 4–20% Criterion TGX Precast Midi Protein Gel, 26 well, 15 ml Bio-rad Cat# 5671095 Trans-Blot Turbo RTA Midi 0.2 mm PVDF Transfer Kit Bio-rad Cat# 1704273 Deposited data Raw and analyzed RNAseq data This paper GSE255383 Custom python script This paper Zenodo: https://zenodo.org/ records/11190462 cryo-EM structural maps and molecular models This paper EMD-50170, EMD-50171, EMD-50259 and PDB: 9F9S (Continued on next page) e2 Molecular Cell 84, 1–18.e1–e9, December 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw gel image files This paper Mendeley Data: https://doi.org/ 10.17632/zj4x3426hv.2 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Experimental models: Organisms/strains BY4741 (MATa his3D1 leu2D0 met15D0 ura3D0) Dharmacon lab N/A mbf1D 319 (BY4741; mbf1D::NAT) This Study N/A gcn2D 619 (BY4741; gcn2D::KAN) Horizon N/A gcn4D (BY4741; gcn4D::KAN) Horizon N/A 703(MatA, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 705(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 923(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-HA) This Study N/A 1080 (matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-DN26-HA) This Study N/A 880 (MatA; GCN4-3XFLAG:KAN, ARG4-myc:His, PCL5D::Leu) This Study N/A 958 (MatA, GCN4-3XFLAG:KAN, ARG4-myc:His, Pho85D:Leu) This Study N/A 725(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1) This Study N/A 874 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1 R89G) This Study N/A 355 (MatA; Mbf1-6xGly-FLAG-mCherry His3) This Study N/A 992 (MatA, Mbf1-R89G-6xGly-FLAG -mCherry::HIS3) This Study N/A 1292 (MatA;Mbf1-mcherry NES::His) This Study N/A Long GCN4 1289 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Long GCN4 FLAG:Kan) This Study N/A Short GCN4 1290 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Short GCN4 FLAG:Kan) This Study N/A Mbf1 WT, GCN4_Short 1316 (BY4741, TBP1-myc::HIS3, GCN4_FLAG_ Short) This Study N/A Mbf1D, GCN4_Short 1318 (BY4741, TBP1-myc::HIS3, MBF1D::NAT, GCN4 Short) This Study N/A 1320 (BY4741, TBP1-myc13::HIS3, MBF1D::NAT, EKD-HA-Mbf1::Met 1; GCN4 Short) This Study N/A 1299 (MatA; GCN4-HA:Kan) This Study N/A 1301(matA; mbf1D::NAT, GCN4-HA:Kan) This Study N/A 1302 (matA; Mbf1:mCherry, GCN4-HA:Kan) This Study N/A 1304 (MatA, Mbf1-R89G-mCherry::HIS3, GCN4-HA:Kan) This Study N/A 1307 (MatA;Mbf1-mcherry NES::His, GCN4-HA:Kan) This Study N/A 690 (MatA, GCN4-3XFLAG:KAN) This Study N/A 693 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN) This Study N/A 919 (MatA, GCN4-3XFLAG:KAN 3, rps3-K108E:His) This Study N/A 1337 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E,L113A) This Study N/A 1338 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E, L113A, G121A) This Study N/A (Continued on next page) Molecular Cell 84, 1–18.e1–e9, December 5, 2024 e3
Article Title: Mitochondrial calcium uptake declines during aging and is directly activated by oleuropein to boost energy metabolism and skeletal muscle performance.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal anti-MCU Cell Signaling Technology Cat#14997; RRID:AB_2721812 Rabbit polyclonal anti-MCUR Booster Cat#A08547-1 Mousse monoclonal anti-TOM20 (F-10) Santa Cruz Cat#sc-17764; RRID:AB_628381 Rabbit polyclonal anti-MICU1 Sigma Aldrich Cat#HPA037479; RRID:AB_2675495 Rabbit polyclonal anti-PDH Cell Signaling Technology Cat#2784; RRID:AB_2162928 Rabbit polyclonal anti-PDH (phospho S293) Abcam Cat#ab92696, RRID:AB_10711672 Rabbit monoclonal anti-TOM20 (D8T4N) Cell Signaling Technology Cat#42406, RRID:AB_2687663 Mouse monoclonal anti-GRP 75 (D-9) Santa Cruz Biotechnology Cat#sc-133137, RRID:AB_2120468 Anti-Rabbit Detection Module ProteinSimple Cat#DM-001 Rabbit polyclonal anti_MCUR1 Cell Signaling Technology Cat#13706S; RRID:AB_2749813 Chemicals, peptides, and recombinant proteins ATP Sigma Aldrich Cat#A9187; CAS #: 74804-12-9 Histamine Sigma Aldrich Cat#H7125; CAS #: 51-45-6 Caffeine Sigma Aldrich Cat#C0750; CAS #: 58-08-2 Epibatidine Sigma Aldrich Cat#E1145;CAS #: 16637-43-2 Oleuropein Extrasynthese Cat#0228S; CAS #:32619-42-4 Oleuropein Aglycone Toronto Research Chemicals Cat#O532945; CAS #:31773-95-2 Hydroxytyrosol Extrasynthese Cat#4999S; CAS #: 10597-60-1 Oligomycin Sigma Aldrich Cat#75351 FCCP Sigma Aldrich Cat#C2920 Rotenone Sigma Aldrich Cat#45656 AntimycinA Sigma Aldrich Cat#A8674 Calcein AM Sigma Aldrich Cat#C0875; CAS#: 154071-48-4 Human Fibronectin Corning Cat#356008 PhosSTOP Merck Cat#4906845001 Fura-2, AM, cell permeant Thermo Fisher Cat#F1221 Gibco MEM, GlutaMAX Supplement Thermo Fisher Cat#41090 GOOD fetal bovine serum - 500 ml PanBiotech Cat#P40-37500 Penicillin-Streptomycin (5,000 U/mL) Thermo Fisher Cat#15070063 Gibco DMEM, high glucose, GlutaMAX Supplement, pyruvate Thermo Fisher Cat#31966 Gibco DMEM, high glucose, HEPES Thermo Fisher Cat#42430 Complete, Mini EDTA-free Protease Inhibitor Cocktail Merck Cat#11836170001 RIPA lysis and extraction buffer Thermo Fisher Cat89901 Non-Fat Dry Milk BioRad Cat#100-04504 PBS 1X PH 7.4 Thermo Fisher Cat# 10010023 Skeletal Muscle Cell Growth Medium Zen-Bio Cat#SKM-M medium Dulbecco’s Modified Eagle Medium F-12 Nutrient Mixture (DMEM/F-12 (1:1) (1x) +GlutaMAX) Thermo Fisher Cat#31331028 FBS Thermo Fisher Cat#10270106 Heat-inactivated Horse Serum Thermo Fisher Cat#26050088 PBS Thermo Fisher Cat#10010023 Tyrode’s salts Sigma Aldrich Cat#T2145 Dulbecco0s Modified Eagle0s Medium Sigma Aldrich Cat#D5030 (Continued on next page) e1 Cell Metabolism 37, 1–19.e1–e11, February 4, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRIzol Reagent Invitrogen, Thermo Fischer Cat#15596026 SuperScript III CellsDirect cDNA Synthesis Kit Invitrogen, Thermo Fisher Cat# 18080300 Master Mix PowerTrack SYBR Green Thermo Fisher Cat# A46109 Coelenterazine n Biotium 10110 CAS #: 55779-48-1 Digitonin Sigma Aldrich D5628; CAS#: 11024-24-1 N-Benzyl-p-toluenesulfonaMide Sigma Aldrich BL3H160B8B26; CAS#: 1576-37-0 Sodium Chloride Sigma Aldrich CAS#: 7647-14-5 Magnesium Chloride Sigma Aldrich CAS#:7791-18-6 HEPES Sigma Aldrich CAS#: 7365-45-9 Glucose Sigma Aldrich CAS#: 50-99-7 Calcium Chloride Sigma Aldrich CAS#: 10043-52-4 Potassium Chloride Sigma Aldrich CAS#: 7447-40-7 Thapsigargin Sigma Aldrich T9033; CAS#: 67526-95-8 EGTA Sigma Aldrich E3889; CAS#: 67-42-5 Collagenase A Roche Cat#COLLA-RO Kaempferol Sigma Aldrich CAS#: 5020-18-3 Olive leaf extract standardized with 40% oleuropein (OLE) Bioactor CAS#: 8060-29-5 JC-10 dye Enzo Lifesciences Cat#ENZ-52305 Hoestch Invitrogen Cat#H33342 Tris(2-carboxyethyl)phosphine (TCEP) Sigma Aldrich Cat#: C4706; CAS#: 51805-45-9 Critical commercial assays BCA protein assay kit Pierce Thermo Fisher Cat#23227 12-230kD Sally Sue Separation Module Protein Simple Cat#SM-S001 Pyruvate dehydrogenase (PDH) Enzyme Activity Microplate Assay Kit (ab109902) Abcam Cat#ab109920 NuPAGE 4 to 12%, Bis-Tris, 1.0–1.5 mm, Mini Protein Gels Invitrogen Cat#NP0336BOX Nitrocellulose membranes BioRad Cat#1704158 12-230 kDa Separation Module Protein Simple Cat#SM-S001 Incucyte Annexin V Green Dye Sartorius Cat#4642 Deposited data RNA-sequencing data Gene Expression Omnibus GSE11016 Source data This paper Data S1 Source Data Experimental models: Cell lines Human Skeletal Muscle Cells, Donor 7, Lot# 655307 Lonza Cat#LZ-CC-2580 Human Skeletal Muscle Cells, Donor 29, Lot # 639629 Lonza Cat#LZ-CC-2580 Human Skeletal Muscle Cells, Donor 215, Lot # SKM070512A Amsbio Cat#SKB-F Human Skeletal Muscle Cells, Donor 712, Lot # SKM062712B Amsbio Cat#SKB-F Human Skeletal Muscle Cells, Donor 211, Lot # SK120211 Amsbio Cat#SKB-F Human Skeletal Muscle Cells, Lot# P01064-69M Cook Myosite Cat#SK-1111 (Continued on next page) Cell Metabolism 37, 1–19.e1–e11, February 4, 2025 e2
Article Title: Hyperpolarization-activated cyclic nucleotide-gated cation channel 3 promotes HCC development in a female-biased manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti Mac-2 (Galectin-3) Cedarlane Labs Cat#CL8942AP; RRID:AB_10060357 Anti IL-6 Santa Cruz Biotechnology Cat#sc-1265; RRID:AB_2127470 Anti Na+/K+-ATPases Santa Cruz Biotechnology Cat#sc-48345; RRID:AB_626712 Anti b-Actin Santa Cruz Biotechnology Cat#sc-47778; RRID:AB_626632 Anti HCN3 Abcam Cat#ab84818; RRID:AB_1861081 Anti HCN3 Alomone Labs Cat#APC-057; RRID:AB_2039904 Anti HCN3 Thermo Fisher Cat#MA3-902; RRID:AB_2115028 Anti HA-tag Cell Signaling Technology Cat#3724; RRID:AB_1549585 Anti AFP Proteintech Cat#14550-1-AP; RRID:AB_2223933 Anti Albumin Proteintech Cat#16475-1-AP; RRID:AB_2242567 Anti Ki-67 Millipore-Sigma Cat#AB9260; RRID:AB_2142366 Anti NCOA5 Bethyl Cat#A300-790A; RRID:AB_2151214 Anti TIP30 Xiao lab (Ito et al.)28 N/A Anti PR Cell Signaling Technology Cat#8757; RRID:AB_2797144 LICOR IRDye 800CW secondary antibodies LICOR Cat#923–32213, 926–32214, 926-32211 LICOR IRDye 680RD secondary antibodies LICOR Cat#926–68072, 925–68074, 925-68076 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat#EC0112 E. coli TOP10 Thermo Fisher Cat#C404010 Biological samples Human HCC tissue array TissueArray.Com LLC Cat#LV1505a Chemicals, peptides, and recombinant proteins RIPA Lysis and Extraction Buffer Thermo Fisher Cat89900 Formalin solution, neutral buffered, 10% Sigma-Aldrich Cat#HT501128 TRIzol Reagent Thermo Fisher Cat#15596026 PowerUp SYBR Green reagent Thermo Fisher Cat#A25742 Lipofectamine 3000 Thermo Fisher Cat#L3000015 QuickExtract DNA Extraction Solution Lucigen Cat#QE0905T SuperScript IV First-Strand Synthesis System Thermo Fisher Cat#18091050 (R)-MG132 Cayman Chemical Cat#13697 ZD7288 Tocris Cat#1000 Polyethyleneimine Polysciences, Inc. Cat#23966-1 Puromycin dihydrochloride Thermo Fisher Cat#A1113803 Nitrotetrazolium Blue chloride Sigma-Aldrich Cat#N6639 Laemmli Sample Buffer BIO-RAD Cat#1610747 Thapsigargin Millipore-Sigma Cat#586005 Critical commercial assays Biorad Protein Assay BIO-RAD Cat#5000006 VECTASTAIN Elite ABC-HRP system Vector Laboratories Cat#PK-6101, PK-6102 Cell Counting Kit-8 Dojindo Cat#CK04 Alanine Transaminase Colorimetric Activity Assay Cayman Chemical Cat#700260 Mouse AFP Quantikine ELISA Kit R&D Systems Cat#MAFP00 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Mouse IL-6 ELISA Kit Proteintech Cat#KE10007 (Continued on next page) 16 Cell Reports 42, 113157, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Raw and processed RNA sequencing data This study GEO: GSE228531 Experimental models: Cell lines NIH/3T3 ATCC Cat#CRL-1658; RRID:CVCL_0594 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 PLC/PRF/5 ATCC Cat#CRL-8024; RRID:CVCL_0485 SNU-387 ATCC Cat#CRL-2237; RRID:CVCL_0250 Experimental models: Organisms/strains Mouse: Ncoa5+/ BALB/c Xiao lab (Gao et al.)8 N/A Mouse: Tip30+/ BALB/c Xiao lab (Ito et al.)28 N/A Mouse: Ncoa5+/ Tip30+/ BALB/c This study N/A Mouse: Hcn3 / C57BL/6 Biel lab (Fenske et al.)49 N/A Mouse: Hcn3 / BALB/c This study N/A Mouse: BALB/cJ Jackson Laboratory Cat#000651; RRID:IMSR_JAX:000651 Oligonucleotides See Table S4 for PCR primer sequences N/A N/A Recombinant DNA HCN3 CDS containing plasmid DF/HCC DNA Resource Core HsCD00348243 pSin-EF2 vector Yu et al.58 Addgene Cat#16579; RRID:Addgene_16579 pSpCas9(BB)-2A-Puro (PX459) V2.0 Ran et al.59 Addgene Cat#62988; RRID:Addgene_62988 pCMV delta R8.2 Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12263; RRID:Addgene_12263 pMD2.G Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12259; RRID:Addgene_12259 pGL2-Basic Promega N/A pcDNA3-TIP30 Xiao lab (Zhang et al.)60 N/A pcDNA3-hPR-A Su et al.61 Addgene Cat#89119; RRID:Addgene_189119 pcDNA3-PRB Su et al.61 Addgene Cat#89130; RRID:Addgene_89130 pRL Promega N/A pT3-EF1a-c-MYC Chen lab (Mendez-Lucas et al.)48 N/A pT3-EF1a-MCL1 Chen lab (Mendez-Lucas et al.)48 N/A pCMV/SB Chen lab (Mendez-Lucas et al.)48 N/A pSin-EF2-HCN3HA This study N/A PX459V2-HCN3-T1 This study N/A PX459V2-HCN3-T2 This study N/A pGL2-promoHCN3 This study N/A pT3-EF1a empty vector This study N/A pT3-EF1a-HCN3HA This study N/A Software and algorithms UCSC Xena Goldman et al.62 https://xena.ucsc.edu/ cBioportal Cerami et al.63; Gao et al.64 https://www.cbioportal.org/ STRING Szklarczyk et al.65 https://string-db.org/ Gene Set Enrichment Analysis Subramanian et al.51 https://www.gsea-msigdb.org/gsea/index.jsp ssGSEA Barbie et al.50 https://gsea-msigdb.github.io/ssGSEA- gpmodule/v10/index.html Trimmomatic Bolger et al.66 http://www.usadellab.org/cms/ ?page=trimmomatic STAR Dobin et al.67 https://github.com/alexdobin/STAR DESeq2 Love et al.68 https://bioconductor.org/packages/release/ bioc/html/DESeq2.html (Continued on next page) Cell Reports 42, 113157, October 31, 2023 17
Extraction:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq. ..
