Virus:Article Title: Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-HA Roche Cat# 1186742300; RRID: AB_390918 Chicken anti-GFP Abcam Cat# Ab13970; RRID: AB_300798 Rabbit anti-NeuN Sigma Aldrich Cat# ABN78; RRID: AB_10807945 Mouse anti-Robo3 R&D Systems Cat# AF3155; RRID: AB_10644167 Mouse anti-GluN1 SySy Cat# 114011; RRID: AB_887750 Goat anti-rat Alexa 555 ThermoFisher Cat# A21434; RRID: AB_2535855 Goat anti-chicken Alexa 488 ThermoFisher Cat# A11039; RRID: AB_2534096 Goat anti-mouse Alexa 647 ThermoFisher Cat# A21235; RRID: AB_2535804 Streptavidin Alexa 647 ThermoFisher Cat# S32357 Bacterial and virus strains scAAV9-hSyn-iCre-HA Boston Children’s Hospital Viral Core N/A scAAV9-hSyn-DiCre-HA Boston Children’s Hospital Viral Core N/A AAV9-hSyn-DN-THR Boston Children’s Hospital Viral Core N/A AAV9-hSyn-WT-THR Boston Children’s Hospital Viral Core N/A AAV9-SIO-nEF-DN-Thrb Janelia Viral Tools N/A AAV9-SIO-nEF-WT-Thrb Janelia Viral Tools N/A AAV9-hSyn-FLEX-CoChR-GFP UNC GTC Vector Core N/A AAVretro-CAG-Cre UNC GTC Vector Core N/A AAV9-hSyn-CoChR-GFP UNC GTC Vector Core N/A pENN.AAV_PHPeB.hSyn.HI.eGFP-Cre.WPRE.SV40 Addgene Addgene 105540 AAV9-S5E2-ChR2-mCherry Addgene Addgene 135634 Chemicals, peptides, and recombinant proteins 3,3’,5-Triiodo-L-thyronine Sigma-Aldrich Cat# T6397 Sobetirome Thomas Scanlan N/A Kolliphor Sigma-Aldrich Cat# C5135 NMP Sigma-Aldrich Cat# 328634 0.15% PTU Diet Inotiv Cat# TD.95125 Control Diet Inotiv Cat# TD.97350 Trizol Life Technologies Cat# 15596018 RIPA buffer ThermoFisher Cat# 89900 cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail Roche Cat# 11836170001 Biocytin Sigma Aldrich Cat# B4261 Critical commercial assays Chromium Next GEM Single Cell 3’ Kit v3 10X Genomics Cat#1000268 RNEasy Micro Kit Qiagen Cat#74004 SuperScript IV VILO Master Mix Kit with ezDNAse enzyme ThermoFisher Cat#11766050 RNAscope Multiplex Fluorescent Reagent Kit v1 (discontinued) and v2 Advanced Cell Diagnostics Cat#323100 (Continued on next page) e1 Cell 187, 1–19.e1–e11, October 3, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data snRNA-seq datasets This paper GEO: GSE271421 snRNA-seq datasets This paper https://cellxgene.cziscience.com/ collections/c450e15d-321a-42d6986b-11409d04896d Moseq, electrophysiology, and 2ABT datasets This paper https://dataverse.harvard.edu/ dataverse/2024_hochbaum_thyroid Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat# 664; RRID:IMSR_JAX:000664 Mouse: Robo3 fl/fl: Robo3tm1.1Ache Alain Chédotal111 MGI:4441335 Oligonucleotides TaqMan probe for Hr: (Mm00498963_m1) ThermoFisher Cat# 4331182 TaqMan probe for Dio1: (Mm00839358_m1) ThermoFisher Cat# 4331182 TaqMan probe for Ier5: (Mm01295615_s1) ThermoFisher Cat# 4331182 TaqMan probe for Gapdh: (Mm99999915_g1) ThermoFisher Cat# 4351370 TaqMan probe for Cyp11a1: (Mm00490735_m1) ThermoFisher Cat# 4331182 FISH probe for Hr Advanced Cell Diagnostics Cat# 883311 FISH probe for Ier5 Advanced Cell Diagnostics Cat# 530401-C3 FISH probe for Robo3 Advanced Cell Diagnostics Cat# 558811-C2 4-plex positive probe Advanced Cell Diagnostics Cat# 321811 4-plex negative control