Article Title: Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads mRNA DIRECT Kit Life Technologies Cat# 61012 Pierce Anti-HA Magnetic Beads ThermoFisher Scientific Cat# 88837 Anti-FLAG M2 Magnetic Beads Sigma Aldrich Cat# M8823 Pierce Anti-c-Myc Magnetic Beads ThermoFisher Scientific Cat# 88842 Dulbecco’s Modified Eagle Medium (DMEM) - high glucose, pyruvate, L-glutamine Thermo Fisher Cat# 11995073 Fetal bovine serum (FBS) Thermo Fisher Cat# 26140079 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher Cat# 13778075 L-Histidinol dihydrochloride Sigma Aldrich Cat# H6647 Anisomycin from Streptomyces griseolus Sigma Aldrich Cat# A9789 RIPA Lysis and Extraction Buffer Thermo Fisher Cat# 89901 Sodium phosphate dibasic Sigma Aldrich Cat# 71640 b-glycerophosphate Sigma Aldrich Cat# G9422 Benzonase nuclease Sigma Aldrich Cat# E1014 TCEP GoldBio Cat# TCEP25 Halt Protease and Phosphatase Inhibitor Cocktail (100X) – EDTA free Thermo Fisher Cat# 78440 10x Tris/Glycine/SDS running buffer Bio-rad Cat# 1610732 Blotto, non-fat dry milk Santa Cruz Biotechnology Cat# sc-2324 Emetine dihydrochloride Sigma Aldrich Cat# 324693 Sodium chloride (NaCl) Sigma Aldrich Cat# S9888 NP-40 Alternative, PROTEIN GRADE Detergent, 10% Solution, Sterile-Filtered Millipore Sigma Cat# 492018 1M Tris-HCl pH 7.0 Thermo Fisher Cat# AM9850G Sucrose Sigma Aldrich Cat# S7903 PBS pH 7.4 Thermo Fisher Cat# 10010049 Triton X-100 Sigma Aldrich Cat# T9284 EDTA (0.5 M), pH 8.0, RNase-free Thermo Fisher Cat# AM9260G TRIzol Reagent Thermo Fisher Cat# 15596026 Chloroform Sigma Cat# C2432 GlycoBlue Coprecipitant (15 mg/mL) Thermo Fisher Cat# AM9515 2-Propanol (HPLC), Fisher Chemical Fisher Scientific Cat# A451SK-4 Ethanol 200 Prf, 24x1 Gl Pint Pharmco Cat# 111000200CSPT Nuclease-Free Water (not DEPC-Treated) Thermo Fisher Cat# 4387936 TURBO DNase (2 U/mL) Thermo Fisher Cat# AM2238 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Thermo Fisher Cat# AM9722 Sodium Acetate (3 M), pH 5.5, RNase-free Thermo Fisher Cat# AM9740 iScript cDNA Synthesis Kit Bio-rad Cat# 1708891 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 4–20% Criterion TGX Precast Midi Protein Gel, 26 well, 15 ml Bio-rad Cat# 5671095 Trans-Blot Turbo RTA Midi 0.2 mm PVDF Transfer Kit Bio-rad Cat# 1704273 Deposited data Raw and analyzed RNAseq data This paper GSE255383 Custom python script This paper Zenodo: https://zenodo.org/ records/11190462 cryo-EM structural maps and molecular models This paper EMD-50170, EMD-50171, EMD-50259 and PDB: 9F9S (Continued on next page) e2 Molecular Cell 84, 1–18.e1–e9, December 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw gel image files This paper Mendeley Data: https://doi.org/ 10.17632/zj4x3426hv.2 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Experimental models: Organisms/strains BY4741 (MATa his3D1 leu2D0 met15D0 ura3D0) Dharmacon lab N/A mbf1D 319 (BY4741; mbf1D::NAT) This Study N/A gcn2D 619 (BY4741; gcn2D::KAN) Horizon N/A gcn4D (BY4741; gcn4D::KAN) Horizon N/A 703(MatA, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 705(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 923(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-HA) This Study N/A 1080 (matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-DN26-HA) This Study N/A 880 (MatA; GCN4-3XFLAG:KAN, ARG4-myc:His, PCL5D::Leu) This Study N/A 958 (MatA, GCN4-3XFLAG:KAN, ARG4-myc:His, Pho85D:Leu) This Study N/A 725(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1) This Study N/A 874 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1 R89G) This Study N/A 355 (MatA; Mbf1-6xGly-FLAG-mCherry His3) This Study N/A 992 (MatA, Mbf1-R89G-6xGly-FLAG -mCherry::HIS3) This Study N/A 1292 (MatA;Mbf1-mcherry NES::His) This Study N/A Long GCN4 1289 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Long GCN4 FLAG:Kan) This Study N/A Short GCN4 1290 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Short GCN4 FLAG:Kan) This Study N/A Mbf1 WT, GCN4_Short 1316 (BY4741, TBP1-myc::HIS3, GCN4_FLAG_ Short) This Study N/A Mbf1D, GCN4_Short 1318 (BY4741, TBP1-myc::HIS3, MBF1D::NAT, GCN4 Short) This Study N/A 1320 (BY4741, TBP1-myc13::HIS3, MBF1D::NAT, EKD-HA-Mbf1::Met 1; GCN4 Short) This Study N/A 1299 (MatA; GCN4-HA:Kan) This Study N/A 1301(matA; mbf1D::NAT, GCN4-HA:Kan) This Study N/A 1302 (matA; Mbf1:mCherry, GCN4-HA:Kan) This Study N/A 1304 (MatA, Mbf1-R89G-mCherry::HIS3, GCN4-HA:Kan) This Study N/A 1307 (MatA;Mbf1-mcherry NES::His, GCN4-HA:Kan) This Study N/A 690 (MatA, GCN4-3XFLAG:KAN) This Study N/A 693 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN) This Study N/A 919 (MatA, GCN4-3XFLAG:KAN 3, rps3-K108E:His) This Study N/A 1337 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E,L113A) This Study N/A 1338 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E, L113A, G121A) This Study N/A (Continued on next page) Molecular Cell 84, 1–18.e1–e9, December 5, 2024 e3
Article Title: Mitochondrial calcium uptake declines during aging and is directly activated by oleuropein to boost energy metabolism and skeletal muscle performance.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal anti-MCU Cell Signaling Technology Cat#14997; RRID:AB_2721812 Rabbit polyclonal anti-MCUR Booster Cat#A08547-1 Mousse monoclonal anti-TOM20 (F-10) Santa Cruz Cat#sc-17764; RRID:AB_628381 Rabbit polyclonal anti-MICU1 Sigma Aldrich Cat#HPA037479; RRID:AB_2675495 Rabbit polyclonal anti-PDH Cell Signaling Technology Cat#2784; RRID:AB_2162928 Rabbit polyclonal anti-PDH (phospho S293) Abcam Cat#ab92696, RRID:AB_10711672 Rabbit monoclonal anti-TOM20 (D8T4N) Cell Signaling Technology Cat#42406, RRID:AB_2687663 Mouse monoclonal anti-GRP 75 (D-9) Santa Cruz Biotechnology Cat#sc-133137, RRID:AB_2120468 Anti-Rabbit Detection Module ProteinSimple Cat#DM-001 Rabbit polyclonal anti_MCUR1 Cell Signaling Technology Cat#13706S; RRID:AB_2749813 Chemicals, peptides, and recombinant proteins ATP Sigma Aldrich Cat#A9187; CAS #: 74804-12-9 Histamine Sigma Aldrich Cat#H7125; CAS #: 51-45-6 Caffeine Sigma Aldrich Cat#C0750; CAS #: 58-08-2 Epibatidine Sigma Aldrich Cat#E1145;CAS #: 16637-43-2 Oleuropein Extrasynthese Cat#0228S; CAS #:32619-42-4 Oleuropein Aglycone Toronto Research Chemicals Cat#O532945; CAS #:31773-95-2 Hydroxytyrosol Extrasynthese Cat#4999S; CAS #: 10597-60-1 Oligomycin Sigma Aldrich Cat#75351 FCCP Sigma Aldrich Cat#C2920 Rotenone Sigma Aldrich Cat#45656 AntimycinA Sigma Aldrich Cat#A8674 Calcein AM Sigma Aldrich Cat#C0875; CAS#: 154071-48-4 Human Fibronectin Corning Cat#356008 PhosSTOP Merck Cat#4906845001 Fura-2, AM, cell permeant Thermo Fisher Cat#F1221 Gibco MEM, GlutaMAX Supplement Thermo Fisher Cat#41090 GOOD fetal bovine serum - 500 ml PanBiotech Cat#P40-37500 Penicillin-Streptomycin (5,000 U/mL) Thermo Fisher Cat#15070063 Gibco DMEM, high glucose, GlutaMAX Supplement, pyruvate Thermo Fisher Cat#31966 Gibco DMEM, high glucose, HEPES Thermo Fisher Cat#42430 Complete, Mini EDTA-free Protease Inhibitor Cocktail Merck Cat#11836170001 RIPA lysis and extraction buffer Thermo Fisher Cat89901 Non-Fat Dry Milk BioRad Cat#100-04504 PBS 1X PH 7.4 Thermo Fisher Cat# 10010023 Skeletal Muscle Cell Growth Medium Zen-Bio Cat#SKM-M medium Dulbecco’s Modified Eagle Medium F-12 Nutrient Mixture (DMEM/F-12 (1:1) (1x) +GlutaMAX) Thermo Fisher Cat#31331028 FBS Thermo Fisher Cat#10270106 Heat-inactivated Horse Serum Thermo Fisher Cat#26050088 PBS Thermo Fisher Cat#10010023 Tyrode’s salts Sigma Aldrich Cat#T2145 Dulbecco0s Modified Eagle0s Medium Sigma Aldrich Cat#D5030 (Continued on next page) e1 Cell Metabolism 37, 1–19.e1–e11, February 4, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRIzol Reagent Invitrogen, Thermo Fischer Cat#15596026 SuperScript III CellsDirect cDNA Synthesis Kit Invitrogen, Thermo Fisher Cat# 18080300 Master Mix PowerTrack SYBR Green Thermo Fisher Cat# A46109 Coelenterazine n Biotium 10110 CAS #: 55779-48-1 Digitonin Sigma Aldrich D5628; CAS#: 11024-24-1 N-Benzyl-p-toluenesulfonaMide Sigma Aldrich BL3H160B8B26; CAS#: 1576-37-0 Sodium Chloride Sigma Aldrich CAS#: 7647-14-5 Magnesium Chloride Sigma Aldrich CAS#:7791-18-6 HEPES Sigma Aldrich CAS#: 7365-45-9 Glucose Sigma Aldrich CAS#: 50-99-7 Calcium Chloride Sigma Aldrich CAS#: 10043-52-4 Potassium Chloride Sigma Aldrich CAS#: 7447-40-7 Thapsigargin Sigma Aldrich T9033; CAS#: 67526-95-8 EGTA Sigma Aldrich E3889; CAS#: 67-42-5 Collagenase A Roche Cat#COLLA-RO Kaempferol Sigma Aldrich CAS#: 5020-18-3 Olive leaf extract standardized with 40% oleuropein (OLE) Bioactor CAS#: 8060-29-5 JC-10 dye Enzo Lifesciences Cat#ENZ-52305 Hoestch Invitrogen Cat#H33342 Tris(2-carboxyethyl)phosphine (TCEP) Sigma Aldrich Cat#: C4706; CAS#: 51805-45-9 Critical commercial assays BCA protein assay kit Pierce Thermo Fisher Cat#23227 12-230kD Sally Sue Separation Module Protein Simple Cat#SM-S001 Pyruvate dehydrogenase (PDH) Enzyme Activity Microplate Assay Kit (ab109902) Abcam Cat#ab109920 NuPAGE 4 to 12%, Bis-Tris, 1.0–1.5 mm, Mini Protein Gels Invitrogen Cat#NP0336BOX Nitrocellulose membranes BioRad Cat#1704158 12-230 kDa Separation Module Protein Simple Cat#SM-S001 Incucyte Annexin V Green Dye Sartorius Cat#4642 Deposited data RNA-sequencing data Gene Expression Omnibus GSE11016 Source data This paper Data S1 Source Data Experimental models: Cell lines Human Skeletal Muscle Cells, Donor 7, Lot# 655307 Lonza Cat#LZ-CC-2580 Human Skeletal Muscle Cells, Donor 29, Lot # 639629 Lonza Cat#LZ-CC-2580 Human Skeletal Muscle Cells, Donor 215, Lot # SKM070512A Amsbio Cat#SKB-F Human Skeletal Muscle Cells, Donor 712, Lot # SKM062712B Amsbio Cat#SKB-F Human Skeletal Muscle Cells, Donor 211, Lot # SK120211 Amsbio Cat#SKB-F Human Skeletal Muscle Cells, Lot# P01064-69M Cook Myosite Cat#SK-1111 (Continued on next page) Cell Metabolism 37, 1–19.e1–e11, February 4, 2025 e2
Article Title: Hyperpolarization-activated cyclic nucleotide-gated cation channel 3 promotes HCC development in a female-biased manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti Mac-2 (Galectin-3) Cedarlane Labs Cat#CL8942AP; RRID:AB_10060357 Anti IL-6 Santa Cruz Biotechnology Cat#sc-1265; RRID:AB_2127470 Anti Na+/K+-ATPases Santa Cruz Biotechnology Cat#sc-48345; RRID:AB_626712 Anti b-Actin Santa Cruz Biotechnology Cat#sc-47778; RRID:AB_626632 Anti HCN3 Abcam Cat#ab84818; RRID:AB_1861081 Anti HCN3 Alomone Labs Cat#APC-057; RRID:AB_2039904 Anti HCN3 Thermo Fisher Cat#MA3-902; RRID:AB_2115028 Anti HA-tag Cell Signaling Technology Cat#3724; RRID:AB_1549585 Anti AFP Proteintech Cat#14550-1-AP; RRID:AB_2223933 Anti Albumin Proteintech Cat#16475-1-AP; RRID:AB_2242567 Anti Ki-67 Millipore-Sigma Cat#AB9260; RRID:AB_2142366 Anti NCOA5 Bethyl Cat#A300-790A; RRID:AB_2151214 Anti TIP30 Xiao lab (Ito et al.)28 N/A Anti PR Cell Signaling Technology Cat#8757; RRID:AB_2797144 LICOR IRDye 800CW secondary antibodies LICOR Cat#923–32213, 926–32214, 926-32211 LICOR IRDye 680RD secondary antibodies LICOR Cat#926–68072, 925–68074, 925-68076 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat#EC0112 E. coli TOP10 Thermo Fisher Cat#C404010 Biological samples Human HCC tissue array TissueArray.Com LLC Cat#LV1505a Chemicals, peptides, and recombinant proteins RIPA Lysis and Extraction Buffer Thermo Fisher Cat89900 Formalin solution, neutral buffered, 10% Sigma-Aldrich Cat#HT501128 TRIzol Reagent Thermo Fisher Cat#15596026 PowerUp SYBR Green reagent Thermo Fisher Cat#A25742 Lipofectamine 3000 Thermo Fisher Cat#L3000015 QuickExtract DNA Extraction Solution Lucigen Cat#QE0905T SuperScript IV First-Strand Synthesis System Thermo Fisher Cat#18091050 (R)-MG132 Cayman Chemical Cat#13697 ZD7288 Tocris Cat#1000 Polyethyleneimine Polysciences, Inc. Cat#23966-1 Puromycin dihydrochloride Thermo Fisher Cat#A1113803 Nitrotetrazolium Blue chloride Sigma-Aldrich Cat#N6639 Laemmli Sample Buffer BIO-RAD Cat#1610747 Thapsigargin Millipore-Sigma Cat#586005 Critical commercial assays Biorad Protein Assay BIO-RAD Cat#5000006 VECTASTAIN Elite ABC-HRP system Vector Laboratories Cat#PK-6101, PK-6102 Cell Counting Kit-8 Dojindo Cat#CK04 Alanine Transaminase Colorimetric Activity Assay Cayman Chemical Cat#700260 Mouse AFP Quantikine ELISA Kit R&D Systems Cat#MAFP00 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Mouse IL-6 ELISA Kit Proteintech Cat#KE10007 (Continued on next page) 16 Cell Reports 42, 113157, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Raw and processed RNA sequencing data This study GEO: GSE228531 Experimental models: Cell lines NIH/3T3 ATCC Cat#CRL-1658; RRID:CVCL_0594 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 PLC/PRF/5 ATCC Cat#CRL-8024; RRID:CVCL_0485 SNU-387 ATCC Cat#CRL-2237; RRID:CVCL_0250 Experimental models: Organisms/strains Mouse: Ncoa5+/ BALB/c Xiao lab (Gao et al.)8 N/A Mouse: Tip30+/ BALB/c Xiao lab (Ito et al.)28 N/A Mouse: Ncoa5+/ Tip30+/ BALB/c This study N/A Mouse: Hcn3 / C57BL/6 Biel lab (Fenske et al.)49 N/A Mouse: Hcn3 / BALB/c This study N/A Mouse: BALB/cJ Jackson Laboratory Cat#000651; RRID:IMSR_JAX:000651 Oligonucleotides See Table S4 for PCR primer sequences N/A N/A Recombinant DNA HCN3 CDS containing plasmid DF/HCC DNA Resource Core HsCD00348243 pSin-EF2 vector Yu et al.58 Addgene Cat#16579; RRID:Addgene_16579 pSpCas9(BB)-2A-Puro (PX459) V2.0 Ran et al.59 Addgene Cat#62988; RRID:Addgene_62988 pCMV delta R8.2 Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12263; RRID:Addgene_12263 pMD2.G Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12259; RRID:Addgene_12259 pGL2-Basic Promega N/A pcDNA3-TIP30 Xiao lab (Zhang et al.)60 N/A pcDNA3-hPR-A Su et al.61 Addgene Cat#89119; RRID:Addgene_189119 pcDNA3-PRB Su et al.61 Addgene Cat#89130; RRID:Addgene_89130 pRL Promega N/A pT3-EF1a-c-MYC Chen lab (Mendez-Lucas et al.)48 N/A pT3-EF1a-MCL1 Chen lab (Mendez-Lucas et al.)48 N/A pCMV/SB Chen lab (Mendez-Lucas et al.)48 N/A pSin-EF2-HCN3HA This study N/A PX459V2-HCN3-T1 This study N/A PX459V2-HCN3-T2 This study N/A pGL2-promoHCN3 This study N/A pT3-EF1a empty vector This study N/A pT3-EF1a-HCN3HA This study N/A Software and algorithms UCSC Xena Goldman et al.62 https://xena.ucsc.edu/ cBioportal Cerami et al.63; Gao et al.64 https://www.cbioportal.org/ STRING Szklarczyk et al.65 https://string-db.org/ Gene Set Enrichment Analysis Subramanian et al.51 https://www.gsea-msigdb.org/gsea/index.jsp ssGSEA Barbie et al.50 https://gsea-msigdb.github.io/ssGSEA- gpmodule/v10/index.html Trimmomatic Bolger et al.66 http://www.usadellab.org/cms/ ?page=trimmomatic STAR Dobin et al.67 https://github.com/alexdobin/STAR DESeq2 Love et al.68 https://bioconductor.org/packages/release/ bioc/html/DESeq2.html (Continued on next page) Cell Reports 42, 113157, October 31, 2023 17
Western Blot:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq. ..
Real-time Polymerase Chain Reaction:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq. ..
Drug discovery:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq. ..
SYBR Green Assay:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq. ..
Article Title: Hyperpolarization-activated cyclic nucleotide-gated cation channel 3 promotes HCC development in a female-biased manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti Mac-2 (Galectin-3) Cedarlane Labs Cat#CL8942AP; RRID:AB_10060357 Anti IL-6 Santa Cruz Biotechnology Cat#sc-1265; RRID:AB_2127470 Anti Na+/K+-ATPases Santa Cruz Biotechnology Cat#sc-48345; RRID:AB_626712 Anti b-Actin Santa Cruz Biotechnology Cat#sc-47778; RRID:AB_626632 Anti HCN3 Abcam Cat#ab84818; RRID:AB_1861081 Anti HCN3 Alomone Labs Cat#APC-057; RRID:AB_2039904 Anti HCN3 Thermo Fisher Cat#MA3-902; RRID:AB_2115028 Anti HA-tag Cell Signaling Technology Cat#3724; RRID:AB_1549585 Anti AFP Proteintech Cat#14550-1-AP; RRID:AB_2223933 Anti Albumin Proteintech Cat#16475-1-AP; RRID:AB_2242567 Anti Ki-67 Millipore-Sigma Cat#AB9260; RRID:AB_2142366 Anti NCOA5 Bethyl Cat#A300-790A; RRID:AB_2151214 Anti TIP30 Xiao lab (Ito et al.)28 N/A Anti PR Cell Signaling Technology Cat#8757; RRID:AB_2797144 LICOR IRDye 800CW secondary antibodies LICOR Cat#923–32213, 926–32214, 926-32211 LICOR IRDye 680RD secondary antibodies LICOR Cat#926–68072, 925–68074, 925-68076 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat#EC0112 E. coli TOP10 Thermo Fisher Cat#C404010 Biological samples Human HCC tissue array TissueArray.Com LLC Cat#LV1505a Chemicals, peptides, and recombinant proteins RIPA Lysis and Extraction Buffer Thermo Fisher Cat89900 Formalin solution, neutral buffered, 10% Sigma-Aldrich Cat#HT501128 TRIzol Reagent Thermo Fisher Cat#15596026 PowerUp SYBR Green reagent Thermo Fisher Cat#A25742 Lipofectamine 3000 Thermo Fisher Cat#L3000015 QuickExtract DNA Extraction Solution Lucigen Cat#QE0905T SuperScript IV First-Strand Synthesis System Thermo Fisher Cat#18091050 (R)-MG132 Cayman Chemical Cat#13697 ZD7288 Tocris Cat#1000 Polyethyleneimine Polysciences, Inc. Cat#23966-1 Puromycin dihydrochloride Thermo Fisher Cat#A1113803 Nitrotetrazolium Blue chloride Sigma-Aldrich Cat#N6639 Laemmli Sample Buffer BIO-RAD Cat#1610747 Thapsigargin Millipore-Sigma Cat#586005 Critical commercial assays Biorad Protein Assay BIO-RAD Cat#5000006 VECTASTAIN Elite ABC-HRP system Vector Laboratories Cat#PK-6101, PK-6102 Cell Counting Kit-8 Dojindo Cat#CK04 Alanine Transaminase Colorimetric Activity Assay Cayman Chemical Cat#700260 Mouse AFP Quantikine ELISA Kit R&D Systems Cat#MAFP00 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Mouse IL-6 ELISA Kit Proteintech Cat#KE10007 (Continued on next page) 16 Cell Reports 42, 113157, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Raw and processed RNA sequencing data This study GEO: GSE228531 Experimental models: Cell lines NIH/3T3 ATCC Cat#CRL-1658; RRID:CVCL_0594 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 PLC/PRF/5 ATCC Cat#CRL-8024; RRID:CVCL_0485 SNU-387 ATCC Cat#CRL-2237; RRID:CVCL_0250 Experimental models: Organisms/strains Mouse: Ncoa5+/ BALB/c Xiao lab (Gao et al.)8 N/A Mouse: Tip30+/ BALB/c Xiao lab (Ito et al.)28 N/A Mouse: Ncoa5+/ Tip30+/ BALB/c This study N/A Mouse: Hcn3 / C57BL/6 Biel lab (Fenske et al.)49 N/A Mouse: Hcn3 / BALB/c This study N/A Mouse: BALB/cJ Jackson Laboratory Cat#000651; RRID:IMSR_JAX:000651 Oligonucleotides See Table S4 for PCR primer sequences N/A N/A Recombinant DNA HCN3 CDS containing plasmid DF/HCC DNA Resource Core HsCD00348243 pSin-EF2 vector Yu et al.58 Addgene Cat#16579; RRID:Addgene_16579 pSpCas9(BB)-2A-Puro (PX459) V2.0 Ran et al.59 Addgene Cat#62988; RRID:Addgene_62988 pCMV delta R8.2 Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12263; RRID:Addgene_12263 pMD2.G Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12259; RRID:Addgene_12259 pGL2-Basic Promega N/A pcDNA3-TIP30 Xiao lab (Zhang et al.)60 N/A pcDNA3-hPR-A Su et al.61 Addgene Cat#89119; RRID:Addgene_189119 pcDNA3-PRB Su et al.61 Addgene Cat#89130; RRID:Addgene_89130 pRL Promega N/A pT3-EF1a-c-MYC Chen lab (Mendez-Lucas et al.)48 N/A pT3-EF1a-MCL1 Chen lab (Mendez-Lucas et al.)48 N/A pCMV/SB Chen lab (Mendez-Lucas et al.)48 N/A pSin-EF2-HCN3HA This study N/A PX459V2-HCN3-T1 This study N/A PX459V2-HCN3-T2 This study N/A pGL2-promoHCN3 This study N/A pT3-EF1a empty vector This study N/A pT3-EF1a-HCN3HA This study N/A Software and algorithms UCSC Xena Goldman et al.62 https://xena.ucsc.edu/ cBioportal Cerami et al.63; Gao et al.64 https://www.cbioportal.org/ STRING Szklarczyk et al.65 https://string-db.org/ Gene Set Enrichment Analysis Subramanian et al.51 https://www.gsea-msigdb.org/gsea/index.jsp ssGSEA Barbie et al.50 https://gsea-msigdb.github.io/ssGSEA- gpmodule/v10/index.html Trimmomatic Bolger et al.66 http://www.usadellab.org/cms/ ?page=trimmomatic STAR Dobin et al.67 https://github.com/alexdobin/STAR DESeq2 Love et al.68 https://bioconductor.org/packages/release/ bioc/html/DESeq2.html (Continued on next page) Cell Reports 42, 113157, October 31, 2023 17
Bicinchoninic Acid Protein Assay:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq. ..
Article Title: Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads mRNA DIRECT Kit Life Technologies Cat# 61012 Pierce Anti-HA Magnetic Beads ThermoFisher Scientific Cat# 88837 Anti-FLAG M2 Magnetic Beads Sigma Aldrich Cat# M8823 Pierce Anti-c-Myc Magnetic Beads ThermoFisher Scientific Cat# 88842 Dulbecco’s Modified Eagle Medium (DMEM) - high glucose, pyruvate, L-glutamine Thermo Fisher Cat# 11995073 Fetal bovine serum (FBS) Thermo Fisher Cat# 26140079 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher Cat# 13778075 L-Histidinol dihydrochloride Sigma Aldrich Cat# H6647 Anisomycin from Streptomyces griseolus Sigma Aldrich Cat# A9789 RIPA Lysis and Extraction Buffer Thermo Fisher Cat# 89901 Sodium phosphate dibasic Sigma Aldrich Cat# 71640 b-glycerophosphate Sigma Aldrich Cat# G9422 Benzonase nuclease Sigma Aldrich Cat# E1014 TCEP GoldBio Cat# TCEP25 Halt Protease and Phosphatase Inhibitor Cocktail (100X) – EDTA free Thermo Fisher Cat# 78440 10x Tris/Glycine/SDS running buffer Bio-rad Cat# 1610732 Blotto, non-fat dry milk Santa Cruz Biotechnology Cat# sc-2324 Emetine dihydrochloride Sigma Aldrich Cat# 324693 Sodium chloride (NaCl) Sigma Aldrich Cat# S9888 NP-40 Alternative, PROTEIN GRADE Detergent, 10% Solution, Sterile-Filtered Millipore Sigma Cat# 492018 1M Tris-HCl pH 7.0 Thermo Fisher Cat# AM9850G Sucrose Sigma Aldrich Cat# S7903 PBS pH 7.4 Thermo Fisher Cat# 10010049 Triton X-100 Sigma Aldrich Cat# T9284 EDTA (0.5 M), pH 8.0, RNase-free Thermo Fisher Cat# AM9260G TRIzol Reagent Thermo Fisher Cat# 15596026 Chloroform Sigma Cat# C2432 GlycoBlue Coprecipitant (15 mg/mL) Thermo Fisher Cat# AM9515 2-Propanol (HPLC), Fisher Chemical Fisher Scientific Cat# A451SK-4 Ethanol 200 Prf, 24x1 Gl Pint Pharmco Cat# 111000200CSPT Nuclease-Free Water (not DEPC-Treated) Thermo Fisher Cat# 4387936 TURBO DNase (2 U/mL) Thermo Fisher Cat# AM2238 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Thermo Fisher Cat# AM9722 Sodium Acetate (3 M), pH 5.5, RNase-free Thermo Fisher Cat# AM9740 iScript cDNA Synthesis Kit Bio-rad Cat# 1708891 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 4–20% Criterion TGX Precast Midi Protein Gel, 26 well, 15 ml Bio-rad Cat# 5671095 Trans-Blot Turbo RTA Midi 0.2 mm PVDF Transfer Kit Bio-rad Cat# 1704273 Deposited data Raw and analyzed RNAseq data This paper GSE255383 Custom python script This paper Zenodo: https://zenodo.org/ records/11190462 cryo-EM structural maps and molecular models This paper EMD-50170, EMD-50171, EMD-50259 and PDB: 9F9S (Continued on next page) e2 Molecular Cell 84, 1–18.e1–e9, December 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw gel image files This paper Mendeley Data: https://doi.org/ 10.17632/zj4x3426hv.2 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Experimental models: Organisms/strains BY4741 (MATa his3D1 leu2D0 met15D0 ura3D0) Dharmacon lab N/A mbf1D 319 (BY4741; mbf1D::NAT) This Study N/A gcn2D 619 (BY4741; gcn2D::KAN) Horizon N/A gcn4D (BY4741; gcn4D::KAN) Horizon N/A 703(MatA, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 705(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 923(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-HA) This Study N/A 1080 (matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-DN26-HA) This Study N/A 880 (MatA; GCN4-3XFLAG:KAN, ARG4-myc:His, PCL5D::Leu) This Study N/A 958 (MatA, GCN4-3XFLAG:KAN, ARG4-myc:His, Pho85D:Leu) This Study N/A 725(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1) This Study N/A 874 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1 R89G) This Study N/A 355 (MatA; Mbf1-6xGly-FLAG-mCherry His3) This Study N/A 992 (MatA, Mbf1-R89G-6xGly-FLAG -mCherry::HIS3) This Study N/A 1292 (MatA;Mbf1-mcherry NES::His) This Study N/A Long GCN4 1289 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Long GCN4 FLAG:Kan) This Study N/A Short GCN4 1290 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Short GCN4 FLAG:Kan) This Study N/A Mbf1 WT, GCN4_Short 1316 (BY4741, TBP1-myc::HIS3, GCN4_FLAG_ Short) This Study N/A Mbf1D, GCN4_Short 1318 (BY4741, TBP1-myc::HIS3, MBF1D::NAT, GCN4 Short) This Study N/A 1320 (BY4741, TBP1-myc13::HIS3, MBF1D::NAT, EKD-HA-Mbf1::Met 1; GCN4 Short) This Study N/A 1299 (MatA; GCN4-HA:Kan) This Study N/A 1301(matA; mbf1D::NAT, GCN4-HA:Kan) This Study N/A 1302 (matA; Mbf1:mCherry, GCN4-HA:Kan) This Study N/A 1304 (MatA, Mbf1-R89G-mCherry::HIS3, GCN4-HA:Kan) This Study N/A 1307 (MatA;Mbf1-mcherry NES::His, GCN4-HA:Kan) This Study N/A 690 (MatA, GCN4-3XFLAG:KAN) This Study N/A 693 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN) This Study N/A 919 (MatA, GCN4-3XFLAG:KAN 3, rps3-K108E:His) This Study N/A 1337 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E,L113A) This Study N/A 1338 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E, L113A, G121A) This Study N/A (Continued on next page) Molecular Cell 84, 1–18.e1–e9, December 5, 2024 e3
Enzyme-linked Immunosorbent Assay:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq. ..
Article Title: Hyperpolarization-activated cyclic nucleotide-gated cation channel 3 promotes HCC development in a female-biased manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti Mac-2 (Galectin-3) Cedarlane Labs Cat#CL8942AP; RRID:AB_10060357 Anti IL-6 Santa Cruz Biotechnology Cat#sc-1265; RRID:AB_2127470 Anti Na+/K+-ATPases Santa Cruz Biotechnology Cat#sc-48345; RRID:AB_626712 Anti b-Actin Santa Cruz Biotechnology Cat#sc-47778; RRID:AB_626632 Anti HCN3 Abcam Cat#ab84818; RRID:AB_1861081 Anti HCN3 Alomone Labs Cat#APC-057; RRID:AB_2039904 Anti HCN3 Thermo Fisher Cat#MA3-902; RRID:AB_2115028 Anti HA-tag Cell Signaling Technology Cat#3724; RRID:AB_1549585 Anti AFP Proteintech Cat#14550-1-AP; RRID:AB_2223933 Anti Albumin Proteintech Cat#16475-1-AP; RRID:AB_2242567 Anti Ki-67 Millipore-Sigma Cat#AB9260; RRID:AB_2142366 Anti NCOA5 Bethyl Cat#A300-790A; RRID:AB_2151214 Anti TIP30 Xiao lab (Ito et al.)28 N/A Anti PR Cell Signaling Technology Cat#8757; RRID:AB_2797144 LICOR IRDye 800CW secondary antibodies LICOR Cat#923–32213, 926–32214, 926-32211 LICOR IRDye 680RD secondary antibodies LICOR Cat#926–68072, 925–68074, 925-68076 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat#EC0112 E. coli TOP10 Thermo Fisher Cat#C404010 Biological samples Human HCC tissue array TissueArray.Com LLC Cat#LV1505a Chemicals, peptides, and recombinant proteins RIPA Lysis and Extraction Buffer Thermo Fisher Cat89900 Formalin solution, neutral buffered, 10% Sigma-Aldrich Cat#HT501128 TRIzol Reagent Thermo Fisher Cat#15596026 PowerUp SYBR Green reagent Thermo Fisher Cat#A25742 Lipofectamine 3000 Thermo Fisher Cat#L3000015 QuickExtract DNA Extraction Solution Lucigen Cat#QE0905T SuperScript IV First-Strand Synthesis System Thermo Fisher Cat#18091050 (R)-MG132 Cayman Chemical Cat#13697 ZD7288 Tocris Cat#1000 Polyethyleneimine Polysciences, Inc. Cat#23966-1 Puromycin dihydrochloride Thermo Fisher Cat#A1113803 Nitrotetrazolium Blue chloride Sigma-Aldrich Cat#N6639 Laemmli Sample Buffer BIO-RAD Cat#1610747 Thapsigargin Millipore-Sigma Cat#586005 Critical commercial assays Biorad Protein Assay BIO-RAD Cat#5000006 VECTASTAIN Elite ABC-HRP system Vector Laboratories Cat#PK-6101, PK-6102 Cell Counting Kit-8 Dojindo Cat#CK04 Alanine Transaminase Colorimetric Activity Assay Cayman Chemical Cat#700260 Mouse AFP Quantikine ELISA Kit R&D Systems Cat#MAFP00 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Mouse IL-6 ELISA Kit Proteintech Cat#KE10007 (Continued on next page) 16 Cell Reports 42, 113157, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Raw and processed RNA sequencing data This study GEO: GSE228531 Experimental models: Cell lines NIH/3T3 ATCC Cat#CRL-1658; RRID:CVCL_0594 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 PLC/PRF/5 ATCC Cat#CRL-8024; RRID:CVCL_0485 SNU-387 ATCC Cat#CRL-2237; RRID:CVCL_0250 Experimental models: Organisms/strains Mouse: Ncoa5+/ BALB/c Xiao lab (Gao et al.)8 N/A Mouse: Tip30+/ BALB/c Xiao lab (Ito et al.)28 N/A Mouse: Ncoa5+/ Tip30+/ BALB/c This study N/A Mouse: Hcn3 / C57BL/6 Biel lab (Fenske et al.)49 N/A Mouse: Hcn3 / BALB/c This study N/A Mouse: BALB/cJ Jackson Laboratory Cat#000651; RRID:IMSR_JAX:000651 Oligonucleotides See Table S4 for PCR primer sequences N/A N/A Recombinant DNA HCN3 CDS containing plasmid DF/HCC DNA Resource Core HsCD00348243 pSin-EF2 vector Yu et al.58 Addgene Cat#16579; RRID:Addgene_16579 pSpCas9(BB)-2A-Puro (PX459) V2.0 Ran et al.59 Addgene Cat#62988; RRID:Addgene_62988 pCMV delta R8.2 Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12263; RRID:Addgene_12263 pMD2.G Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12259; RRID:Addgene_12259 pGL2-Basic Promega N/A pcDNA3-TIP30 Xiao lab (Zhang et al.)60 N/A pcDNA3-hPR-A Su et al.61 Addgene Cat#89119; RRID:Addgene_189119 pcDNA3-PRB Su et al.61 Addgene Cat#89130; RRID:Addgene_89130 pRL Promega N/A pT3-EF1a-c-MYC Chen lab (Mendez-Lucas et al.)48 N/A pT3-EF1a-MCL1 Chen lab (Mendez-Lucas et al.)48 N/A pCMV/SB Chen lab (Mendez-Lucas et al.)48 N/A pSin-EF2-HCN3HA This study N/A PX459V2-HCN3-T1 This study N/A PX459V2-HCN3-T2 This study N/A pGL2-promoHCN3 This study N/A pT3-EF1a empty vector This study N/A pT3-EF1a-HCN3HA This study N/A Software and algorithms UCSC Xena Goldman et al.62 https://xena.ucsc.edu/ cBioportal Cerami et al.63; Gao et al.64 https://www.cbioportal.org/ STRING Szklarczyk et al.65 https://string-db.org/ Gene Set Enrichment Analysis Subramanian et al.51 https://www.gsea-msigdb.org/gsea/index.jsp ssGSEA Barbie et al.50 https://gsea-msigdb.github.io/ssGSEA- gpmodule/v10/index.html Trimmomatic Bolger et al.66 http://www.usadellab.org/cms/ ?page=trimmomatic STAR Dobin et al.67 https://github.com/alexdobin/STAR DESeq2 Love et al.68 https://bioconductor.org/packages/release/ bioc/html/DESeq2.html (Continued on next page) Cell Reports 42, 113157, October 31, 2023 17
Reverse Transcription:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq. ..
Luciferase:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq. ..
RNA Sequencing:Article Title: Identification of nonsense-mediated decay inhibitors that alter the tumor immune landscape
Article Snippet: See ‘Resource availability’ Chemical compound, drug LY3023414 Selleckchem Cat #S8322 Chemical compound, drug Matrigel Phenol Red Free Standard Formulation Corning Cat #356237 Chemical compound, drug MEGM Mammary Epithelial Cell Growth Medium BulletKit Lonza Cat #CC3150 Chemical compound, drug Methylcellulose Sigma- Aldrich Cat #M6385 Chemical compound, drug Phosphate- buffered saline (PBS) Thermo Fisher Cat #J60465.K2 Other Phusion Flash High- Fidelity PCR Master Mix Thermo Fisher Cat #F548S PCR reagent Other Pierce ECL Western Blotting Substrate Thermo Fisher Cat #32106 Western blot reagent Other PRIMETIME Gene Expression master mix Integrated DNA Technologies Cat #1055770 Real- time PCR reagent Chemical compound, drug Protease inhibitor Millipore Sigma Cat #4693159001 Other QIAshredder QIAGEN Cat #79656 Western blot reagent Recombinant protein Recombinant IL- 2 protein Prometheus Therapeutics and Diagnostics Cat #aldesleukin Recombinant protein Recombinant IL- 7 protein BioLegend Cat #581908 Continued on next page Continued Cook et al. eLife 2024;13:RP95952. .. DOI: https://doi.org/10.7554/eLife.95952 16 of 32 Reagent type (species) or resource Designation Source or reference Identifiers Additional information Chemical compound, drug RediJect D- Luciferin Ultra Bioluminescent Substrate PerkinElmer Cat #770505 Chemical compound, drug RIPA Lysis and Extraction buffer Thermo Fisher Cat #89901 Western blot and real- time PCR reagent Chemical compound, drug RNA Later Invitrogen Cat #AM7020 Real- time PCR reagent Chemical compound, drug RPMI 1640 medium Gibco Cat #11875- 119 Chemical compound, drug Selleckchem Bioactive Compound library (Supplementary file 2) Selleckchem Cat #L1700 Chemical compound, drug SMG1- specific inhibitor: 11j Ascendex LLC N/A Other SsoAdvanced Universal SYBR Green Supermix Bio- Rad Cat #1725270 Real- time PCR reagent Chemical compound, drug Trypsin Gibco Cat #25300054 Commercial assay or kit AllPrep DNA/RNA Mini Kit QIAGEN Cat #80204 Commercial assay or kit Agilent RNA ScreenTape Agilent Cat #5067- 5576 Commercial assay or kit Agilent RNA ScreenTape Sample Buffer Agilent Cat #5067- 5577 Commercial assay or kit Agilent RNA Ladder Agilent Cat #5067- 5578 Commercial assay or kit BCA Protein Assay Kit Thermo Fisher Cat #23227 Commercial assay or kit Bio- Rad SingleShot Cell Lysis kit Bio- Rad Cat #1725080 Commercial assay or kit ELISA R&D Systems Cat #SIF50C Commercial assay or kit High- Capacity cDNA Reverse Transcription Kit Advanced Biosystems Cat #4368814 Commercial assay or kit Illumina RNA library prep kit Illumina Cat #RS- 122- 2001 Commercial assay or kit Kinase kinativ assay ActivX Biosciences N/A Commercial assay or kit Luciferase Assay System Promega Cat #E1501 Commercial assay or kit RNeasy QIAGEN Cat #74104 Other Whole transcriptome RNA- seq: NCI- H358 This study FASTQ files for RNA- seq. ..