probe Advanced Cell Diagnostics Cat# 321831 Recombinant DNA DRH001_scAAV-hSyn-iCre-HA This paper Addgene 225086 DRH002_scAAV-hSyn-DiCre-HA This paper Addgene 225087 DRH015_ AAV-hSyn-WT-THR This paper Addgene 225088 DRH016_ AAV-hSyn-DN-THR This paper Addgene 225089 DRH031_ AAV-SIO-nEF-WT-THR This paper Addgene 225090 DRH032_ AAV-SIO-nEF-DN-THR This paper Addgene 225091 Software and algorithms Custom software This paper https://github.com/bernardosabatinilab/ hochbaum_thyroid_2024 NeuroInfo MBF Bioscience https://www.mbfbioscience.com/ products/neuroinfo/; RRID:SCR_017346 MoSeq behavior analysis pipeline Lin et al.54 http://www.moseq4all.org/ ImageJ (Fiji) Schindelin et al.112 https://imagej.net/; RRID: SCR_003070 CellRanger v.5 pipeline 10x Genomics https://www.10xgenomics.com/support/ software/cell-ranger/latest Modified Seurat v.2 workflow Gazestani et al.113 N/A fGSEA package version 1.24.0 Korotkevich et al.114 N/A MATLAB version R2021b MathWorks https://www.mathworks.com/ products/matlab.html R version 4.2.2 R Foundation https://cran.r-project.org/bin/ windows/base/old/4.2.2/ Python version 3.9 Python Software Foundation https://www.python.org ll OPEN ACCESS Please cite this article in press as: Hochbaum et al., Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration, Cell (2024), https://doi.org/10.1016/j.cell.2024.07.041
Article Title: VPS33B regulates MHC class II antigen presentation in dendritic cells to drive CD4 T cell immunity
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Fc shield CD16/CD32 Tonbo biosciences Cat#70-0161-U500; RRID:AB_2621487 anti-CD90.2 biotin BioLegend 105304; RRID:AB_313175 anti-NK1.1 biotin BioLegend Cat#108703; RRID:AB_313390 anti-Ly6G biotin BioLegend Cat#127603; RRID:AB_1186105 anti-Ter119 biotin BioLegend Cat#116203; RRID:AB_313704 anti-F4/80 biotin BioLegend Cat#123105; RRID:AB_893499 anti-CD317 biotin BioLegend Cat#127006; RRID:AB_2028466 anti-CD19 biotin BioLegend Cat#115503; RRID:AB_313638 anti-CD11b (BV785) BioLegend Cat#101243; RRID:AB_2561373 anti-CD11c (BV650) BioLegend Cat#117339; RRID:AB_2562414 anti-CD45.1(PE) BioLegend Cat#110707; RRID:AB_313496 anti-CD45.2 (AF700) BioLegend Cat#109821; RRID:AB_493730 anti-CD90.2 (BV785) BioLegend Cat#105331; RRID:AB_2562900 anti-CD8α (APC/Cyanine7) BioLegend Cat#100713; RRID:AB_312752 anti-CD4 (PE) BioLegend Cat#100511; RRID:AB_312714 anti-15G4 (PE) Santa Cruz Cat#sc-53946 PE; RRID:AB_831549 anti-CD44 (APC) BioLegend Cat#103011; RRID:AB_312962 anti-MHCII (AF700) BioLegend Cat#107622; RRID:493727 anti-MHCI (FITC) BioLegend Cat#114605; RRID:AB_313596 anti-CD86 (PE) BioLegend Cat#105106; RRID:AB_313159 anti-XCR1 (BV421) BioLegend Cat#148216; RRID:AB_2565230 anti-SIRPα (PE/Cyanine7) Invitrogen Cat#251721-82; RRID: AB_2762640 anti-Tbet (PE/Cyanine7) BioLegend Cat#644824; RRID:AB_2561761 anti-GranzymeB (FITC) BioLegend Cat#515403; RRID:AB_2114575 anti-TCR Vα2 BioLegnd Cat#127810; RRID:AB_1089250 anti-TNFα (APC) BioLegend Cat#506307; RRID:AB_315428 Anti-IFNγ (PE/Cyanine7) BioLegend Cat#505825; RRID:AB_1595591 anti-IL-12/IL-23 p40 (AF700) BioLegend Cat#505213; RRID:AB_2894642 