Magnetic Beads:Article Title: Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads mRNA DIRECT Kit Life Technologies Cat# 61012 Pierce Anti-HA Magnetic Beads ThermoFisher Scientific Cat# 88837 Anti-FLAG M2 Magnetic Beads Sigma Aldrich Cat# M8823 Pierce Anti-c-Myc Magnetic Beads ThermoFisher Scientific Cat# 88842 Dulbecco’s Modified Eagle Medium (DMEM) - high glucose, pyruvate, L-glutamine Thermo Fisher Cat# 11995073 Fetal bovine serum (FBS) Thermo Fisher Cat# 26140079 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher Cat# 13778075 L-Histidinol dihydrochloride Sigma Aldrich Cat# H6647 Anisomycin from Streptomyces griseolus Sigma Aldrich Cat# A9789 RIPA Lysis and Extraction Buffer Thermo Fisher Cat# 89901 Sodium phosphate dibasic Sigma Aldrich Cat# 71640 b-glycerophosphate Sigma Aldrich Cat# G9422 Benzonase nuclease Sigma Aldrich Cat# E1014 TCEP GoldBio Cat# TCEP25 Halt Protease and Phosphatase Inhibitor Cocktail (100X) – EDTA free Thermo Fisher Cat# 78440 10x Tris/Glycine/SDS running buffer Bio-rad Cat# 1610732 Blotto, non-fat dry milk Santa Cruz Biotechnology Cat# sc-2324 Emetine dihydrochloride Sigma Aldrich Cat# 324693 Sodium chloride (NaCl) Sigma Aldrich Cat# S9888 NP-40 Alternative, PROTEIN GRADE Detergent, 10% Solution, Sterile-Filtered Millipore Sigma Cat# 492018 1M Tris-HCl pH 7.0 Thermo Fisher Cat# AM9850G Sucrose Sigma Aldrich Cat# S7903 PBS pH 7.4 Thermo Fisher Cat# 10010049 Triton X-100 Sigma Aldrich Cat# T9284 EDTA (0.5 M), pH 8.0, RNase-free Thermo Fisher Cat# AM9260G TRIzol Reagent Thermo Fisher Cat# 15596026 Chloroform Sigma Cat# C2432 GlycoBlue Coprecipitant (15 mg/mL) Thermo Fisher Cat# AM9515 2-Propanol (HPLC), Fisher Chemical Fisher Scientific Cat# A451SK-4 Ethanol 200 Prf, 24x1 Gl Pint Pharmco Cat# 111000200CSPT Nuclease-Free Water (not DEPC-Treated) Thermo Fisher Cat# 4387936 TURBO DNase (2 U/mL) Thermo Fisher Cat# AM2238 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Thermo Fisher Cat# AM9722 Sodium Acetate (3 M), pH 5.5, RNase-free Thermo Fisher Cat# AM9740 iScript cDNA Synthesis Kit Bio-rad Cat# 1708891 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 4–20% Criterion TGX Precast Midi Protein Gel, 26 well, 15 ml Bio-rad Cat# 5671095 Trans-Blot Turbo RTA Midi 0.2 mm PVDF Transfer Kit Bio-rad Cat# 1704273 Deposited data Raw and analyzed RNAseq data This paper GSE255383 Custom python script This paper Zenodo: https://zenodo.org/ records/11190462 cryo-EM structural maps and molecular models This paper EMD-50170, EMD-50171, EMD-50259 and PDB: 9F9S (Continued on next page) e2 Molecular Cell 84, 1–18.e1–e9, December 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw gel image files This paper Mendeley Data: https://doi.org/ 10.17632/zj4x3426hv.2 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Experimental models: Organisms/strains BY4741 (MATa his3D1 leu2D0 met15D0 ura3D0) Dharmacon lab N/A mbf1D 319 (BY4741; mbf1D::NAT) This Study N/A gcn2D 619 (BY4741; gcn2D::KAN) Horizon N/A gcn4D (BY4741; gcn4D::KAN) Horizon N/A 703(MatA, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 705(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 923(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-HA) This Study N/A 1080 (matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-DN26-HA) This Study N/A 880 (MatA; GCN4-3XFLAG:KAN, ARG4-myc:His, PCL5D::Leu) This Study N/A 958 (MatA, GCN4-3XFLAG:KAN, ARG4-myc:His, Pho85D:Leu) This Study N/A 725(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1) This Study N/A 874 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1 R89G) This Study N/A 355 (MatA; Mbf1-6xGly-FLAG-mCherry His3) This Study N/A 992 (MatA, Mbf1-R89G-6xGly-FLAG -mCherry::HIS3) This Study N/A 1292 (MatA;Mbf1-mcherry NES::His) This Study N/A Long GCN4 1289 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Long GCN4 FLAG:Kan) This Study N/A Short GCN4 1290 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Short GCN4 FLAG:Kan) This Study N/A Mbf1 WT, GCN4_Short 1316 (BY4741, TBP1-myc::HIS3, GCN4_FLAG_ Short) This Study N/A Mbf1D, GCN4_Short 1318 (BY4741, TBP1-myc::HIS3, MBF1D::NAT, GCN4 Short) This Study N/A 1320 (BY4741, TBP1-myc13::HIS3, MBF1D::NAT, EKD-HA-Mbf1::Met 1; GCN4 Short) This Study N/A 1299 (MatA; GCN4-HA:Kan) This Study N/A 1301(matA; mbf1D::NAT, GCN4-HA:Kan) This Study N/A 1302 (matA; Mbf1:mCherry, GCN4-HA:Kan) This Study N/A 1304 (MatA, Mbf1-R89G-mCherry::HIS3, GCN4-HA:Kan) This Study N/A 1307 (MatA;Mbf1-mcherry NES::His, GCN4-HA:Kan) This Study N/A 690 (MatA, GCN4-3XFLAG:KAN) This Study N/A 693 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN) This Study N/A 919 (MatA, GCN4-3XFLAG:KAN 3, rps3-K108E:His) This Study N/A 1337 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E,L113A) This Study N/A 1338 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E, L113A, G121A) This Study N/A (Continued on next page) Molecular Cell 84, 1–18.e1–e9, December 5, 2024 e3
Modification:Article Title: Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads mRNA DIRECT Kit Life Technologies Cat# 61012 Pierce Anti-HA Magnetic Beads ThermoFisher Scientific Cat# 88837 Anti-FLAG M2 Magnetic Beads Sigma Aldrich Cat# M8823 Pierce Anti-c-Myc Magnetic Beads ThermoFisher Scientific Cat# 88842 Dulbecco’s Modified Eagle Medium (DMEM) - high glucose, pyruvate, L-glutamine Thermo Fisher Cat# 11995073 Fetal bovine serum (FBS) Thermo Fisher Cat# 26140079 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher Cat# 13778075 L-Histidinol dihydrochloride Sigma Aldrich Cat# H6647 Anisomycin from Streptomyces griseolus Sigma Aldrich Cat# A9789 RIPA Lysis and Extraction Buffer Thermo Fisher Cat# 89901 Sodium phosphate dibasic Sigma Aldrich Cat# 71640 b-glycerophosphate Sigma Aldrich Cat# G9422 Benzonase nuclease Sigma Aldrich Cat# E1014 TCEP GoldBio Cat# TCEP25 Halt Protease and Phosphatase Inhibitor Cocktail (100X) – EDTA free Thermo Fisher Cat# 78440 10x Tris/Glycine/SDS running buffer Bio-rad Cat# 1610732 Blotto, non-fat dry milk Santa Cruz Biotechnology Cat# sc-2324 Emetine dihydrochloride Sigma Aldrich Cat# 324693 Sodium chloride (NaCl) Sigma Aldrich Cat# S9888 NP-40 Alternative, PROTEIN GRADE Detergent, 10% Solution, Sterile-Filtered Millipore Sigma Cat# 492018 1M Tris-HCl pH 7.0 Thermo Fisher Cat# AM9850G Sucrose Sigma Aldrich Cat# S7903 PBS pH 7.4 Thermo Fisher Cat# 10010049 Triton X-100 Sigma Aldrich Cat# T9284 EDTA (0.5 M), pH 8.0, RNase-free Thermo Fisher Cat# AM9260G TRIzol Reagent Thermo Fisher Cat# 15596026 Chloroform Sigma Cat# C2432 GlycoBlue Coprecipitant (15 mg/mL) Thermo Fisher Cat# AM9515 2-Propanol (HPLC), Fisher Chemical Fisher Scientific Cat# A451SK-4 Ethanol 200 Prf, 24x1 Gl Pint Pharmco Cat# 111000200CSPT Nuclease-Free Water (not DEPC-Treated) Thermo Fisher Cat# 4387936 TURBO DNase (2 U/mL) Thermo Fisher Cat# AM2238 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Thermo Fisher Cat# AM9722 Sodium Acetate (3 M), pH 5.5, RNase-free Thermo Fisher Cat# AM9740 iScript cDNA Synthesis Kit Bio-rad Cat# 1708891 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 4–20% Criterion TGX Precast Midi Protein Gel, 26 well, 15 ml Bio-rad Cat# 5671095 Trans-Blot Turbo RTA Midi 0.2 mm PVDF Transfer Kit Bio-rad Cat# 1704273 Deposited data Raw and analyzed RNAseq data This paper GSE255383 Custom python script This paper Zenodo: https://zenodo.org/ records/11190462 cryo-EM structural maps and molecular models This paper EMD-50170, EMD-50171, EMD-50259 and PDB: 9F9S (Continued on next page) e2 Molecular Cell 84, 1–18.e1–e9, December 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw gel image files This paper Mendeley Data: https://doi.org/ 10.17632/zj4x3426hv.2 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Experimental models: Organisms/strains BY4741 (MATa his3D1 leu2D0 met15D0 ura3D0) Dharmacon lab N/A mbf1D 319 (BY4741; mbf1D::NAT) This Study N/A gcn2D 619 (BY4741; gcn2D::KAN) Horizon N/A gcn4D (BY4741; gcn4D::KAN) Horizon N/A 703(MatA, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 705(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 923(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-HA) This Study N/A 1080 (matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-DN26-HA) This Study N/A 880 (MatA; GCN4-3XFLAG:KAN, ARG4-myc:His, PCL5D::Leu) This Study N/A 958 (MatA, GCN4-3XFLAG:KAN, ARG4-myc:His, Pho85D:Leu) This Study N/A 725(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1) This Study N/A 874 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1 R89G) This Study N/A 355 (MatA; Mbf1-6xGly-FLAG-mCherry His3) This Study N/A 992 (MatA, Mbf1-R89G-6xGly-FLAG -mCherry::HIS3) This Study N/A 1292 (MatA;Mbf1-mcherry NES::His) This Study N/A Long GCN4 1289 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Long GCN4 FLAG:Kan) This Study N/A Short GCN4 1290 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Short GCN4 FLAG:Kan) This Study N/A Mbf1 WT, GCN4_Short 1316 (BY4741, TBP1-myc::HIS3, GCN4_FLAG_ Short) This Study N/A Mbf1D, GCN4_Short 1318 (BY4741, TBP1-myc::HIS3, MBF1D::NAT, GCN4 Short) This Study N/A 1320 (BY4741, TBP1-myc13::HIS3, MBF1D::NAT, EKD-HA-Mbf1::Met 1; GCN4 Short) This Study N/A 1299 (MatA; GCN4-HA:Kan) This Study N/A 1301(matA; mbf1D::NAT, GCN4-HA:Kan) This Study N/A 1302 (matA; Mbf1:mCherry, GCN4-HA:Kan) This Study N/A 1304 (MatA, Mbf1-R89G-mCherry::HIS3, GCN4-HA:Kan) This Study N/A 1307 (MatA;Mbf1-mcherry NES::His, GCN4-HA:Kan) This Study N/A 690 (MatA, GCN4-3XFLAG:KAN) This Study N/A 693 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN) This Study N/A 919 (MatA, GCN4-3XFLAG:KAN 3, rps3-K108E:His) This Study N/A 1337 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E,L113A) This Study N/A 1338 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E, L113A, G121A) This Study N/A (Continued on next page) Molecular Cell 84, 1–18.e1–e9, December 5, 2024 e3
Article Title: Mitochondrial calcium uptake declines during aging and is directly activated by oleuropein to boost energy metabolism and skeletal muscle performance.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal anti-MCU Cell Signaling Technology Cat#14997; RRID:AB_2721812 Rabbit polyclonal anti-MCUR Booster Cat#A08547-1 Mousse monoclonal anti-TOM20 (F-10) Santa Cruz Cat#sc-17764; RRID:AB_628381 Rabbit polyclonal anti-MICU1 Sigma Aldrich Cat#HPA037479; RRID:AB_2675495 Rabbit polyclonal anti-PDH Cell Signaling Technology Cat#2784; RRID:AB_2162928 Rabbit polyclonal anti-PDH (phospho S293) Abcam Cat#ab92696, RRID:AB_10711672 Rabbit monoclonal anti-TOM20 (D8T4N) Cell Signaling Technology Cat#42406, RRID:AB_2687663 Mouse monoclonal anti-GRP 75 (D-9) Santa Cruz Biotechnology Cat#sc-133137, RRID:AB_2120468 Anti-Rabbit Detection Module ProteinSimple Cat#DM-001 Rabbit polyclonal anti_MCUR1 Cell Signaling Technology Cat#13706S; RRID:AB_2749813 Chemicals, peptides, and recombinant proteins ATP Sigma Aldrich Cat#A9187; CAS #: 74804-12-9 Histamine Sigma Aldrich Cat#H7125; CAS #: 51-45-6 Caffeine Sigma Aldrich Cat#C0750; CAS #: 58-08-2 Epibatidine Sigma Aldrich Cat#E1145;CAS #: 16637-43-2 Oleuropein Extrasynthese Cat#0228S; CAS #:32619-42-4 Oleuropein Aglycone Toronto Research Chemicals Cat#O532945; CAS #:31773-95-2 Hydroxytyrosol Extrasynthese Cat#4999S; CAS #: 10597-60-1 Oligomycin Sigma Aldrich Cat#75351 FCCP Sigma Aldrich Cat#C2920 Rotenone Sigma Aldrich Cat#45656 AntimycinA Sigma Aldrich Cat#A8674 Calcein AM Sigma Aldrich Cat#C0875; CAS#: 154071-48-4 Human Fibronectin Corning Cat#356008 PhosSTOP Merck Cat#4906845001 Fura-2, AM, cell permeant Thermo Fisher Cat#F1221 Gibco MEM, GlutaMAX Supplement Thermo Fisher Cat#41090 GOOD fetal bovine serum - 500 ml PanBiotech Cat#P40-37500 Penicillin-Streptomycin (5,000 U/mL) Thermo Fisher Cat#15070063 Gibco DMEM, high glucose, GlutaMAX Supplement, pyruvate Thermo Fisher Cat#31966 Gibco DMEM, high glucose, HEPES Thermo Fisher Cat#42430 Complete, Mini EDTA-free Protease Inhibitor Cocktail Merck Cat#11836170001 RIPA lysis and extraction buffer Thermo Fisher Cat89901 Non-Fat Dry Milk BioRad Cat#100-04504 PBS 1X PH 7.4 Thermo Fisher Cat# 10010023 Skeletal Muscle Cell Growth Medium Zen-Bio Cat#SKM-M medium Dulbecco’s Modified Eagle Medium F-12 Nutrient Mixture (DMEM/F-12 (1:1) (1x) +GlutaMAX) Thermo Fisher Cat#31331028 FBS Thermo Fisher Cat#10270106 Heat-inactivated Horse Serum Thermo Fisher Cat#26050088 PBS Thermo Fisher Cat#10010023 Tyrode’s salts Sigma Aldrich Cat#T2145 Dulbecco0s Modified Eagle0s Medium Sigma Aldrich Cat#D5030 (Continued on next page) e1 Cell Metabolism 37, 1–19.e1–e11, February 4, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRIzol Reagent Invitrogen, Thermo Fischer Cat#15596026 SuperScript III CellsDirect cDNA Synthesis Kit Invitrogen, Thermo Fisher Cat# 18080300 Master Mix PowerTrack SYBR Green Thermo Fisher Cat# A46109 Coelenterazine n Biotium 10110 CAS #: 55779-48-1 Digitonin Sigma Aldrich D5628; CAS#: 11024-24-1 N-Benzyl-p-toluenesulfonaMide Sigma Aldrich BL3H160B8B26; CAS#: 1576-37-0 Sodium Chloride Sigma Aldrich CAS#: 7647-14-5 Magnesium Chloride Sigma Aldrich CAS#:7791-18-6 HEPES Sigma Aldrich CAS#: 7365-45-9 Glucose Sigma Aldrich CAS#: 50-99-7 Calcium Chloride Sigma Aldrich CAS#: 10043-52-4 Potassium Chloride Sigma Aldrich CAS#: 7447-40-7 Thapsigargin Sigma Aldrich T9033; CAS#: 67526-95-8 EGTA Sigma Aldrich E3889; CAS#: 67-42-5 Collagenase A Roche Cat#COLLA-RO Kaempferol Sigma Aldrich CAS#: 5020-18-3 Olive leaf extract standardized with 40% oleuropein (OLE) Bioactor CAS#: 8060-29-5 JC-10 dye Enzo Lifesciences Cat#ENZ-52305 Hoestch Invitrogen Cat#H33342 Tris(2-carboxyethyl)phosphine (TCEP) Sigma Aldrich Cat#: C4706; CAS#: 51805-45-9 Critical commercial assays BCA protein assay kit Pierce Thermo Fisher Cat#23227 12-230kD Sally Sue Separation Module Protein Simple Cat#SM-S001 Pyruvate dehydrogenase (PDH) Enzyme Activity Microplate Assay Kit (ab109902) Abcam Cat#ab109920 NuPAGE 4 to 12%, Bis-Tris, 1.0–1.5 mm, Mini Protein Gels Invitrogen Cat#NP0336BOX Nitrocellulose membranes BioRad Cat#1704158 12-230 kDa Separation Module Protein Simple Cat#SM-S001 Incucyte Annexin V Green Dye Sartorius Cat#4642 Deposited data RNA-sequencing data Gene Expression Omnibus GSE11016 Source data This paper Data S1 Source Data Experimental models: Cell lines Human Skeletal Muscle Cells, Donor 7, Lot# 655307 Lonza Cat#LZ-CC-2580 Human Skeletal Muscle Cells, Donor 29, Lot # 639629 Lonza Cat#LZ-CC-2580 Human Skeletal Muscle Cells, Donor 215, Lot # SKM070512A Amsbio Cat#SKB-F Human Skeletal Muscle Cells, Donor 712, Lot # SKM062712B Amsbio Cat#SKB-F Human Skeletal Muscle Cells, Donor 211, Lot # SK120211 Amsbio Cat#SKB-F Human Skeletal Muscle Cells, Lot# P01064-69M Cook Myosite Cat#SK-1111 (Continued on next page) Cell Metabolism 37, 1–19.e1–e11, February 4, 2025 e2
Transfection:Article Title: Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads mRNA DIRECT Kit Life Technologies Cat# 61012 Pierce Anti-HA Magnetic Beads ThermoFisher Scientific Cat# 88837 Anti-FLAG M2 Magnetic Beads Sigma Aldrich Cat# M8823 Pierce Anti-c-Myc Magnetic Beads ThermoFisher Scientific Cat# 88842 Dulbecco’s Modified Eagle Medium (DMEM) - high glucose, pyruvate, L-glutamine Thermo Fisher Cat# 11995073 Fetal bovine serum (FBS) Thermo Fisher Cat# 26140079 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher Cat# 13778075 L-Histidinol dihydrochloride Sigma Aldrich Cat# H6647 Anisomycin from Streptomyces griseolus Sigma Aldrich Cat# A9789 RIPA Lysis and Extraction Buffer Thermo Fisher Cat# 89901 Sodium phosphate dibasic Sigma Aldrich Cat# 71640 b-glycerophosphate Sigma Aldrich Cat# G9422 Benzonase nuclease Sigma Aldrich Cat# E1014 TCEP GoldBio Cat# TCEP25 Halt Protease and Phosphatase Inhibitor Cocktail (100X) – EDTA free Thermo Fisher Cat# 78440 10x Tris/Glycine/SDS running buffer Bio-rad Cat# 1610732 Blotto, non-fat dry milk Santa Cruz Biotechnology Cat# sc-2324 Emetine dihydrochloride Sigma Aldrich Cat# 324693 Sodium chloride (NaCl) Sigma Aldrich Cat# S9888 NP-40 Alternative, PROTEIN GRADE Detergent, 10% Solution, Sterile-Filtered Millipore Sigma Cat# 492018 1M Tris-HCl pH 7.0 Thermo Fisher Cat# AM9850G Sucrose Sigma Aldrich Cat# S7903 PBS pH 7.4 Thermo Fisher Cat# 10010049 Triton X-100 Sigma Aldrich Cat# T9284 EDTA (0.5 M), pH 8.0, RNase-free Thermo Fisher Cat# AM9260G TRIzol Reagent Thermo Fisher Cat# 15596026 Chloroform Sigma Cat# C2432 GlycoBlue Coprecipitant (15 mg/mL) Thermo Fisher Cat# AM9515 2-Propanol (HPLC), Fisher Chemical Fisher Scientific Cat# A451SK-4 Ethanol 200 Prf, 24x1 Gl Pint Pharmco Cat# 111000200CSPT Nuclease-Free Water (not DEPC-Treated) Thermo Fisher Cat# 4387936 TURBO DNase (2 U/mL) Thermo Fisher Cat# AM2238 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Thermo Fisher Cat# AM9722 Sodium Acetate (3 M), pH 5.5, RNase-free Thermo Fisher Cat# AM9740 iScript cDNA Synthesis Kit Bio-rad Cat# 1708891 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 4–20% Criterion TGX Precast Midi Protein Gel, 26 well, 15 ml Bio-rad Cat# 5671095 Trans-Blot Turbo RTA Midi 0.2 mm PVDF Transfer Kit Bio-rad Cat# 1704273 Deposited data Raw and analyzed RNAseq data This paper GSE255383 Custom python script This paper Zenodo: https://zenodo.org/ records/11190462 cryo-EM structural maps and molecular models This paper EMD-50170, EMD-50171, EMD-50259 and PDB: 9F9S (Continued on next page) e2 Molecular Cell 84, 1–18.e1–e9, December 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw gel image files This paper Mendeley Data: https://doi.org/ 10.17632/zj4x3426hv.2 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Experimental models: Organisms/strains BY4741 (MATa his3D1 leu2D0 met15D0 ura3D0) Dharmacon lab N/A mbf1D 319 (BY4741; mbf1D::NAT) This Study N/A gcn2D 619 (BY4741; gcn2D::KAN) Horizon N/A gcn4D (BY4741; gcn4D::KAN) Horizon N/A 703(MatA, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 705(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 923(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-HA) This Study N/A 1080 (matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-DN26-HA) This Study N/A 880 (MatA; GCN4-3XFLAG:KAN, ARG4-myc:His, PCL5D::Leu) This Study N/A 958 (MatA, GCN4-3XFLAG:KAN, ARG4-myc:His, Pho85D:Leu) This Study N/A 725(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1) This Study N/A 874 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1 R89G) This Study N/A 355 (MatA; Mbf1-6xGly-FLAG-mCherry His3) This Study N/A 992 (MatA, Mbf1-R89G-6xGly-FLAG -mCherry::HIS3) This Study N/A 1292 (MatA;Mbf1-mcherry NES::His) This Study N/A Long GCN4 1289 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Long GCN4 FLAG:Kan) This Study N/A Short GCN4 1290 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Short GCN4 FLAG:Kan) This Study N/A Mbf1 WT, GCN4_Short 1316 (BY4741, TBP1-myc::HIS3, GCN4_FLAG_ Short) This Study N/A Mbf1D, GCN4_Short 1318 (BY4741, TBP1-myc::HIS3, MBF1D::NAT, GCN4 Short) This Study N/A 1320 (BY4741, TBP1-myc13::HIS3, MBF1D::NAT, EKD-HA-Mbf1::Met 1; GCN4 Short) This Study N/A 1299 (MatA; GCN4-HA:Kan) This Study N/A 1301(matA; mbf1D::NAT, GCN4-HA:Kan) This Study N/A 1302 (matA; Mbf1:mCherry, GCN4-HA:Kan) This Study N/A 1304 (MatA, Mbf1-R89G-mCherry::HIS3, GCN4-HA:Kan) This Study N/A 1307 (MatA;Mbf1-mcherry NES::His, GCN4-HA:Kan) This Study N/A 690 (MatA, GCN4-3XFLAG:KAN) This Study N/A 693 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN) This Study N/A 919 (MatA, GCN4-3XFLAG:KAN 3, rps3-K108E:His) This Study N/A 1337 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E,L113A) This Study N/A 1338 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E, L113A, G121A) This Study N/A (Continued on next page) Molecular Cell 84, 1–18.e1–e9, December 5, 2024 e3
Sterility:Article Title: Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads mRNA DIRECT Kit Life Technologies Cat# 61012 Pierce Anti-HA Magnetic Beads ThermoFisher Scientific Cat# 88837 Anti-FLAG M2 Magnetic Beads Sigma Aldrich Cat# M8823 Pierce Anti-c-Myc Magnetic Beads ThermoFisher Scientific Cat# 88842 Dulbecco’s Modified Eagle Medium (DMEM) - high glucose, pyruvate, L-glutamine Thermo Fisher Cat# 11995073 Fetal bovine serum (FBS) Thermo Fisher Cat# 26140079 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher Cat# 13778075 L-Histidinol dihydrochloride Sigma Aldrich Cat# H6647 Anisomycin from Streptomyces griseolus Sigma Aldrich Cat# A9789 RIPA Lysis and Extraction Buffer Thermo Fisher Cat# 89901 Sodium phosphate dibasic Sigma Aldrich Cat# 71640 b-glycerophosphate Sigma Aldrich Cat# G9422 Benzonase nuclease Sigma Aldrich Cat# E1014 TCEP GoldBio Cat# TCEP25 Halt Protease and Phosphatase Inhibitor Cocktail (100X) – EDTA free Thermo Fisher Cat# 78440 10x Tris/Glycine/SDS running buffer Bio-rad Cat# 1610732 Blotto, non-fat dry milk Santa Cruz Biotechnology Cat# sc-2324 Emetine dihydrochloride Sigma Aldrich Cat# 324693 Sodium chloride (NaCl) Sigma Aldrich Cat# S9888 NP-40 Alternative, PROTEIN GRADE Detergent, 10% Solution, Sterile-Filtered Millipore Sigma Cat# 492018 1M Tris-HCl pH 7.0 Thermo Fisher Cat# AM9850G Sucrose Sigma Aldrich Cat# S7903 PBS pH 7.4 Thermo Fisher Cat# 10010049 Triton X-100 Sigma Aldrich Cat# T9284 EDTA (0.5 M), pH 8.0, RNase-free Thermo Fisher Cat# AM9260G TRIzol Reagent Thermo Fisher Cat# 15596026 Chloroform Sigma Cat# C2432 GlycoBlue Coprecipitant (15 mg/mL) Thermo Fisher Cat# AM9515 2-Propanol (HPLC), Fisher Chemical Fisher Scientific Cat# A451SK-4 Ethanol 200 Prf, 24x1 Gl Pint Pharmco Cat# 111000200CSPT Nuclease-Free Water (not DEPC-Treated) Thermo Fisher Cat# 4387936 TURBO DNase (2 U/mL) Thermo Fisher Cat# AM2238 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Thermo Fisher Cat# AM9722 Sodium Acetate (3 M), pH 5.5, RNase-free Thermo Fisher Cat# AM9740 iScript cDNA Synthesis Kit Bio-rad Cat# 1708891 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 4–20% Criterion TGX Precast Midi Protein Gel, 26 well, 15 ml Bio-rad Cat# 5671095 Trans-Blot Turbo RTA Midi 0.2 mm PVDF Transfer Kit Bio-rad Cat# 1704273 Deposited data Raw and analyzed RNAseq data This paper GSE255383 Custom python script This paper Zenodo: https://zenodo.org/ records/11190462 cryo-EM structural maps and molecular models This paper EMD-50170, EMD-50171, EMD-50259 and PDB: 9F9S (Continued on next page) e2 Molecular Cell 84, 1–18.e1–e9, December 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw gel image files This paper Mendeley Data: https://doi.org/ 10.17632/zj4x3426hv.2 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Experimental models: Organisms/strains BY4741 (MATa his3D1 leu2D0 met15D0 ura3D0) Dharmacon lab N/A mbf1D 319 (BY4741; mbf1D::NAT) This Study N/A gcn2D 619 (BY4741; gcn2D::KAN) Horizon N/A gcn4D (BY4741; gcn4D::KAN) Horizon N/A 703(MatA, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 705(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 923(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-HA) This Study N/A 1080 (matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-DN26-HA) This Study N/A 880 (MatA; GCN4-3XFLAG:KAN, ARG4-myc:His, PCL5D::Leu) This Study N/A 958 (MatA, GCN4-3XFLAG:KAN, ARG4-myc:His, Pho85D:Leu) This Study N/A 725(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1) This Study N/A 874 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1 R89G) This Study N/A 355 (MatA; Mbf1-6xGly-FLAG-mCherry His3) This Study N/A 992 (MatA, Mbf1-R89G-6xGly-FLAG -mCherry::HIS3) This Study N/A 1292 (MatA;Mbf1-mcherry NES::His) This Study N/A Long GCN4 1289 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Long GCN4 FLAG:Kan) This Study N/A Short GCN4 1290 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Short GCN4 FLAG:Kan) This Study N/A Mbf1 WT, GCN4_Short 1316 (BY4741, TBP1-myc::HIS3, GCN4_FLAG_ Short) This Study N/A Mbf1D, GCN4_Short 1318 (BY4741, TBP1-myc::HIS3, MBF1D::NAT, GCN4 Short) This Study N/A 1320 (BY4741, TBP1-myc13::HIS3, MBF1D::NAT, EKD-HA-Mbf1::Met 1; GCN4 Short) This Study N/A 1299 (MatA; GCN4-HA:Kan) This Study N/A 1301(matA; mbf1D::NAT, GCN4-HA:Kan) This Study N/A 1302 (matA; Mbf1:mCherry, GCN4-HA:Kan) This Study N/A 1304 (MatA, Mbf1-R89G-mCherry::HIS3, GCN4-HA:Kan) This Study N/A 1307 (MatA;Mbf1-mcherry NES::His, GCN4-HA:Kan) This Study N/A 690 (MatA, GCN4-3XFLAG:KAN) This Study N/A 693 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN) This Study N/A 919 (MatA, GCN4-3XFLAG:KAN 3, rps3-K108E:His) This Study N/A 1337 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E,L113A) This Study N/A 1338 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E, L113A, G121A) This Study N/A (Continued on next page) Molecular Cell 84, 1–18.e1–e9, December 5, 2024 e3
High Performance Liquid Chromatography:Article Title: Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads mRNA DIRECT Kit Life Technologies Cat# 61012 Pierce Anti-HA Magnetic Beads ThermoFisher Scientific Cat# 88837 Anti-FLAG M2 Magnetic Beads Sigma Aldrich Cat# M8823 Pierce Anti-c-Myc Magnetic Beads ThermoFisher Scientific Cat# 88842 Dulbecco’s Modified Eagle Medium (DMEM) - high glucose, pyruvate, L-glutamine Thermo Fisher Cat# 11995073 Fetal bovine serum (FBS) Thermo Fisher Cat# 26140079 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher Cat# 13778075 L-Histidinol dihydrochloride Sigma Aldrich Cat# H6647 Anisomycin from Streptomyces griseolus Sigma Aldrich Cat# A9789 RIPA Lysis and Extraction Buffer Thermo Fisher Cat# 89901 Sodium phosphate dibasic Sigma Aldrich Cat# 71640 b-glycerophosphate Sigma Aldrich Cat# G9422 Benzonase nuclease Sigma Aldrich Cat# E1014 TCEP GoldBio Cat# TCEP25 Halt Protease and Phosphatase Inhibitor Cocktail (100X) – EDTA free Thermo Fisher Cat# 78440 10x Tris/Glycine/SDS running buffer Bio-rad Cat# 1610732 Blotto, non-fat dry milk Santa Cruz Biotechnology Cat# sc-2324 Emetine dihydrochloride Sigma Aldrich Cat# 324693 Sodium chloride (NaCl) Sigma Aldrich Cat# S9888 NP-40 Alternative, PROTEIN GRADE Detergent, 10% Solution, Sterile-Filtered Millipore Sigma Cat# 492018 1M Tris-HCl pH 7.0 Thermo Fisher Cat# AM9850G Sucrose Sigma Aldrich Cat# S7903 PBS pH 7.4 Thermo Fisher Cat# 10010049 Triton X-100 Sigma Aldrich Cat# T9284 EDTA (0.5 M), pH 8.0, RNase-free Thermo Fisher Cat# AM9260G TRIzol Reagent Thermo Fisher Cat# 15596026 Chloroform Sigma Cat# C2432 GlycoBlue Coprecipitant (15 mg/mL) Thermo Fisher Cat# AM9515 2-Propanol (HPLC), Fisher Chemical Fisher Scientific Cat# A451SK-4 Ethanol 200 Prf, 24x1 Gl Pint Pharmco Cat# 111000200CSPT Nuclease-Free Water (not DEPC-Treated) Thermo Fisher Cat# 4387936 TURBO DNase (2 U/mL) Thermo Fisher Cat# AM2238 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Thermo Fisher Cat# AM9722 Sodium Acetate (3 M), pH 5.5, RNase-free Thermo Fisher Cat# AM9740 iScript cDNA Synthesis Kit Bio-rad Cat# 1708891 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 4–20% Criterion TGX Precast Midi Protein Gel, 26 well, 15 ml Bio-rad Cat# 5671095 Trans-Blot Turbo RTA Midi 0.2 mm PVDF Transfer Kit Bio-rad Cat# 1704273 Deposited data Raw and analyzed RNAseq data This paper GSE255383 Custom python script This paper Zenodo: https://zenodo.org/ records/11190462 cryo-EM structural maps and molecular models This paper EMD-50170, EMD-50171, EMD-50259 and PDB: 9F9S (Continued on next page) e2 Molecular Cell 84, 1–18.e1–e9, December 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw gel image files This paper Mendeley Data: https://doi.org/ 10.17632/zj4x3426hv.2 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Experimental models: Organisms/strains BY4741 (MATa his3D1 leu2D0 met15D0 ura3D0) Dharmacon lab N/A mbf1D 319 (BY4741; mbf1D::NAT) This Study N/A gcn2D 619 (BY4741; gcn2D::KAN) Horizon N/A gcn4D (BY4741; gcn4D::KAN) Horizon N/A 703(MatA, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 705(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 923(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-HA) This Study N/A 1080 (matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-DN26-HA) This Study N/A 880 (MatA; GCN4-3XFLAG:KAN, ARG4-myc:His, PCL5D::Leu) This Study N/A 958 (MatA, GCN4-3XFLAG:KAN, ARG4-myc:His, Pho85D:Leu) This Study N/A 725(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1) This Study N/A 874 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1 R89G) This Study N/A 355 (MatA; Mbf1-6xGly-FLAG-mCherry His3) This Study N/A 992 (MatA, Mbf1-R89G-6xGly-FLAG -mCherry::HIS3) This Study N/A 1292 (MatA;Mbf1-mcherry NES::His) This Study N/A Long GCN4 1289 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Long GCN4 FLAG:Kan) This Study N/A Short GCN4 1290 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Short GCN4 FLAG:Kan) This Study N/A Mbf1 WT, GCN4_Short 1316 (BY4741, TBP1-myc::HIS3, GCN4_FLAG_ Short) This Study N/A Mbf1D, GCN4_Short 1318 (BY4741, TBP1-myc::HIS3, MBF1D::NAT, GCN4 Short) This Study N/A 1320 (BY4741, TBP1-myc13::HIS3, MBF1D::NAT, EKD-HA-Mbf1::Met 1; GCN4 Short) This Study N/A 1299 (MatA; GCN4-HA:Kan) This Study N/A 1301(matA; mbf1D::NAT, GCN4-HA:Kan) This Study N/A 1302 (matA; Mbf1:mCherry, GCN4-HA:Kan) This Study N/A 1304 (MatA, Mbf1-R89G-mCherry::HIS3, GCN4-HA:Kan) This Study N/A 1307 (MatA;Mbf1-mcherry NES::His, GCN4-HA:Kan) This Study N/A 690 (MatA, GCN4-3XFLAG:KAN) This Study N/A 693 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN) This Study N/A 919 (MatA, GCN4-3XFLAG:KAN 3, rps3-K108E:His) This Study N/A 1337 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E,L113A) This Study N/A 1338 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E, L113A, G121A) This Study N/A (Continued on next page) Molecular Cell 84, 1–18.e1–e9, December 5, 2024 e3
cDNA Synthesis:Article Title: Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads mRNA DIRECT Kit Life Technologies Cat# 61012 Pierce Anti-HA Magnetic Beads ThermoFisher Scientific Cat# 88837 Anti-FLAG M2 Magnetic Beads Sigma Aldrich Cat# M8823 Pierce Anti-c-Myc Magnetic Beads ThermoFisher Scientific Cat# 88842 Dulbecco’s Modified Eagle Medium (DMEM) - high glucose, pyruvate, L-glutamine Thermo Fisher Cat# 11995073 Fetal bovine serum (FBS) Thermo Fisher Cat# 26140079 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher Cat# 13778075 L-Histidinol dihydrochloride Sigma Aldrich Cat# H6647 Anisomycin from Streptomyces griseolus Sigma Aldrich Cat# A9789 RIPA Lysis and Extraction Buffer Thermo Fisher Cat# 89901 Sodium phosphate dibasic Sigma Aldrich Cat# 71640 b-glycerophosphate Sigma Aldrich Cat# G9422 Benzonase nuclease Sigma Aldrich Cat# E1014 TCEP GoldBio Cat# TCEP25 Halt Protease and Phosphatase Inhibitor Cocktail (100X) – EDTA free Thermo Fisher Cat# 78440 10x Tris/Glycine/SDS running buffer Bio-rad Cat# 1610732 Blotto, non-fat dry milk Santa Cruz Biotechnology Cat# sc-2324 Emetine dihydrochloride Sigma Aldrich Cat# 324693 Sodium chloride (NaCl) Sigma Aldrich Cat# S9888 NP-40 Alternative, PROTEIN GRADE Detergent, 10% Solution, Sterile-Filtered Millipore Sigma Cat# 492018 1M Tris-HCl pH 7.0 Thermo Fisher Cat# AM9850G Sucrose Sigma Aldrich Cat# S7903 PBS pH 7.4 Thermo Fisher Cat# 10010049 Triton X-100 Sigma Aldrich Cat# T9284 EDTA (0.5 M), pH 8.0, RNase-free Thermo Fisher Cat# AM9260G TRIzol Reagent Thermo Fisher Cat# 15596026 Chloroform Sigma Cat# C2432 GlycoBlue Coprecipitant (15 mg/mL) Thermo Fisher Cat# AM9515 2-Propanol (HPLC), Fisher Chemical Fisher Scientific Cat# A451SK-4 Ethanol 200 Prf, 24x1 Gl Pint Pharmco Cat# 111000200CSPT Nuclease-Free Water (not DEPC-Treated) Thermo Fisher Cat# 4387936 TURBO DNase (2 U/mL) Thermo Fisher Cat# AM2238 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Thermo Fisher Cat# AM9722 Sodium Acetate (3 M), pH 5.5, RNase-free Thermo Fisher Cat# AM9740 iScript cDNA Synthesis Kit Bio-rad Cat# 1708891 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 4–20% Criterion TGX Precast Midi Protein Gel, 26 well, 15 ml Bio-rad Cat# 5671095 Trans-Blot Turbo RTA Midi 0.2 mm PVDF Transfer Kit Bio-rad Cat# 1704273 Deposited data Raw and analyzed RNAseq data This paper GSE255383 Custom python script This paper Zenodo: https://zenodo.org/ records/11190462 cryo-EM structural maps and molecular models This paper EMD-50170, EMD-50171, EMD-50259 and PDB: 9F9S (Continued on next page) e2 Molecular Cell 84, 1–18.e1–e9, December 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw gel image files This paper Mendeley Data: https://doi.org/ 10.17632/zj4x3426hv.2 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Experimental models: Organisms/strains BY4741 (MATa his3D1 leu2D0 met15D0 ura3D0) Dharmacon lab N/A mbf1D 319 (BY4741; mbf1D::NAT) This Study N/A gcn2D 619 (BY4741; gcn2D::KAN) Horizon N/A gcn4D (BY4741; gcn4D::KAN) Horizon N/A 703(MatA, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 705(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 923(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-HA) This Study N/A 1080 (matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-DN26-HA) This Study N/A 880 (MatA; GCN4-3XFLAG:KAN, ARG4-myc:His, PCL5D::Leu) This Study N/A 958 (MatA, GCN4-3XFLAG:KAN, ARG4-myc:His, Pho85D:Leu) This Study N/A 725(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1) This Study N/A 874 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1 R89G) This Study N/A 355 (MatA; Mbf1-6xGly-FLAG-mCherry His3) This Study N/A 992 (MatA, Mbf1-R89G-6xGly-FLAG -mCherry::HIS3) This Study N/A 1292 (MatA;Mbf1-mcherry NES::His) This Study N/A Long GCN4 1289 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Long GCN4 FLAG:Kan) This Study N/A Short GCN4 1290 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Short GCN4 FLAG:Kan) This Study N/A Mbf1 WT, GCN4_Short 1316 (BY4741, TBP1-myc::HIS3, GCN4_FLAG_ Short) This Study N/A Mbf1D, GCN4_Short 1318 (BY4741, TBP1-myc::HIS3, MBF1D::NAT, GCN4 Short) This Study N/A 1320 (BY4741, TBP1-myc13::HIS3, MBF1D::NAT, EKD-HA-Mbf1::Met 1; GCN4 Short) This Study N/A 1299 (MatA; GCN4-HA:Kan) This Study N/A 1301(matA; mbf1D::NAT, GCN4-HA:Kan) This Study N/A 1302 (matA; Mbf1:mCherry, GCN4-HA:Kan) This Study N/A 1304 (MatA, Mbf1-R89G-mCherry::HIS3, GCN4-HA:Kan) This Study N/A 1307 (MatA;Mbf1-mcherry NES::His, GCN4-HA:Kan) This Study N/A 690 (MatA, GCN4-3XFLAG:KAN) This Study N/A 693 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN) This Study N/A 919 (MatA, GCN4-3XFLAG:KAN 3, rps3-K108E:His) This Study N/A 1337 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E,L113A) This Study N/A 1338 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E, L113A, G121A) This Study N/A (Continued on next page) Molecular Cell 84, 1–18.e1–e9, December 5, 2024 e3