anti-H3 Cell Signaling Cat#5192S; RRID:AB_1950410 anti-VPS33B Gift from Helmut Kramer UTSW Medical Center – anti-IFNγ capture antibody BioLegend Cat#505701; RRID:AB_315389 Biotinylated anti-IFNγ detection antibody BioLegend 505803; RRID:AB_315397 Biotinylated anti-CD19 antibody BioLegend Cat#115504; RRID:313639 YAe biotin Invitrogen Cat#13-5741-82; RRID:AB_657821 Streptavidin (BV421) BioLegend Cat#405226; RRID:AB_3662382 Streptavidin nanobeads BioLegend Cat#480015 Anti-biotin MicroBeads Miltenyi Biotec Cat#130-097-046 Bacterial and virus strains LCMV Armstrong Gift from Koichi Araki Lab CCHMC Araki et al.70 Chemicals, peptides, and recombinant proteins Zombie Yellow BioLegend Cat#423104 RIPA buffer ThermoFisher Cat89901 Protease inhibitor Cocktail Tablets Roche Cat#1169748001 (Continued on next page) iScience 29, 116052, June 19, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Phosphatase inhibitor Cocktail Tablets Roche Cat#4906845001 Dynabeads Protein G Invitrogen Cat#10003D NuPAGE LDS buffer Invitrogen Cat#NP0007 Fetal calf serum (FCS) Sigma-Aldrich Cat#F0926 DNAse I Sigma-Aldrich Cat#D8515 Recombinant GM-CSF BioLegend Cat#576306 2-Mercaptoethanol (BME) Sigma-Aldrich Cat#M6250 Paraformaldehyde aqueous solution ThermoFischer Cat#15710 Fluorescein isothiocyanate (FITC) isomer I Sigma-Aldrich Cat#F7250 Dibutyl Phthalate Sigma-Aldrich Cat#524980 Acetone Sigma-Aldrich Cat#179124 PBS ThermoFisher Cat#14190250 Hyclone RPMI-1640 with L-Glutamine Cytiva Cat#SH3002701 Bovine Serum Albumin (BSA) Sigma-Aldrich Cat#A7906 Phosphatase inhibitor Roche Cat#4906845001 Collagenase IV Worthington Cat#LS004188 DNase I Roche Cat#10104159001 TRIzol Reagent Invitrogen Cat#15596026 DMEM, high glucose ThermoFisher Cat#11965118 Gibco HEPES ThermoFisher Cat#15630080 OPD Sigma-Aldrich Cat#P1526 EDTA Sigma-Aldrich Cat#E9884 RBC lysis buffer Sigma-Aldrich Cat#R7757 IL-2 BioLegend Cat#575402 PMA Invivogen Cat#tlrl-pma Ionomycin Invivogen Cat#inh-ion Brefeldin A BioLegend Cat#420601 CD4 T cell isolation kit BioLegend Cat#480039 CD8 T cell isolation kit BioLegend Cat#480043 Cell Trace Violet Invitrogen Cat#C34557 EndoFitTM OVA Invivogen Cat#vac-pova DQ-OVA Invitrogen Cat#D12053 OVA 323-339 Invivogen Cat#vac-isq Lipopolysaccharide Sigma-Aldrich Cat#L288 CpG-B Invivogen Cat#Tlrl-1668 Experimental models: Organisms/strains fL Sanger Institute Mouse Genetics project RRID:IMSR_EM:07849 CSF1R Cre Jackson Lab RRID:IMSR_JAX:029206 Vav Cre Jackson Lab RRID:IMSR_JAX:008610 OT-II Jackson Lab RRID:IMSR_JAX:004194 OTI Jackson Lab RRID:IMSR_JAX:003831 SMARTA Jackson Lab RRID:IMSR_JAX:030450 P14 Jackson Lab RRID:MMRRC_037394-JAX Software and algorithms FlowJo 10 https://www.flowjo.com N/A GraphPad Prism v10 https://www.graphpad.com N/A Adobe Illustrator CC 2024 https://www.adobe.com/ N/A (Continued on next page) e2 iScience 29, 116052, June 19, 2026