RNA sequencing:Article Title: Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Dynabeads mRNA DIRECT Kit Life Technologies Cat# 61012 Pierce Anti-HA Magnetic Beads ThermoFisher Scientific Cat# 88837 Anti-FLAG M2 Magnetic Beads Sigma Aldrich Cat# M8823 Pierce Anti-c-Myc Magnetic Beads ThermoFisher Scientific Cat# 88842 Dulbecco’s Modified Eagle Medium (DMEM) - high glucose, pyruvate, L-glutamine Thermo Fisher Cat# 11995073 Fetal bovine serum (FBS) Thermo Fisher Cat# 26140079 Lipofectamine RNAiMAX Transfection Reagent Thermo Fisher Cat# 13778075 L-Histidinol dihydrochloride Sigma Aldrich Cat# H6647 Anisomycin from Streptomyces griseolus Sigma Aldrich Cat# A9789 RIPA Lysis and Extraction Buffer Thermo Fisher Cat# 89901 Sodium phosphate dibasic Sigma Aldrich Cat# 71640 b-glycerophosphate Sigma Aldrich Cat# G9422 Benzonase nuclease Sigma Aldrich Cat# E1014 TCEP GoldBio Cat# TCEP25 Halt Protease and Phosphatase Inhibitor Cocktail (100X) – EDTA free Thermo Fisher Cat# 78440 10x Tris/Glycine/SDS running buffer Bio-rad Cat# 1610732 Blotto, non-fat dry milk Santa Cruz Biotechnology Cat# sc-2324 Emetine dihydrochloride Sigma Aldrich Cat# 324693 Sodium chloride (NaCl) Sigma Aldrich Cat# S9888 NP-40 Alternative, PROTEIN GRADE Detergent, 10% Solution, Sterile-Filtered Millipore Sigma Cat# 492018 1M Tris-HCl pH 7.0 Thermo Fisher Cat# AM9850G Sucrose Sigma Aldrich Cat# S7903 PBS pH 7.4 Thermo Fisher Cat# 10010049 Triton X-100 Sigma Aldrich Cat# T9284 EDTA (0.5 M), pH 8.0, RNase-free Thermo Fisher Cat# AM9260G TRIzol Reagent Thermo Fisher Cat# 15596026 Chloroform Sigma Cat# C2432 GlycoBlue Coprecipitant (15 mg/mL) Thermo Fisher Cat# AM9515 2-Propanol (HPLC), Fisher Chemical Fisher Scientific Cat# A451SK-4 Ethanol 200 Prf, 24x1 Gl Pint Pharmco Cat# 111000200CSPT Nuclease-Free Water (not DEPC-Treated) Thermo Fisher Cat# 4387936 TURBO DNase (2 U/mL) Thermo Fisher Cat# AM2238 Acid-Phenol:Chloroform, pH 4.5 (with IAA, 125:24:1) Thermo Fisher Cat# AM9722 Sodium Acetate (3 M), pH 5.5, RNase-free Thermo Fisher Cat# AM9740 iScript cDNA Synthesis Kit Bio-rad Cat# 1708891 Critical commercial assays Pierce BCA Protein Assay Kit Thermo Fisher Cat# 23225 4–20% Criterion TGX Precast Midi Protein Gel, 26 well, 15 ml Bio-rad Cat# 5671095 Trans-Blot Turbo RTA Midi 0.2 mm PVDF Transfer Kit Bio-rad Cat# 1704273 Deposited data Raw and analyzed RNAseq data This paper GSE255383 Custom python script This paper Zenodo: https://zenodo.org/ records/11190462 cryo-EM structural maps and molecular models This paper EMD-50170, EMD-50171, EMD-50259 and PDB: 9F9S (Continued on next page) e2 Molecular Cell 84, 1–18.e1–e9, December 5, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Raw gel image files This paper Mendeley Data: https://doi.org/ 10.17632/zj4x3426hv.2 Experimental models: Cell lines HEK293T ATCC Cat# CRL-3216 Experimental models: Organisms/strains BY4741 (MATa his3D1 leu2D0 met15D0 ura3D0) Dharmacon lab N/A mbf1D 319 (BY4741; mbf1D::NAT) This Study N/A gcn2D 619 (BY4741; gcn2D::KAN) Horizon N/A gcn4D (BY4741; gcn4D::KAN) Horizon N/A 703(MatA, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 705(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His) This Study N/A 923(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-HA) This Study N/A 1080 (matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His, EKD Mbf1-DN26-HA) This Study N/A 880 (MatA; GCN4-3XFLAG:KAN, ARG4-myc:His, PCL5D::Leu) This Study N/A 958 (MatA, GCN4-3XFLAG:KAN, ARG4-myc:His, Pho85D:Leu) This Study N/A 725(matA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1) This Study N/A 874 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN, ARG4-myc:His EKD-HA-Mbf1 R89G) This Study N/A 355 (MatA; Mbf1-6xGly-FLAG-mCherry His3) This Study N/A 992 (MatA, Mbf1-R89G-6xGly-FLAG -mCherry::HIS3) This Study N/A 1292 (MatA;Mbf1-mcherry NES::His) This Study N/A Long GCN4 1289 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Long GCN4 FLAG:Kan) This Study N/A Short GCN4 1290 (BY4741; mbf1D::NAT;EKD-HA-Mbf1:Met, Arg4-myc:His, Short GCN4 FLAG:Kan) This Study N/A Mbf1 WT, GCN4_Short 1316 (BY4741, TBP1-myc::HIS3, GCN4_FLAG_ Short) This Study N/A Mbf1D, GCN4_Short 1318 (BY4741, TBP1-myc::HIS3, MBF1D::NAT, GCN4 Short) This Study N/A 1320 (BY4741, TBP1-myc13::HIS3, MBF1D::NAT, EKD-HA-Mbf1::Met 1; GCN4 Short) This Study N/A 1299 (MatA; GCN4-HA:Kan) This Study N/A 1301(matA; mbf1D::NAT, GCN4-HA:Kan) This Study N/A 1302 (matA; Mbf1:mCherry, GCN4-HA:Kan) This Study N/A 1304 (MatA, Mbf1-R89G-mCherry::HIS3, GCN4-HA:Kan) This Study N/A 1307 (MatA;Mbf1-mcherry NES::His, GCN4-HA:Kan) This Study N/A 690 (MatA, GCN4-3XFLAG:KAN) This Study N/A 693 (MatA; mbf1D:NAT, GCN4-3XFLAG:KAN) This Study N/A 919 (MatA, GCN4-3XFLAG:KAN 3, rps3-K108E:His) This Study N/A 1337 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E,L113A) This Study N/A 1338 (MatA, GCN4-3XFLAG:KAN, RPS3 K108E, L113A, G121A) This Study N/A (Continued on next page) Molecular Cell 84, 1–18.e1–e9, December 5, 2024 e3
Recombinant:Article Title: Mitochondrial calcium uptake declines during aging and is directly activated by oleuropein to boost energy metabolism and skeletal muscle performance.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal anti-MCU Cell Signaling Technology Cat#14997; RRID:AB_2721812 Rabbit polyclonal anti-MCUR Booster Cat#A08547-1 Mousse monoclonal anti-TOM20 (F-10) Santa Cruz Cat#sc-17764; RRID:AB_628381 Rabbit polyclonal anti-MICU1 Sigma Aldrich Cat#HPA037479; RRID:AB_2675495 Rabbit polyclonal anti-PDH Cell Signaling Technology Cat#2784; RRID:AB_2162928 Rabbit polyclonal anti-PDH (phospho S293) Abcam Cat#ab92696, RRID:AB_10711672 Rabbit monoclonal anti-TOM20 (D8T4N) Cell Signaling Technology Cat#42406, RRID:AB_2687663 Mouse monoclonal anti-GRP 75 (D-9) Santa Cruz Biotechnology Cat#sc-133137, RRID:AB_2120468 Anti-Rabbit Detection Module ProteinSimple Cat#DM-001 Rabbit polyclonal anti_MCUR1 Cell Signaling Technology Cat#13706S; RRID:AB_2749813 Chemicals, peptides, and recombinant proteins ATP Sigma Aldrich Cat#A9187; CAS #: 74804-12-9 Histamine Sigma Aldrich Cat#H7125; CAS #: 51-45-6 Caffeine Sigma Aldrich Cat#C0750; CAS #: 58-08-2 Epibatidine Sigma Aldrich Cat#E1145;CAS #: 16637-43-2 Oleuropein Extrasynthese Cat#0228S; CAS #:32619-42-4 Oleuropein Aglycone Toronto Research Chemicals Cat#O532945; CAS #:31773-95-2 Hydroxytyrosol Extrasynthese Cat#4999S; CAS #: 10597-60-1 Oligomycin Sigma Aldrich Cat#75351 FCCP Sigma Aldrich Cat#C2920 Rotenone Sigma Aldrich Cat#45656 AntimycinA Sigma Aldrich Cat#A8674 Calcein AM Sigma Aldrich Cat#C0875; CAS#: 154071-48-4 Human Fibronectin Corning Cat#356008 PhosSTOP Merck Cat#4906845001 Fura-2, AM, cell permeant Thermo Fisher Cat#F1221 Gibco MEM, GlutaMAX Supplement Thermo Fisher Cat#41090 GOOD fetal bovine serum - 500 ml PanBiotech Cat#P40-37500 Penicillin-Streptomycin (5,000 U/mL) Thermo Fisher Cat#15070063 Gibco DMEM, high glucose, GlutaMAX Supplement, pyruvate Thermo Fisher Cat#31966 Gibco DMEM, high glucose, HEPES Thermo Fisher Cat#42430 Complete, Mini EDTA-free Protease Inhibitor Cocktail Merck Cat#11836170001 RIPA lysis and extraction buffer Thermo Fisher Cat89901 Non-Fat Dry Milk BioRad Cat#100-04504 PBS 1X PH 7.4 Thermo Fisher Cat# 10010023 Skeletal Muscle Cell Growth Medium Zen-Bio Cat#SKM-M medium Dulbecco’s Modified Eagle Medium F-12 Nutrient Mixture (DMEM/F-12 (1:1) (1x) +GlutaMAX) Thermo Fisher Cat#31331028 FBS Thermo Fisher Cat#10270106 Heat-inactivated Horse Serum Thermo Fisher Cat#26050088 PBS Thermo Fisher Cat#10010023 Tyrode’s salts Sigma Aldrich Cat#T2145 Dulbecco0s Modified Eagle0s Medium Sigma Aldrich Cat#D5030 (Continued on next page) e1 Cell Metabolism 37, 1–19.e1–e11, February 4, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRIzol Reagent Invitrogen, Thermo Fischer Cat#15596026 SuperScript III CellsDirect cDNA Synthesis Kit Invitrogen, Thermo Fisher Cat# 18080300 Master Mix PowerTrack SYBR Green Thermo Fisher Cat# A46109 Coelenterazine n Biotium 10110 CAS #: 55779-48-1 Digitonin Sigma Aldrich D5628; CAS#: 11024-24-1 N-Benzyl-p-toluenesulfonaMide Sigma Aldrich BL3H160B8B26; CAS#: 1576-37-0 Sodium Chloride Sigma Aldrich CAS#: 7647-14-5 Magnesium Chloride Sigma Aldrich CAS#:7791-18-6 HEPES Sigma Aldrich CAS#: 7365-45-9 Glucose Sigma Aldrich CAS#: 50-99-7 Calcium Chloride Sigma Aldrich CAS#: 10043-52-4 Potassium Chloride Sigma Aldrich CAS#: 7447-40-7 Thapsigargin Sigma Aldrich T9033; CAS#: 67526-95-8 EGTA Sigma Aldrich E3889; CAS#: 67-42-5 Collagenase A Roche Cat#COLLA-RO Kaempferol Sigma Aldrich CAS#: 5020-18-3 Olive leaf extract standardized with 40% oleuropein (OLE) Bioactor CAS#: 8060-29-5 JC-10 dye Enzo Lifesciences Cat#ENZ-52305 Hoestch Invitrogen Cat#H33342 Tris(2-carboxyethyl)phosphine (TCEP) Sigma Aldrich Cat#: C4706; CAS#: 51805-45-9 Critical commercial assays BCA protein assay kit Pierce Thermo Fisher Cat#23227 12-230kD Sally Sue Separation Module Protein Simple Cat#SM-S001 Pyruvate dehydrogenase (PDH) Enzyme Activity Microplate Assay Kit (ab109902) Abcam Cat#ab109920 NuPAGE 4 to 12%, Bis-Tris, 1.0–1.5 mm, Mini Protein Gels Invitrogen Cat#NP0336BOX Nitrocellulose membranes BioRad Cat#1704158 12-230 kDa Separation Module Protein Simple Cat#SM-S001 Incucyte Annexin V Green Dye Sartorius Cat#4642 Deposited data RNA-sequencing data Gene Expression Omnibus GSE11016 Source data This paper Data S1 Source Data Experimental models: Cell lines Human Skeletal Muscle Cells, Donor 7, Lot# 655307 Lonza Cat#LZ-CC-2580 Human Skeletal Muscle Cells, Donor 29, Lot # 639629 Lonza Cat#LZ-CC-2580 Human Skeletal Muscle Cells, Donor 215, Lot # SKM070512A Amsbio Cat#SKB-F Human Skeletal Muscle Cells, Donor 712, Lot # SKM062712B Amsbio Cat#SKB-F Human Skeletal Muscle Cells, Donor 211, Lot # SK120211 Amsbio Cat#SKB-F Human Skeletal Muscle Cells, Lot# P01064-69M Cook Myosite Cat#SK-1111 (Continued on next page) Cell Metabolism 37, 1–19.e1–e11, February 4, 2025 e2
Article Title: Hyperpolarization-activated cyclic nucleotide-gated cation channel 3 promotes HCC development in a female-biased manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti Mac-2 (Galectin-3) Cedarlane Labs Cat#CL8942AP; RRID:AB_10060357 Anti IL-6 Santa Cruz Biotechnology Cat#sc-1265; RRID:AB_2127470 Anti Na+/K+-ATPases Santa Cruz Biotechnology Cat#sc-48345; RRID:AB_626712 Anti b-Actin Santa Cruz Biotechnology Cat#sc-47778; RRID:AB_626632 Anti HCN3 Abcam Cat#ab84818; RRID:AB_1861081 Anti HCN3 Alomone Labs Cat#APC-057; RRID:AB_2039904 Anti HCN3 Thermo Fisher Cat#MA3-902; RRID:AB_2115028 Anti HA-tag Cell Signaling Technology Cat#3724; RRID:AB_1549585 Anti AFP Proteintech Cat#14550-1-AP; RRID:AB_2223933 Anti Albumin Proteintech Cat#16475-1-AP; RRID:AB_2242567 Anti Ki-67 Millipore-Sigma Cat#AB9260; RRID:AB_2142366 Anti NCOA5 Bethyl Cat#A300-790A; RRID:AB_2151214 Anti TIP30 Xiao lab (Ito et al.)28 N/A Anti PR Cell Signaling Technology Cat#8757; RRID:AB_2797144 LICOR IRDye 800CW secondary antibodies LICOR Cat#923–32213, 926–32214, 926-32211 LICOR IRDye 680RD secondary antibodies LICOR Cat#926–68072, 925–68074, 925-68076 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat#EC0112 E. coli TOP10 Thermo Fisher Cat#C404010 Biological samples Human HCC tissue array TissueArray.Com LLC Cat#LV1505a Chemicals, peptides, and recombinant proteins RIPA Lysis and Extraction Buffer Thermo Fisher Cat89900 Formalin solution, neutral buffered, 10% Sigma-Aldrich Cat#HT501128 TRIzol Reagent Thermo Fisher Cat#15596026 PowerUp SYBR Green reagent Thermo Fisher Cat#A25742 Lipofectamine 3000 Thermo Fisher Cat#L3000015 QuickExtract DNA Extraction Solution Lucigen Cat#QE0905T SuperScript IV First-Strand Synthesis System Thermo Fisher Cat#18091050 (R)-MG132 Cayman Chemical Cat#13697 ZD7288 Tocris Cat#1000 Polyethyleneimine Polysciences, Inc. Cat#23966-1 Puromycin dihydrochloride Thermo Fisher Cat#A1113803 Nitrotetrazolium Blue chloride Sigma-Aldrich Cat#N6639 Laemmli Sample Buffer BIO-RAD Cat#1610747 Thapsigargin Millipore-Sigma Cat#586005 Critical commercial assays Biorad Protein Assay BIO-RAD Cat#5000006 VECTASTAIN Elite ABC-HRP system Vector Laboratories Cat#PK-6101, PK-6102 Cell Counting Kit-8 Dojindo Cat#CK04 Alanine Transaminase Colorimetric Activity Assay Cayman Chemical Cat#700260 Mouse AFP Quantikine ELISA Kit R&D Systems Cat#MAFP00 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Mouse IL-6 ELISA Kit Proteintech Cat#KE10007 (Continued on next page) 16 Cell Reports 42, 113157, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Raw and processed RNA sequencing data This study GEO: GSE228531 Experimental models: Cell lines NIH/3T3 ATCC Cat#CRL-1658; RRID:CVCL_0594 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 PLC/PRF/5 ATCC Cat#CRL-8024; RRID:CVCL_0485 SNU-387 ATCC Cat#CRL-2237; RRID:CVCL_0250 Experimental models: Organisms/strains Mouse: Ncoa5+/ BALB/c Xiao lab (Gao et al.)8 N/A Mouse: Tip30+/ BALB/c Xiao lab (Ito et al.)28 N/A Mouse: Ncoa5+/ Tip30+/ BALB/c This study N/A Mouse: Hcn3 / C57BL/6 Biel lab (Fenske et al.)49 N/A Mouse: Hcn3 / BALB/c This study N/A Mouse: BALB/cJ Jackson Laboratory Cat#000651; RRID:IMSR_JAX:000651 Oligonucleotides See Table S4 for PCR primer sequences N/A N/A Recombinant DNA HCN3 CDS containing plasmid DF/HCC DNA Resource Core HsCD00348243 pSin-EF2 vector Yu et al.58 Addgene Cat#16579; RRID:Addgene_16579 pSpCas9(BB)-2A-Puro (PX459) V2.0 Ran et al.59 Addgene Cat#62988; RRID:Addgene_62988 pCMV delta R8.2 Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12263; RRID:Addgene_12263 pMD2.G Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12259; RRID:Addgene_12259 pGL2-Basic Promega N/A pcDNA3-TIP30 Xiao lab (Zhang et al.)60 N/A pcDNA3-hPR-A Su et al.61 Addgene Cat#89119; RRID:Addgene_189119 pcDNA3-PRB Su et al.61 Addgene Cat#89130; RRID:Addgene_89130 pRL Promega N/A pT3-EF1a-c-MYC Chen lab (Mendez-Lucas et al.)48 N/A pT3-EF1a-MCL1 Chen lab (Mendez-Lucas et al.)48 N/A pCMV/SB Chen lab (Mendez-Lucas et al.)48 N/A pSin-EF2-HCN3HA This study N/A PX459V2-HCN3-T1 This study N/A PX459V2-HCN3-T2 This study N/A pGL2-promoHCN3 This study N/A pT3-EF1a empty vector This study N/A pT3-EF1a-HCN3HA This study N/A Software and algorithms UCSC Xena Goldman et al.62 https://xena.ucsc.edu/ cBioportal Cerami et al.63; Gao et al.64 https://www.cbioportal.org/ STRING Szklarczyk et al.65 https://string-db.org/ Gene Set Enrichment Analysis Subramanian et al.51 https://www.gsea-msigdb.org/gsea/index.jsp ssGSEA Barbie et al.50 https://gsea-msigdb.github.io/ssGSEA- gpmodule/v10/index.html Trimmomatic Bolger et al.66 http://www.usadellab.org/cms/ ?page=trimmomatic STAR Dobin et al.67 https://github.com/alexdobin/STAR DESeq2 Love et al.68 https://bioconductor.org/packages/release/ bioc/html/DESeq2.html (Continued on next page) Cell Reports 42, 113157, October 31, 2023 17
Protease Inhibitor:Article Title: Mitochondrial calcium uptake declines during aging and is directly activated by oleuropein to boost energy metabolism and skeletal muscle performance.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal anti-MCU Cell Signaling Technology Cat#14997; RRID:AB_2721812 Rabbit polyclonal anti-MCUR Booster Cat#A08547-1 Mousse monoclonal anti-TOM20 (F-10) Santa Cruz Cat#sc-17764; RRID:AB_628381 Rabbit polyclonal anti-MICU1 Sigma Aldrich Cat#HPA037479; RRID:AB_2675495 Rabbit polyclonal anti-PDH Cell Signaling Technology Cat#2784; RRID:AB_2162928 Rabbit polyclonal anti-PDH (phospho S293) Abcam Cat#ab92696, RRID:AB_10711672 Rabbit monoclonal anti-TOM20 (D8T4N) Cell Signaling Technology Cat#42406, RRID:AB_2687663 Mouse monoclonal anti-GRP 75 (D-9) Santa Cruz Biotechnology Cat#sc-133137, RRID:AB_2120468 Anti-Rabbit Detection Module ProteinSimple Cat#DM-001 Rabbit polyclonal anti_MCUR1 Cell Signaling Technology Cat#13706S; RRID:AB_2749813 Chemicals, peptides, and recombinant proteins ATP Sigma Aldrich Cat#A9187; CAS #: 74804-12-9 Histamine Sigma Aldrich Cat#H7125; CAS #: 51-45-6 Caffeine Sigma Aldrich Cat#C0750; CAS #: 58-08-2 Epibatidine Sigma Aldrich Cat#E1145;CAS #: 16637-43-2 Oleuropein Extrasynthese Cat#0228S; CAS #:32619-42-4 Oleuropein Aglycone Toronto Research Chemicals Cat#O532945; CAS #:31773-95-2 Hydroxytyrosol Extrasynthese Cat#4999S; CAS #: 10597-60-1 Oligomycin Sigma Aldrich Cat#75351 FCCP Sigma Aldrich Cat#C2920 Rotenone Sigma Aldrich Cat#45656 AntimycinA Sigma Aldrich Cat#A8674 Calcein AM Sigma Aldrich Cat#C0875; CAS#: 154071-48-4 Human Fibronectin Corning Cat#356008 PhosSTOP Merck Cat#4906845001 Fura-2, AM, cell permeant Thermo Fisher Cat#F1221 Gibco MEM, GlutaMAX Supplement Thermo Fisher Cat#41090 GOOD fetal bovine serum - 500 ml PanBiotech Cat#P40-37500 Penicillin-Streptomycin (5,000 U/mL) Thermo Fisher Cat#15070063 Gibco DMEM, high glucose, GlutaMAX Supplement, pyruvate Thermo Fisher Cat#31966 Gibco DMEM, high glucose, HEPES Thermo Fisher Cat#42430 Complete, Mini EDTA-free Protease Inhibitor Cocktail Merck Cat#11836170001 RIPA lysis and extraction buffer Thermo Fisher Cat89901 Non-Fat Dry Milk BioRad Cat#100-04504 PBS 1X PH 7.4 Thermo Fisher Cat# 10010023 Skeletal Muscle Cell Growth Medium Zen-Bio Cat#SKM-M medium Dulbecco’s Modified Eagle Medium F-12 Nutrient Mixture (DMEM/F-12 (1:1) (1x) +GlutaMAX) Thermo Fisher Cat#31331028 FBS Thermo Fisher Cat#10270106 Heat-inactivated Horse Serum Thermo Fisher Cat#26050088 PBS Thermo Fisher Cat#10010023 Tyrode’s salts Sigma Aldrich Cat#T2145 Dulbecco0s Modified Eagle0s Medium Sigma Aldrich Cat#D5030 (Continued on next page) e1 Cell Metabolism 37, 1–19.e1–e11, February 4, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRIzol Reagent Invitrogen, Thermo Fischer Cat#15596026 SuperScript III CellsDirect cDNA Synthesis Kit Invitrogen, Thermo Fisher Cat# 18080300 Master Mix PowerTrack SYBR Green Thermo Fisher Cat# A46109 Coelenterazine n Biotium 10110 CAS #: 55779-48-1 Digitonin Sigma Aldrich D5628; CAS#: 11024-24-1 N-Benzyl-p-toluenesulfonaMide Sigma Aldrich BL3H160B8B26; CAS#: 1576-37-0 Sodium Chloride Sigma Aldrich CAS#: 7647-14-5 Magnesium Chloride Sigma Aldrich CAS#:7791-18-6 HEPES Sigma Aldrich CAS#: 7365-45-9 Glucose Sigma Aldrich CAS#: 50-99-7 Calcium Chloride Sigma Aldrich CAS#: 10043-52-4 Potassium Chloride Sigma Aldrich CAS#: 7447-40-7 Thapsigargin Sigma Aldrich T9033; CAS#: 67526-95-8 EGTA Sigma Aldrich E3889; CAS#: 67-42-5 Collagenase A Roche Cat#COLLA-RO Kaempferol Sigma Aldrich CAS#: 5020-18-3 Olive leaf extract standardized with 40% oleuropein (OLE) Bioactor CAS#: 8060-29-5 JC-10 dye Enzo Lifesciences Cat#ENZ-52305 Hoestch Invitrogen Cat#H33342 Tris(2-carboxyethyl)phosphine (TCEP) Sigma Aldrich Cat#: C4706; CAS#: 51805-45-9 Critical commercial assays BCA protein assay kit Pierce Thermo Fisher Cat#23227 12-230kD Sally Sue Separation Module Protein Simple Cat#SM-S001 Pyruvate dehydrogenase (PDH) Enzyme Activity Microplate Assay Kit (ab109902) Abcam Cat#ab109920 NuPAGE 4 to 12%, Bis-Tris, 1.0–1.5 mm, Mini Protein Gels Invitrogen Cat#NP0336BOX Nitrocellulose membranes BioRad Cat#1704158 12-230 kDa Separation Module Protein Simple Cat#SM-S001 Incucyte Annexin V Green Dye Sartorius Cat#4642 Deposited data RNA-sequencing data Gene Expression Omnibus GSE11016 Source data This paper Data S1 Source Data Experimental models: Cell lines Human Skeletal Muscle Cells, Donor 7, Lot# 655307 Lonza Cat#LZ-CC-2580 Human Skeletal Muscle Cells, Donor 29, Lot # 639629 Lonza Cat#LZ-CC-2580 Human Skeletal Muscle Cells, Donor 215, Lot # SKM070512A Amsbio Cat#SKB-F Human Skeletal Muscle Cells, Donor 712, Lot # SKM062712B Amsbio Cat#SKB-F Human Skeletal Muscle Cells, Donor 211, Lot # SK120211 Amsbio Cat#SKB-F Human Skeletal Muscle Cells, Lot# P01064-69M Cook Myosite Cat#SK-1111 (Continued on next page) Cell Metabolism 37, 1–19.e1–e11, February 4, 2025 e2
Milk:Article Title: Mitochondrial calcium uptake declines during aging and is directly activated by oleuropein to boost energy metabolism and skeletal muscle performance.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit monoclonal anti-MCU Cell Signaling Technology Cat#14997; RRID:AB_2721812 Rabbit polyclonal anti-MCUR Booster Cat#A08547-1 Mousse monoclonal anti-TOM20 (F-10) Santa Cruz Cat#sc-17764; RRID:AB_628381 Rabbit polyclonal anti-MICU1 Sigma Aldrich Cat#HPA037479; RRID:AB_2675495 Rabbit polyclonal anti-PDH Cell Signaling Technology Cat#2784; RRID:AB_2162928 Rabbit polyclonal anti-PDH (phospho S293) Abcam Cat#ab92696, RRID:AB_10711672 Rabbit monoclonal anti-TOM20 (D8T4N) Cell Signaling Technology Cat#42406, RRID:AB_2687663 Mouse monoclonal anti-GRP 75 (D-9) Santa Cruz Biotechnology Cat#sc-133137, RRID:AB_2120468 Anti-Rabbit Detection Module ProteinSimple Cat#DM-001 Rabbit polyclonal anti_MCUR1 Cell Signaling Technology Cat#13706S; RRID:AB_2749813 Chemicals, peptides, and recombinant proteins ATP Sigma Aldrich Cat#A9187; CAS #: 74804-12-9 Histamine Sigma Aldrich Cat#H7125; CAS #: 51-45-6 Caffeine Sigma Aldrich Cat#C0750; CAS #: 58-08-2 Epibatidine Sigma Aldrich Cat#E1145;CAS #: 16637-43-2 Oleuropein Extrasynthese Cat#0228S; CAS #:32619-42-4 Oleuropein Aglycone Toronto Research Chemicals Cat#O532945; CAS #:31773-95-2 Hydroxytyrosol Extrasynthese Cat#4999S; CAS #: 10597-60-1 Oligomycin Sigma Aldrich Cat#75351 FCCP Sigma Aldrich Cat#C2920 Rotenone Sigma Aldrich Cat#45656 AntimycinA Sigma Aldrich Cat#A8674 Calcein AM Sigma Aldrich Cat#C0875; CAS#: 154071-48-4 Human Fibronectin Corning Cat#356008 PhosSTOP Merck Cat#4906845001 Fura-2, AM, cell permeant Thermo Fisher Cat#F1221 Gibco MEM, GlutaMAX Supplement Thermo Fisher Cat#41090 GOOD fetal bovine serum - 500 ml PanBiotech Cat#P40-37500 Penicillin-Streptomycin (5,000 U/mL) Thermo Fisher Cat#15070063 Gibco DMEM, high glucose, GlutaMAX Supplement, pyruvate Thermo Fisher Cat#31966 Gibco DMEM, high glucose, HEPES Thermo Fisher Cat#42430 Complete, Mini EDTA-free Protease Inhibitor Cocktail Merck Cat#11836170001 RIPA lysis and extraction buffer Thermo Fisher Cat89901 Non-Fat Dry Milk BioRad Cat#100-04504 PBS 1X PH 7.4 Thermo Fisher Cat# 10010023 Skeletal Muscle Cell Growth Medium Zen-Bio Cat#SKM-M medium Dulbecco’s Modified Eagle Medium F-12 Nutrient Mixture (DMEM/F-12 (1:1) (1x) +GlutaMAX) Thermo Fisher Cat#31331028 FBS Thermo Fisher Cat#10270106 Heat-inactivated Horse Serum Thermo Fisher Cat#26050088 PBS Thermo Fisher Cat#10010023 Tyrode’s salts Sigma Aldrich Cat#T2145 Dulbecco0s Modified Eagle0s Medium Sigma Aldrich Cat#D5030 (Continued on next page) e1 Cell Metabolism 37, 1–19.e1–e11, February 4, 2025 .. REAGENT or RESOURCE SOURCE IDENTIFIER TRIzol Reagent Invitrogen, Thermo Fischer Cat#15596026 SuperScript III CellsDirect cDNA Synthesis Kit Invitrogen, Thermo Fisher Cat# 18080300 Master Mix PowerTrack SYBR Green Thermo Fisher Cat# A46109 Coelenterazine n Biotium 10110 CAS #: 55779-48-1 Digitonin Sigma Aldrich D5628; CAS#: 11024-24-1 N-Benzyl-p-toluenesulfonaMide Sigma Aldrich BL3H160B8B26; CAS#: 1576-37-0 Sodium Chloride Sigma Aldrich CAS#: 7647-14-5 Magnesium Chloride Sigma Aldrich CAS#:7791-18-6 HEPES Sigma Aldrich CAS#: 7365-45-9 Glucose Sigma Aldrich CAS#: 50-99-7 Calcium Chloride Sigma Aldrich CAS#: 10043-52-4 Potassium Chloride Sigma Aldrich CAS#: 7447-40-7 Thapsigargin Sigma Aldrich T9033; CAS#: 67526-95-8 EGTA Sigma Aldrich E3889; CAS#: 67-42-5 Collagenase A Roche Cat#COLLA-RO Kaempferol Sigma Aldrich CAS#: 5020-18-3 Olive leaf extract standardized with 40% oleuropein (OLE) Bioactor CAS#: 8060-29-5 JC-10 dye Enzo Lifesciences Cat#ENZ-52305 Hoestch Invitrogen Cat#H33342 Tris(2-carboxyethyl)phosphine (TCEP) Sigma Aldrich Cat#: C4706; CAS#: 51805-45-9 Critical commercial assays BCA protein assay kit Pierce Thermo Fisher Cat#23227 12-230kD Sally Sue Separation Module Protein Simple Cat#SM-S001 Pyruvate dehydrogenase (PDH) Enzyme Activity Microplate Assay Kit (ab109902) Abcam Cat#ab109920 NuPAGE 4 to 12%, Bis-Tris, 1.0–1.5 mm, Mini Protein Gels Invitrogen Cat#NP0336BOX Nitrocellulose membranes BioRad Cat#1704158 12-230 kDa Separation Module Protein Simple Cat#SM-S001 Incucyte Annexin V Green Dye Sartorius Cat#4642 Deposited data RNA-sequencing data Gene Expression Omnibus GSE11016 Source data This paper Data S1 Source Data Experimental models: Cell lines Human Skeletal Muscle Cells, Donor 7, Lot# 655307 Lonza Cat#LZ-CC-2580 Human Skeletal Muscle Cells, Donor 29, Lot # 639629 Lonza Cat#LZ-CC-2580 Human Skeletal Muscle Cells, Donor 215, Lot # SKM070512A Amsbio Cat#SKB-F Human Skeletal Muscle Cells, Donor 712, Lot # SKM062712B Amsbio Cat#SKB-F Human Skeletal Muscle Cells, Donor 211, Lot # SK120211 Amsbio Cat#SKB-F Human Skeletal Muscle Cells, Lot# P01064-69M Cook Myosite Cat#SK-1111 (Continued on next page) Cell Metabolism 37, 1–19.e1–e11, February 4, 2025 e2
Virus:Article Title: Hyperpolarization-activated cyclic nucleotide-gated cation channel 3 promotes HCC development in a female-biased manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti Mac-2 (Galectin-3) Cedarlane Labs Cat#CL8942AP; RRID:AB_10060357 Anti IL-6 Santa Cruz Biotechnology Cat#sc-1265; RRID:AB_2127470 Anti Na+/K+-ATPases Santa Cruz Biotechnology Cat#sc-48345; RRID:AB_626712 Anti b-Actin Santa Cruz Biotechnology Cat#sc-47778; RRID:AB_626632 Anti HCN3 Abcam Cat#ab84818; RRID:AB_1861081 Anti HCN3 Alomone Labs Cat#APC-057; RRID:AB_2039904 Anti HCN3 Thermo Fisher Cat#MA3-902; RRID:AB_2115028 Anti HA-tag Cell Signaling Technology Cat#3724; RRID:AB_1549585 Anti AFP Proteintech Cat#14550-1-AP; RRID:AB_2223933 Anti Albumin Proteintech Cat#16475-1-AP; RRID:AB_2242567 Anti Ki-67 Millipore-Sigma Cat#AB9260; RRID:AB_2142366 Anti NCOA5 Bethyl Cat#A300-790A; RRID:AB_2151214 Anti TIP30 Xiao lab (Ito et al.)28 N/A Anti PR Cell Signaling Technology Cat#8757; RRID:AB_2797144 LICOR IRDye 800CW secondary antibodies LICOR Cat#923–32213, 926–32214, 926-32211 LICOR IRDye 680RD secondary antibodies LICOR Cat#926–68072, 925–68074, 925-68076 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat#EC0112 E. coli TOP10 Thermo Fisher Cat#C404010 Biological samples Human HCC tissue array TissueArray.Com LLC Cat#LV1505a Chemicals, peptides, and recombinant proteins RIPA Lysis and Extraction Buffer Thermo Fisher Cat89900 Formalin solution, neutral buffered, 10% Sigma-Aldrich Cat#HT501128 TRIzol Reagent Thermo Fisher Cat#15596026 PowerUp SYBR Green reagent Thermo Fisher Cat#A25742 Lipofectamine 3000 Thermo Fisher Cat#L3000015 QuickExtract DNA Extraction Solution Lucigen Cat#QE0905T SuperScript IV First-Strand Synthesis System Thermo Fisher Cat#18091050 (R)-MG132 Cayman Chemical Cat#13697 ZD7288 Tocris Cat#1000 Polyethyleneimine Polysciences, Inc. Cat#23966-1 Puromycin dihydrochloride Thermo Fisher Cat#A1113803 Nitrotetrazolium Blue chloride Sigma-Aldrich Cat#N6639 Laemmli Sample Buffer BIO-RAD Cat#1610747 Thapsigargin Millipore-Sigma Cat#586005 Critical commercial assays Biorad Protein Assay BIO-RAD Cat#5000006 VECTASTAIN Elite ABC-HRP system Vector Laboratories Cat#PK-6101, PK-6102 Cell Counting Kit-8 Dojindo Cat#CK04 Alanine Transaminase Colorimetric Activity Assay Cayman Chemical Cat#700260 Mouse AFP Quantikine ELISA Kit R&D Systems Cat#MAFP00 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Mouse IL-6 ELISA Kit Proteintech Cat#KE10007 (Continued on next page) 16 Cell Reports 42, 113157, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Raw and processed RNA sequencing data This study GEO: GSE228531 Experimental models: Cell lines NIH/3T3 ATCC Cat#CRL-1658; RRID:CVCL_0594 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 PLC/PRF/5 ATCC Cat#CRL-8024; RRID:CVCL_0485 SNU-387 ATCC Cat#CRL-2237; RRID:CVCL_0250 Experimental models: Organisms/strains Mouse: Ncoa5+/ BALB/c Xiao lab (Gao et al.)8 N/A Mouse: Tip30+/ BALB/c Xiao lab (Ito et al.)28 N/A Mouse: Ncoa5+/ Tip30+/ BALB/c This study N/A Mouse: Hcn3 / C57BL/6 Biel lab (Fenske et al.)49 N/A Mouse: Hcn3 / BALB/c This study N/A Mouse: BALB/cJ Jackson Laboratory Cat#000651; RRID:IMSR_JAX:000651 Oligonucleotides See Table S4 for PCR primer sequences N/A N/A Recombinant DNA HCN3 CDS containing plasmid DF/HCC DNA Resource Core HsCD00348243 pSin-EF2 vector Yu et al.58 Addgene Cat#16579; RRID:Addgene_16579 pSpCas9(BB)-2A-Puro (PX459) V2.0 Ran et al.59 Addgene Cat#62988; RRID:Addgene_62988 pCMV delta R8.2 Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12263; RRID:Addgene_12263 pMD2.G Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12259; RRID:Addgene_12259 pGL2-Basic Promega N/A pcDNA3-TIP30 Xiao lab (Zhang et al.)60 N/A pcDNA3-hPR-A Su et al.61 Addgene Cat#89119; RRID:Addgene_189119 pcDNA3-PRB Su et al.61 Addgene Cat#89130; RRID:Addgene_89130 pRL Promega N/A pT3-EF1a-c-MYC Chen lab (Mendez-Lucas et al.)48 N/A pT3-EF1a-MCL1 Chen lab (Mendez-Lucas et al.)48 N/A pCMV/SB Chen lab (Mendez-Lucas et al.)48 N/A pSin-EF2-HCN3HA This study N/A PX459V2-HCN3-T1 This study N/A PX459V2-HCN3-T2 This study N/A pGL2-promoHCN3 This study N/A pT3-EF1a empty vector This study N/A pT3-EF1a-HCN3HA This study N/A Software and algorithms UCSC Xena Goldman et al.62 https://xena.ucsc.edu/ cBioportal Cerami et al.63; Gao et al.64 https://www.cbioportal.org/ STRING Szklarczyk et al.65 https://string-db.org/ Gene Set Enrichment Analysis Subramanian et al.51 https://www.gsea-msigdb.org/gsea/index.jsp ssGSEA Barbie et al.50 https://gsea-msigdb.github.io/ssGSEA- gpmodule/v10/index.html Trimmomatic Bolger et al.66 http://www.usadellab.org/cms/ ?page=trimmomatic STAR Dobin et al.67 https://github.com/alexdobin/STAR DESeq2 Love et al.68 https://bioconductor.org/packages/release/ bioc/html/DESeq2.html (Continued on next page) Cell Reports 42, 113157, October 31, 2023 17
DNA Extraction:Article Title: Hyperpolarization-activated cyclic nucleotide-gated cation channel 3 promotes HCC development in a female-biased manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti Mac-2 (Galectin-3) Cedarlane Labs Cat#CL8942AP; RRID:AB_10060357 Anti IL-6 Santa Cruz Biotechnology Cat#sc-1265; RRID:AB_2127470 Anti Na+/K+-ATPases Santa Cruz Biotechnology Cat#sc-48345; RRID:AB_626712 Anti b-Actin Santa Cruz Biotechnology Cat#sc-47778; RRID:AB_626632 Anti HCN3 Abcam Cat#ab84818; RRID:AB_1861081 Anti HCN3 Alomone Labs Cat#APC-057; RRID:AB_2039904 Anti HCN3 Thermo Fisher Cat#MA3-902; RRID:AB_2115028 Anti HA-tag Cell Signaling Technology Cat#3724; RRID:AB_1549585 Anti AFP Proteintech Cat#14550-1-AP; RRID:AB_2223933 Anti Albumin Proteintech Cat#16475-1-AP; RRID:AB_2242567 Anti Ki-67 Millipore-Sigma Cat#AB9260; RRID:AB_2142366 Anti NCOA5 Bethyl Cat#A300-790A; RRID:AB_2151214 Anti TIP30 Xiao lab (Ito et al.)28 N/A Anti PR Cell Signaling Technology Cat#8757; RRID:AB_2797144 LICOR IRDye 800CW secondary antibodies LICOR Cat#923–32213, 926–32214, 926-32211 LICOR IRDye 680RD secondary antibodies LICOR Cat#926–68072, 925–68074, 925-68076 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat#EC0112 E. coli TOP10 Thermo Fisher Cat#C404010 Biological samples Human HCC tissue array TissueArray.Com LLC Cat#LV1505a Chemicals, peptides, and recombinant proteins RIPA Lysis and Extraction Buffer Thermo Fisher Cat89900 Formalin solution, neutral buffered, 10% Sigma-Aldrich Cat#HT501128 TRIzol Reagent Thermo Fisher Cat#15596026 PowerUp SYBR Green reagent Thermo Fisher Cat#A25742 Lipofectamine 3000 Thermo Fisher Cat#L3000015 QuickExtract DNA Extraction Solution Lucigen Cat#QE0905T SuperScript IV First-Strand Synthesis System Thermo Fisher Cat#18091050 (R)-MG132 Cayman Chemical Cat#13697 ZD7288 Tocris Cat#1000 Polyethyleneimine Polysciences, Inc. Cat#23966-1 Puromycin dihydrochloride Thermo Fisher Cat#A1113803 Nitrotetrazolium Blue chloride Sigma-Aldrich Cat#N6639 Laemmli Sample Buffer BIO-RAD Cat#1610747 Thapsigargin Millipore-Sigma Cat#586005 Critical commercial assays Biorad Protein Assay BIO-RAD Cat#5000006 VECTASTAIN Elite ABC-HRP system Vector Laboratories Cat#PK-6101, PK-6102 Cell Counting Kit-8 Dojindo Cat#CK04 Alanine Transaminase Colorimetric Activity Assay Cayman Chemical Cat#700260 Mouse AFP Quantikine ELISA Kit R&D Systems Cat#MAFP00 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Mouse IL-6 ELISA Kit Proteintech Cat#KE10007 (Continued on next page) 16 Cell Reports 42, 113157, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Raw and processed RNA sequencing data This study GEO: GSE228531 Experimental models: Cell lines NIH/3T3 ATCC Cat#CRL-1658; RRID:CVCL_0594 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 PLC/PRF/5 ATCC Cat#CRL-8024; RRID:CVCL_0485 SNU-387 ATCC Cat#CRL-2237; RRID:CVCL_0250 Experimental models: Organisms/strains Mouse: Ncoa5+/ BALB/c Xiao lab (Gao et al.)8 N/A Mouse: Tip30+/ BALB/c Xiao lab (Ito et al.)28 N/A Mouse: Ncoa5+/ Tip30+/ BALB/c This study N/A Mouse: Hcn3 / C57BL/6 Biel lab (Fenske et al.)49 N/A Mouse: Hcn3 / BALB/c This study N/A Mouse: BALB/cJ Jackson Laboratory Cat#000651; RRID:IMSR_JAX:000651 Oligonucleotides See Table S4 for PCR primer sequences N/A N/A Recombinant DNA HCN3 CDS containing plasmid DF/HCC DNA Resource Core HsCD00348243 pSin-EF2 vector Yu et al.58 Addgene Cat#16579; RRID:Addgene_16579 pSpCas9(BB)-2A-Puro (PX459) V2.0 Ran et al.59 Addgene Cat#62988; RRID:Addgene_62988 pCMV delta R8.2 Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12263; RRID:Addgene_12263 pMD2.G Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12259; RRID:Addgene_12259 pGL2-Basic Promega N/A pcDNA3-TIP30 Xiao lab (Zhang et al.)60 N/A pcDNA3-hPR-A Su et al.61 Addgene Cat#89119; RRID:Addgene_189119 pcDNA3-PRB Su et al.61 Addgene Cat#89130; RRID:Addgene_89130 pRL Promega N/A pT3-EF1a-c-MYC Chen lab (Mendez-Lucas et al.)48 N/A pT3-EF1a-MCL1 Chen lab (Mendez-Lucas et al.)48 N/A pCMV/SB Chen lab (Mendez-Lucas et al.)48 N/A pSin-EF2-HCN3HA This study N/A PX459V2-HCN3-T1 This study N/A PX459V2-HCN3-T2 This study N/A pGL2-promoHCN3 This study N/A pT3-EF1a empty vector This study N/A pT3-EF1a-HCN3HA This study N/A Software and algorithms UCSC Xena Goldman et al.62 https://xena.ucsc.edu/ cBioportal Cerami et al.63; Gao et al.64 https://www.cbioportal.org/ STRING Szklarczyk et al.65 https://string-db.org/ Gene Set Enrichment Analysis Subramanian et al.51 https://www.gsea-msigdb.org/gsea/index.jsp ssGSEA Barbie et al.50 https://gsea-msigdb.github.io/ssGSEA- gpmodule/v10/index.html Trimmomatic Bolger et al.66 http://www.usadellab.org/cms/ ?page=trimmomatic STAR Dobin et al.67 https://github.com/alexdobin/STAR DESeq2 Love et al.68 https://bioconductor.org/packages/release/ bioc/html/DESeq2.html (Continued on next page) Cell Reports 42, 113157, October 31, 2023 17