Recombinant:Article Title: Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-HA Roche Cat# 1186742300; RRID: AB_390918 Chicken anti-GFP Abcam Cat# Ab13970; RRID: AB_300798 Rabbit anti-NeuN Sigma Aldrich Cat# ABN78; RRID: AB_10807945 Mouse anti-Robo3 R&D Systems Cat# AF3155; RRID: AB_10644167 Mouse anti-GluN1 SySy Cat# 114011; RRID: AB_887750 Goat anti-rat Alexa 555 ThermoFisher Cat# A21434; RRID: AB_2535855 Goat anti-chicken Alexa 488 ThermoFisher Cat# A11039; RRID: AB_2534096 Goat anti-mouse Alexa 647 ThermoFisher Cat# A21235; RRID: AB_2535804 Streptavidin Alexa 647 ThermoFisher Cat# S32357 Bacterial and virus strains scAAV9-hSyn-iCre-HA Boston Children’s Hospital Viral Core N/A scAAV9-hSyn-DiCre-HA Boston Children’s Hospital Viral Core N/A AAV9-hSyn-DN-THR Boston Children’s Hospital Viral Core N/A AAV9-hSyn-WT-THR Boston Children’s Hospital Viral Core N/A AAV9-SIO-nEF-DN-Thrb Janelia Viral Tools N/A AAV9-SIO-nEF-WT-Thrb Janelia Viral Tools N/A AAV9-hSyn-FLEX-CoChR-GFP UNC GTC Vector Core N/A AAVretro-CAG-Cre UNC GTC Vector Core N/A AAV9-hSyn-CoChR-GFP UNC GTC Vector Core N/A pENN.AAV_PHPeB.hSyn.HI.eGFP-Cre.WPRE.SV40 Addgene Addgene 105540 AAV9-S5E2-ChR2-mCherry Addgene Addgene 135634 Chemicals, peptides, and recombinant proteins 3,3’,5-Triiodo-L-thyronine Sigma-Aldrich Cat# T6397 Sobetirome Thomas Scanlan N/A Kolliphor Sigma-Aldrich Cat# C5135 NMP Sigma-Aldrich Cat# 328634 0.15% PTU Diet Inotiv Cat# TD.95125 Control Diet Inotiv Cat# TD.97350 Trizol Life Technologies Cat# 15596018 RIPA buffer ThermoFisher Cat# 89900 cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail Roche Cat# 11836170001 Biocytin Sigma Aldrich Cat# B4261 Critical commercial assays Chromium Next GEM Single Cell 3’ Kit v3 10X Genomics Cat#1000268 RNEasy Micro Kit Qiagen Cat#74004 SuperScript IV VILO Master Mix Kit with ezDNAse enzyme ThermoFisher Cat#11766050 RNAscope Multiplex Fluorescent Reagent Kit v1 (discontinued) and v2 Advanced Cell Diagnostics Cat#323100 (Continued on next page) e1 Cell 187, 1–19.e1–e11, October 3, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data snRNA-seq datasets This paper GEO: GSE271421 snRNA-seq datasets This paper https://cellxgene.cziscience.com/ collections/c450e15d-321a-42d6986b-11409d04896d Moseq, electrophysiology, and 2ABT datasets This paper https://dataverse.harvard.edu/ dataverse/2024_hochbaum_thyroid Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat# 664; RRID:IMSR_JAX:000664 Mouse: Robo3 fl/fl: Robo3tm1.1Ache Alain Chédotal111 MGI:4441335 Oligonucleotides TaqMan probe for Hr: (Mm00498963_m1) ThermoFisher Cat# 4331182 TaqMan probe for Dio1: (Mm00839358_m1) ThermoFisher Cat# 4331182 TaqMan probe for Ier5: (Mm01295615_s1) ThermoFisher Cat# 4331182 TaqMan probe for Gapdh: (Mm99999915_g1) ThermoFisher Cat# 4351370 TaqMan probe for Cyp11a1: (Mm00490735_m1) ThermoFisher Cat# 4331182 FISH probe for Hr Advanced Cell Diagnostics Cat# 883311 FISH probe for Ier5 Advanced Cell Diagnostics Cat# 530401-C3 FISH probe for Robo3 Advanced Cell Diagnostics Cat# 558811-C2 4-plex positive probe Advanced Cell Diagnostics Cat# 321811 4-plex negative control probe Advanced Cell Diagnostics Cat# 321831 Recombinant DNA DRH001_scAAV-hSyn-iCre-HA This paper Addgene 225086 DRH002_scAAV-hSyn-DiCre-HA This paper Addgene 225087 DRH015_ AAV-hSyn-WT-THR This paper Addgene 225088 DRH016_ AAV-hSyn-DN-THR This paper Addgene 225089 DRH031_ AAV-SIO-nEF-WT-THR This paper Addgene 225090 DRH032_ AAV-SIO-nEF-DN-THR This paper Addgene 225091 Software and algorithms Custom software This paper https://github.com/bernardosabatinilab/ hochbaum_thyroid_2024 NeuroInfo MBF Bioscience https://www.mbfbioscience.com/ products/neuroinfo/; RRID:SCR_017346 MoSeq behavior analysis pipeline Lin et al.54 http://www.moseq4all.org/ ImageJ (Fiji) Schindelin et al.112 https://imagej.net/; RRID: SCR_003070 CellRanger v.5 pipeline 10x Genomics https://www.10xgenomics.com/support/ software/cell-ranger/latest Modified Seurat v.2 workflow Gazestani et al.113 N/A fGSEA package version 1.24.0 Korotkevich et al.114 N/A MATLAB version R2021b MathWorks https://www.mathworks.com/ products/matlab.html R version 4.2.2 R Foundation https://cran.r-project.org/bin/ windows/base/old/4.2.2/ Python version 3.9 Python Software Foundation https://www.python.org ll OPEN ACCESS Please cite this article in press as: Hochbaum et al., Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration, Cell (2024), https://doi.org/10.1016/j.cell.2024.07.041
Article Title: YY1 Lactylation in Microglia Promotes Angiogenesis Through Transcription Activation-Mediated Upregulation of FGF2
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal Anti-CD31 Abcam Cat# ab9498; RRID: AB_307284 Rabbit polyclonal Anti-SIRT1 Abcam Cat# ab7343; RRID: AB_305867 Rabbit monoclonal Anti-Ki67 Abcam Cat# ab16667; RRID: AB_302459 Rabbit polyclonal Anti-PCAF Abcam Cat# ab12188; RRID: AB_298918 Goat polyclonal Anti-Iba1 Abcam Cat# ab5076; RRID: AB_2224402 VeriBlot for IP Detection Reagent (HRP) Abcam Cat# 131366 Mouse monoclonal Anti-β-Actin Abcam Cat# ab8226, RRID: AB_306371 Mouse monoclonal Anti-YY1 Proteintech Cat# 66281-1-lg; RRID: AB_2737053 Mouse monoclonal Anti-HDAC6 Santa Cruz Biotechnology Cat# sc-28386; RRID: AB_627708 Mouse monoclonal Anti-FGF2 Santa Cruz Biotechnology Cat# sc-74412; RRID: AB_1122854 Mouse monoclonal Anti-p300 Santa Cruz Biotechnology Cat# sc-48343; RRID: AB_628075 Mouse monoclonal Anti-TIP60 Santa Cruz Biotechnology Cat# sc-166323; RRID: AB_2296327 Rabbit monoclonal Anti-Iba1 FUJIFILM Wako Shibayagi Cat# 019-19741; RRID: AB_839504 Rabbit Pan-Kla PTM BIO Cat# PTM-1401; RRID: AB_2868521 Rabbit (DA1E) mAb IgG XP Isotype Control antibody Cell Signaling Technology Cat# 3900; RRID: AB_1550038 Rabbit monoclonal Anti-YY1 Cell Signaling Technology Cat# 46395; RRID: AB_2799302 Goat Anti-Mouse Alexa Flour 488 Bioss Cat# bs-0368G-A488,RRID:AB_10892893 Goat Anti-Rabbit Alexa Flour 488 Bioss Cat# bs-0295G A488;RRID:AB_10893781 Donkey Anti-Goat Cy3 Bioss Cat# bs-0294D-Cy3;RRID:AB_10894752 Goat Anti-Mouse Cy3 Bioss Cat# bs-0296G-Cy3;RRID:AB_10892835 Goat Anti-Rabbit Cy3 Bioss Cat# bs-0295G-Cy3;RRID:AB_10892956 Chemicals, peptides, and recombinant proteins EMEM ATCC Cat# 30-2003 Complete Classic Medium with Serum & CultureBoost Cell Systems Cat# 4Z0-500 Trypsin-EDTA (0.05%) Gibco Cat# 25300054 FBS Gibco Cat# 10099141 Penicillin-Streptomycin-Glutam(100X) Gibco Cat# 10378016 DMSO Solarbio Cat# 67-68-5 TRIzol Thermofisher Cat# 15596026 