CCK-8 Assay:Article Title: Hyperpolarization-activated cyclic nucleotide-gated cation channel 3 promotes HCC development in a female-biased manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti Mac-2 (Galectin-3) Cedarlane Labs Cat#CL8942AP; RRID:AB_10060357 Anti IL-6 Santa Cruz Biotechnology Cat#sc-1265; RRID:AB_2127470 Anti Na+/K+-ATPases Santa Cruz Biotechnology Cat#sc-48345; RRID:AB_626712 Anti b-Actin Santa Cruz Biotechnology Cat#sc-47778; RRID:AB_626632 Anti HCN3 Abcam Cat#ab84818; RRID:AB_1861081 Anti HCN3 Alomone Labs Cat#APC-057; RRID:AB_2039904 Anti HCN3 Thermo Fisher Cat#MA3-902; RRID:AB_2115028 Anti HA-tag Cell Signaling Technology Cat#3724; RRID:AB_1549585 Anti AFP Proteintech Cat#14550-1-AP; RRID:AB_2223933 Anti Albumin Proteintech Cat#16475-1-AP; RRID:AB_2242567 Anti Ki-67 Millipore-Sigma Cat#AB9260; RRID:AB_2142366 Anti NCOA5 Bethyl Cat#A300-790A; RRID:AB_2151214 Anti TIP30 Xiao lab (Ito et al.)28 N/A Anti PR Cell Signaling Technology Cat#8757; RRID:AB_2797144 LICOR IRDye 800CW secondary antibodies LICOR Cat#923–32213, 926–32214, 926-32211 LICOR IRDye 680RD secondary antibodies LICOR Cat#926–68072, 925–68074, 925-68076 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat#EC0112 E. coli TOP10 Thermo Fisher Cat#C404010 Biological samples Human HCC tissue array TissueArray.Com LLC Cat#LV1505a Chemicals, peptides, and recombinant proteins RIPA Lysis and Extraction Buffer Thermo Fisher Cat89900 Formalin solution, neutral buffered, 10% Sigma-Aldrich Cat#HT501128 TRIzol Reagent Thermo Fisher Cat#15596026 PowerUp SYBR Green reagent Thermo Fisher Cat#A25742 Lipofectamine 3000 Thermo Fisher Cat#L3000015 QuickExtract DNA Extraction Solution Lucigen Cat#QE0905T SuperScript IV First-Strand Synthesis System Thermo Fisher Cat#18091050 (R)-MG132 Cayman Chemical Cat#13697 ZD7288 Tocris Cat#1000 Polyethyleneimine Polysciences, Inc. Cat#23966-1 Puromycin dihydrochloride Thermo Fisher Cat#A1113803 Nitrotetrazolium Blue chloride Sigma-Aldrich Cat#N6639 Laemmli Sample Buffer BIO-RAD Cat#1610747 Thapsigargin Millipore-Sigma Cat#586005 Critical commercial assays Biorad Protein Assay BIO-RAD Cat#5000006 VECTASTAIN Elite ABC-HRP system Vector Laboratories Cat#PK-6101, PK-6102 Cell Counting Kit-8 Dojindo Cat#CK04 Alanine Transaminase Colorimetric Activity Assay Cayman Chemical Cat#700260 Mouse AFP Quantikine ELISA Kit R&D Systems Cat#MAFP00 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Mouse IL-6 ELISA Kit Proteintech Cat#KE10007 (Continued on next page) 16 Cell Reports 42, 113157, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Raw and processed RNA sequencing data This study GEO: GSE228531 Experimental models: Cell lines NIH/3T3 ATCC Cat#CRL-1658; RRID:CVCL_0594 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 PLC/PRF/5 ATCC Cat#CRL-8024; RRID:CVCL_0485 SNU-387 ATCC Cat#CRL-2237; RRID:CVCL_0250 Experimental models: Organisms/strains Mouse: Ncoa5+/ BALB/c Xiao lab (Gao et al.)8 N/A Mouse: Tip30+/ BALB/c Xiao lab (Ito et al.)28 N/A Mouse: Ncoa5+/ Tip30+/ BALB/c This study N/A Mouse: Hcn3 / C57BL/6 Biel lab (Fenske et al.)49 N/A Mouse: Hcn3 / BALB/c This study N/A Mouse: BALB/cJ Jackson Laboratory Cat#000651; RRID:IMSR_JAX:000651 Oligonucleotides See Table S4 for PCR primer sequences N/A N/A Recombinant DNA HCN3 CDS containing plasmid DF/HCC DNA Resource Core HsCD00348243 pSin-EF2 vector Yu et al.58 Addgene Cat#16579; RRID:Addgene_16579 pSpCas9(BB)-2A-Puro (PX459) V2.0 Ran et al.59 Addgene Cat#62988; RRID:Addgene_62988 pCMV delta R8.2 Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12263; RRID:Addgene_12263 pMD2.G Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12259; RRID:Addgene_12259 pGL2-Basic Promega N/A pcDNA3-TIP30 Xiao lab (Zhang et al.)60 N/A pcDNA3-hPR-A Su et al.61 Addgene Cat#89119; RRID:Addgene_189119 pcDNA3-PRB Su et al.61 Addgene Cat#89130; RRID:Addgene_89130 pRL Promega N/A pT3-EF1a-c-MYC Chen lab (Mendez-Lucas et al.)48 N/A pT3-EF1a-MCL1 Chen lab (Mendez-Lucas et al.)48 N/A pCMV/SB Chen lab (Mendez-Lucas et al.)48 N/A pSin-EF2-HCN3HA This study N/A PX459V2-HCN3-T1 This study N/A PX459V2-HCN3-T2 This study N/A pGL2-promoHCN3 This study N/A pT3-EF1a empty vector This study N/A pT3-EF1a-HCN3HA This study N/A Software and algorithms UCSC Xena Goldman et al.62 https://xena.ucsc.edu/ cBioportal Cerami et al.63; Gao et al.64 https://www.cbioportal.org/ STRING Szklarczyk et al.65 https://string-db.org/ Gene Set Enrichment Analysis Subramanian et al.51 https://www.gsea-msigdb.org/gsea/index.jsp ssGSEA Barbie et al.50 https://gsea-msigdb.github.io/ssGSEA- gpmodule/v10/index.html Trimmomatic Bolger et al.66 http://www.usadellab.org/cms/ ?page=trimmomatic STAR Dobin et al.67 https://github.com/alexdobin/STAR DESeq2 Love et al.68 https://bioconductor.org/packages/release/ bioc/html/DESeq2.html (Continued on next page) Cell Reports 42, 113157, October 31, 2023 17
Activity Assay:Article Title: Hyperpolarization-activated cyclic nucleotide-gated cation channel 3 promotes HCC development in a female-biased manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti Mac-2 (Galectin-3) Cedarlane Labs Cat#CL8942AP; RRID:AB_10060357 Anti IL-6 Santa Cruz Biotechnology Cat#sc-1265; RRID:AB_2127470 Anti Na+/K+-ATPases Santa Cruz Biotechnology Cat#sc-48345; RRID:AB_626712 Anti b-Actin Santa Cruz Biotechnology Cat#sc-47778; RRID:AB_626632 Anti HCN3 Abcam Cat#ab84818; RRID:AB_1861081 Anti HCN3 Alomone Labs Cat#APC-057; RRID:AB_2039904 Anti HCN3 Thermo Fisher Cat#MA3-902; RRID:AB_2115028 Anti HA-tag Cell Signaling Technology Cat#3724; RRID:AB_1549585 Anti AFP Proteintech Cat#14550-1-AP; RRID:AB_2223933 Anti Albumin Proteintech Cat#16475-1-AP; RRID:AB_2242567 Anti Ki-67 Millipore-Sigma Cat#AB9260; RRID:AB_2142366 Anti NCOA5 Bethyl Cat#A300-790A; RRID:AB_2151214 Anti TIP30 Xiao lab (Ito et al.)28 N/A Anti PR Cell Signaling Technology Cat#8757; RRID:AB_2797144 LICOR IRDye 800CW secondary antibodies LICOR Cat#923–32213, 926–32214, 926-32211 LICOR IRDye 680RD secondary antibodies LICOR Cat#926–68072, 925–68074, 925-68076 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat#EC0112 E. coli TOP10 Thermo Fisher Cat#C404010 Biological samples Human HCC tissue array TissueArray.Com LLC Cat#LV1505a Chemicals, peptides, and recombinant proteins RIPA Lysis and Extraction Buffer Thermo Fisher Cat89900 Formalin solution, neutral buffered, 10% Sigma-Aldrich Cat#HT501128 TRIzol Reagent Thermo Fisher Cat#15596026 PowerUp SYBR Green reagent Thermo Fisher Cat#A25742 Lipofectamine 3000 Thermo Fisher Cat#L3000015 QuickExtract DNA Extraction Solution Lucigen Cat#QE0905T SuperScript IV First-Strand Synthesis System Thermo Fisher Cat#18091050 (R)-MG132 Cayman Chemical Cat#13697 ZD7288 Tocris Cat#1000 Polyethyleneimine Polysciences, Inc. Cat#23966-1 Puromycin dihydrochloride Thermo Fisher Cat#A1113803 Nitrotetrazolium Blue chloride Sigma-Aldrich Cat#N6639 Laemmli Sample Buffer BIO-RAD Cat#1610747 Thapsigargin Millipore-Sigma Cat#586005 Critical commercial assays Biorad Protein Assay BIO-RAD Cat#5000006 VECTASTAIN Elite ABC-HRP system Vector Laboratories Cat#PK-6101, PK-6102 Cell Counting Kit-8 Dojindo Cat#CK04 Alanine Transaminase Colorimetric Activity Assay Cayman Chemical Cat#700260 Mouse AFP Quantikine ELISA Kit R&D Systems Cat#MAFP00 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Mouse IL-6 ELISA Kit Proteintech Cat#KE10007 (Continued on next page) 16 Cell Reports 42, 113157, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Raw and processed RNA sequencing data This study GEO: GSE228531 Experimental models: Cell lines NIH/3T3 ATCC Cat#CRL-1658; RRID:CVCL_0594 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 PLC/PRF/5 ATCC Cat#CRL-8024; RRID:CVCL_0485 SNU-387 ATCC Cat#CRL-2237; RRID:CVCL_0250 Experimental models: Organisms/strains Mouse: Ncoa5+/ BALB/c Xiao lab (Gao et al.)8 N/A Mouse: Tip30+/ BALB/c Xiao lab (Ito et al.)28 N/A Mouse: Ncoa5+/ Tip30+/ BALB/c This study N/A Mouse: Hcn3 / C57BL/6 Biel lab (Fenske et al.)49 N/A Mouse: Hcn3 / BALB/c This study N/A Mouse: BALB/cJ Jackson Laboratory Cat#000651; RRID:IMSR_JAX:000651 Oligonucleotides See Table S4 for PCR primer sequences N/A N/A Recombinant DNA HCN3 CDS containing plasmid DF/HCC DNA Resource Core HsCD00348243 pSin-EF2 vector Yu et al.58 Addgene Cat#16579; RRID:Addgene_16579 pSpCas9(BB)-2A-Puro (PX459) V2.0 Ran et al.59 Addgene Cat#62988; RRID:Addgene_62988 pCMV delta R8.2 Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12263; RRID:Addgene_12263 pMD2.G Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12259; RRID:Addgene_12259 pGL2-Basic Promega N/A pcDNA3-TIP30 Xiao lab (Zhang et al.)60 N/A pcDNA3-hPR-A Su et al.61 Addgene Cat#89119; RRID:Addgene_189119 pcDNA3-PRB Su et al.61 Addgene Cat#89130; RRID:Addgene_89130 pRL Promega N/A pT3-EF1a-c-MYC Chen lab (Mendez-Lucas et al.)48 N/A pT3-EF1a-MCL1 Chen lab (Mendez-Lucas et al.)48 N/A pCMV/SB Chen lab (Mendez-Lucas et al.)48 N/A pSin-EF2-HCN3HA This study N/A PX459V2-HCN3-T1 This study N/A PX459V2-HCN3-T2 This study N/A pGL2-promoHCN3 This study N/A pT3-EF1a empty vector This study N/A pT3-EF1a-HCN3HA This study N/A Software and algorithms UCSC Xena Goldman et al.62 https://xena.ucsc.edu/ cBioportal Cerami et al.63; Gao et al.64 https://www.cbioportal.org/ STRING Szklarczyk et al.65 https://string-db.org/ Gene Set Enrichment Analysis Subramanian et al.51 https://www.gsea-msigdb.org/gsea/index.jsp ssGSEA Barbie et al.50 https://gsea-msigdb.github.io/ssGSEA- gpmodule/v10/index.html Trimmomatic Bolger et al.66 http://www.usadellab.org/cms/ ?page=trimmomatic STAR Dobin et al.67 https://github.com/alexdobin/STAR DESeq2 Love et al.68 https://bioconductor.org/packages/release/ bioc/html/DESeq2.html (Continued on next page) Cell Reports 42, 113157, October 31, 2023 17
Reporter Assay:Article Title: Hyperpolarization-activated cyclic nucleotide-gated cation channel 3 promotes HCC development in a female-biased manner.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti Mac-2 (Galectin-3) Cedarlane Labs Cat#CL8942AP; RRID:AB_10060357 Anti IL-6 Santa Cruz Biotechnology Cat#sc-1265; RRID:AB_2127470 Anti Na+/K+-ATPases Santa Cruz Biotechnology Cat#sc-48345; RRID:AB_626712 Anti b-Actin Santa Cruz Biotechnology Cat#sc-47778; RRID:AB_626632 Anti HCN3 Abcam Cat#ab84818; RRID:AB_1861081 Anti HCN3 Alomone Labs Cat#APC-057; RRID:AB_2039904 Anti HCN3 Thermo Fisher Cat#MA3-902; RRID:AB_2115028 Anti HA-tag Cell Signaling Technology Cat#3724; RRID:AB_1549585 Anti AFP Proteintech Cat#14550-1-AP; RRID:AB_2223933 Anti Albumin Proteintech Cat#16475-1-AP; RRID:AB_2242567 Anti Ki-67 Millipore-Sigma Cat#AB9260; RRID:AB_2142366 Anti NCOA5 Bethyl Cat#A300-790A; RRID:AB_2151214 Anti TIP30 Xiao lab (Ito et al.)28 N/A Anti PR Cell Signaling Technology Cat#8757; RRID:AB_2797144 LICOR IRDye 800CW secondary antibodies LICOR Cat#923–32213, 926–32214, 926-32211 LICOR IRDye 680RD secondary antibodies LICOR Cat#926–68072, 925–68074, 925-68076 Bacterial and virus strains E. coli DH5a Thermo Fisher Cat#EC0112 E. coli TOP10 Thermo Fisher Cat#C404010 Biological samples Human HCC tissue array TissueArray.Com LLC Cat#LV1505a Chemicals, peptides, and recombinant proteins RIPA Lysis and Extraction Buffer Thermo Fisher Cat89900 Formalin solution, neutral buffered, 10% Sigma-Aldrich Cat#HT501128 TRIzol Reagent Thermo Fisher Cat#15596026 PowerUp SYBR Green reagent Thermo Fisher Cat#A25742 Lipofectamine 3000 Thermo Fisher Cat#L3000015 QuickExtract DNA Extraction Solution Lucigen Cat#QE0905T SuperScript IV First-Strand Synthesis System Thermo Fisher Cat#18091050 (R)-MG132 Cayman Chemical Cat#13697 ZD7288 Tocris Cat#1000 Polyethyleneimine Polysciences, Inc. Cat#23966-1 Puromycin dihydrochloride Thermo Fisher Cat#A1113803 Nitrotetrazolium Blue chloride Sigma-Aldrich Cat#N6639 Laemmli Sample Buffer BIO-RAD Cat#1610747 Thapsigargin Millipore-Sigma Cat#586005 Critical commercial assays Biorad Protein Assay BIO-RAD Cat#5000006 VECTASTAIN Elite ABC-HRP system Vector Laboratories Cat#PK-6101, PK-6102 Cell Counting Kit-8 Dojindo Cat#CK04 Alanine Transaminase Colorimetric Activity Assay Cayman Chemical Cat#700260 Mouse AFP Quantikine ELISA Kit R&D Systems Cat#MAFP00 Dual-Luciferase Reporter Assay System Promega Cat#E1910 Mouse IL-6 ELISA Kit Proteintech Cat#KE10007 (Continued on next page) 16 Cell Reports 42, 113157, October 31, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data Raw and processed RNA sequencing data This study GEO: GSE228531 Experimental models: Cell lines NIH/3T3 ATCC Cat#CRL-1658; RRID:CVCL_0594 HEK293T ATCC Cat#CRL-3216; RRID:CVCL_0063 PLC/PRF/5 ATCC Cat#CRL-8024; RRID:CVCL_0485 SNU-387 ATCC Cat#CRL-2237; RRID:CVCL_0250 Experimental models: Organisms/strains Mouse: Ncoa5+/ BALB/c Xiao lab (Gao et al.)8 N/A Mouse: Tip30+/ BALB/c Xiao lab (Ito et al.)28 N/A Mouse: Ncoa5+/ Tip30+/ BALB/c This study N/A Mouse: Hcn3 / C57BL/6 Biel lab (Fenske et al.)49 N/A Mouse: Hcn3 / BALB/c This study N/A Mouse: BALB/cJ Jackson Laboratory Cat#000651; RRID:IMSR_JAX:000651 Oligonucleotides See Table S4 for PCR primer sequences N/A N/A Recombinant DNA HCN3 CDS containing plasmid DF/HCC DNA Resource Core HsCD00348243 pSin-EF2 vector Yu et al.58 Addgene Cat#16579; RRID:Addgene_16579 pSpCas9(BB)-2A-Puro (PX459) V2.0 Ran et al.59 Addgene Cat#62988; RRID:Addgene_62988 pCMV delta R8.2 Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12263; RRID:Addgene_12263 pMD2.G Trono Lab Packaging and Envelope Plasmids (unpublished) Addgene Cat#12259; RRID:Addgene_12259 pGL2-Basic Promega N/A pcDNA3-TIP30 Xiao lab (Zhang et al.)60 N/A pcDNA3-hPR-A Su et al.61 Addgene Cat#89119; RRID:Addgene_189119 pcDNA3-PRB Su et al.61 Addgene Cat#89130; RRID:Addgene_89130 pRL Promega N/A pT3-EF1a-c-MYC Chen lab (Mendez-Lucas et al.)48 N/A pT3-EF1a-MCL1 Chen lab (Mendez-Lucas et al.)48 N/A pCMV/SB Chen lab (Mendez-Lucas et al.)48 N/A pSin-EF2-HCN3HA This study N/A PX459V2-HCN3-T1 This study N/A PX459V2-HCN3-T2 This study N/A pGL2-promoHCN3 This study N/A pT3-EF1a empty vector This study N/A pT3-EF1a-HCN3HA This study N/A Software and algorithms UCSC Xena Goldman et al.62 https://xena.ucsc.edu/ cBioportal Cerami et al.63; Gao et al.64 https://www.cbioportal.org/ STRING Szklarczyk et al.65 https://string-db.org/ Gene Set Enrichment Analysis Subramanian et al.51 https://www.gsea-msigdb.org/gsea/index.jsp ssGSEA Barbie et al.50 https://gsea-msigdb.github.io/ssGSEA- gpmodule/v10/index.html Trimmomatic Bolger et al.66 http://www.usadellab.org/cms/ ?page=trimmomatic STAR Dobin et al.67 https://github.com/alexdobin/STAR DESeq2 Love et al.68 https://bioconductor.org/packages/release/ bioc/html/DESeq2.html (Continued on next page) Cell Reports 42, 113157, October 31, 2023 17
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