DAPI Thermofisher Cat# 62248 RIPA buffer Thermofisher Cat# 89900 Rotenone Rhawn Cat# R006873 Sodium Dichloroacetate Rhawn Cat# R052025 PLX3397 MedChemExpress Cat# HY-16749 PEG-300 Sigma-Aldrich 90878-250ML-F Puromycin Sigma-Aldrich Cat#P8833 Tween 80 Sigma-Aldrich Cat# P1754 TritonX-100 Sigma-Aldrich Cat# 648466 Lipofectamine 2000 Invitrogen Cat#11668019 Critical commercial assays RT Master Mix for qPCR MedChemExpress Cat# HY-K0511 SYBR Green qPCR Master Mix MedChemExpress Cat# HY-K0522 This preprint research paper has not been peer reviewed. .. Electronic copy available at: https://ssrn.com/abstract=4044116 Pr pr in t n ot p ee r r ev ie we d Ultra High Sensitivity ECL Kit MedChemExpress Cat# HY-K1005 Immunoprecipitation kit Abcam Cat# ab206996 SimpleChIP Plus Enzymatic Chromatin IP Kit Cell Signaling Technology Cat# 9004S Dual-Luciferase Reporter Assay System Promega Cat# E2920 The LA Assay Kit Solarbio Cat# BC2235 4% paraformaldehyde Biosharp Cat# 143174 Goat serum Boster Cat# AR0009 Experimental models: Cell lines HMC3 cells ATCC Cat# CRL-3304 HRMECs Cell Systems Cat# ACBRI 181 Experimental models: Organisms/strains Mouse: C57BL/6J The Experimental Animal Center of Chongqing Medical University N/A Oligonucleotides Primers used for qRT-PCR, see Table S2 Shanghai Sangon Biotech N/A Primers used for ChIP-qPCR, see Table S2 Shanghai Sangon Biotech N/A Recombinant DNA Ubi-MCS(YY1 WT)-3FLAG-CBh-gcGFP-IRES-puromycin Shanghai Genechem Co, Ltd N/A Ubi-MCS(YY1 K183R)-3FLAG-CBh-gcGFP-IRESpuromycin Shanghai Genechem Co, Ltd N/A MCS-SV40-firefly_Luciferase-PloyA-Tk-Renilla_LuciferasePolyA (FGF2 promoter luciferase reporter) Shanghai Genechem Co, Ltd N/A CAS9-Easy-Lentivirus(SAM)(EP300): Lenti-dCAS9puro; U6-sgRNA-SV40-MS2-P65-HSF1-CMV-EGFP Shanghai Genechem Co, Ltd N/A Software and algorithms GraphPad Prism 8.0 https://www.graphpad.com N/A NIH ImageJ https://imagej.nih.gov/ij/ N/A cellSens Dimension https://www.olympuslifescience.com.cn/en/software/ cellsens/ N/A ZEN https://www.zeiss.com/microsc opy/int/ downloads.html N/A IBM.SPSS.V20. https://spssau.com/?10200000 0&b_scene_zt=1 N/A This preprint research paper has not been peer reviewed.
Article Title: VPS33B regulates MHC class II antigen presentation in dendritic cells to drive CD4 T cell immunity
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Fc shield CD16/CD32 Tonbo biosciences Cat#70-0161-U500; RRID:AB_2621487 anti-CD90.2 biotin BioLegend 105304; RRID:AB_313175 anti-NK1.1 biotin BioLegend Cat#108703; RRID:AB_313390 anti-Ly6G biotin BioLegend Cat#127603; RRID:AB_1186105 anti-Ter119 biotin BioLegend Cat#116203; RRID:AB_313704 anti-F4/80 biotin BioLegend Cat#123105; RRID:AB_893499 anti-CD317 biotin BioLegend Cat#127006; RRID:AB_2028466 anti-CD19 biotin BioLegend Cat#115503; RRID:AB_313638 anti-CD11b (BV785) BioLegend Cat#101243; RRID:AB_2561373 anti-CD11c (BV650) BioLegend Cat#117339; RRID:AB_2562414 anti-CD45.1(PE) BioLegend Cat#110707; RRID:AB_313496 anti-CD45.2 (AF700) BioLegend Cat#109821; RRID:AB_493730 anti-CD90.2 (BV785) BioLegend Cat#105331; RRID:AB_2562900 anti-CD8α (APC/Cyanine7) BioLegend Cat#100713; RRID:AB_312752 anti-CD4 (PE) BioLegend Cat#100511; RRID:AB_312714 anti-15G4 (PE) Santa Cruz Cat#sc-53946 PE; RRID:AB_831549 anti-CD44 (APC) BioLegend Cat#103011; RRID:AB_312962 anti-MHCII (AF700) BioLegend Cat#107622; RRID:493727 anti-MHCI (FITC) BioLegend Cat#114605; RRID:AB_313596 anti-CD86 (PE) BioLegend Cat#105106; RRID:AB_313159 anti-XCR1 (BV421) BioLegend Cat#148216; RRID:AB_2565230 anti-SIRPα (PE/Cyanine7) Invitrogen Cat#251721-82; RRID: AB_2762640 anti-Tbet (PE/Cyanine7) BioLegend Cat#644824; RRID:AB_2561761 anti-GranzymeB (FITC) BioLegend Cat#515403; RRID:AB_2114575 anti-TCR Vα2 BioLegnd Cat#127810; RRID:AB_1089250 anti-TNFα (APC) BioLegend Cat#506307; RRID:AB_315428 Anti-IFNγ (PE/Cyanine7) BioLegend Cat#505825; RRID:AB_1595591 anti-IL-12/IL-23 p40 (AF700) BioLegend Cat#505213; RRID:AB_2894642 anti-H3 Cell Signaling Cat#5192S; RRID:AB_1950410 anti-VPS33B Gift from Helmut Kramer UTSW Medical Center – anti-IFNγ capture antibody BioLegend Cat#505701; RRID:AB_315389 Biotinylated anti-IFNγ detection antibody BioLegend 505803; RRID:AB_315397 Biotinylated anti-CD19 antibody BioLegend Cat#115504; RRID:313639 YAe biotin Invitrogen Cat#13-5741-82; RRID:AB_657821 Streptavidin (BV421) BioLegend Cat#405226; RRID:AB_3662382 Streptavidin nanobeads BioLegend Cat#480015 Anti-biotin MicroBeads Miltenyi Biotec Cat#130-097-046 Bacterial and virus strains LCMV Armstrong Gift from Koichi Araki Lab CCHMC Araki et al.70 Chemicals, peptides, and recombinant proteins Zombie Yellow BioLegend Cat#423104 RIPA buffer ThermoFisher Cat89901 Protease inhibitor Cocktail Tablets Roche Cat#1169748001 (Continued on next page) iScience 29, 116052, June 19, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Phosphatase inhibitor Cocktail Tablets Roche Cat#4906845001 Dynabeads Protein G Invitrogen Cat#10003D NuPAGE LDS buffer Invitrogen Cat#NP0007 Fetal calf serum (FCS) Sigma-Aldrich Cat#F0926 DNAse I Sigma-Aldrich Cat#D8515 Recombinant GM-CSF BioLegend Cat#576306 2-Mercaptoethanol (BME) Sigma-Aldrich Cat#M6250 Paraformaldehyde aqueous solution ThermoFischer Cat#15710 Fluorescein isothiocyanate (FITC) isomer I Sigma-Aldrich Cat#F7250 Dibutyl Phthalate Sigma-Aldrich Cat#524980 Acetone Sigma-Aldrich Cat#179124 PBS ThermoFisher Cat#14190250 Hyclone RPMI-1640 with L-Glutamine Cytiva Cat#SH3002701 Bovine Serum Albumin (BSA) Sigma-Aldrich Cat#A7906 Phosphatase inhibitor Roche Cat#4906845001 Collagenase IV Worthington Cat#LS004188 DNase I Roche Cat#10104159001 TRIzol Reagent Invitrogen Cat#15596026 DMEM, high glucose ThermoFisher Cat#11965118 Gibco HEPES ThermoFisher Cat#15630080 OPD Sigma-Aldrich Cat#P1526 EDTA Sigma-Aldrich Cat#E9884 RBC lysis buffer Sigma-Aldrich Cat#R7757 IL-2 BioLegend Cat#575402 PMA Invivogen Cat#tlrl-pma Ionomycin Invivogen Cat#inh-ion Brefeldin A BioLegend Cat#420601 CD4 T cell isolation kit BioLegend Cat#480039 CD8 T cell isolation kit BioLegend Cat#480043 Cell Trace Violet Invitrogen Cat#C34557 EndoFitTM OVA Invivogen Cat#vac-pova DQ-OVA Invitrogen Cat#D12053 OVA 323-339 Invivogen Cat#vac-isq Lipopolysaccharide Sigma-Aldrich Cat#L288 CpG-B Invivogen Cat#Tlrl-1668 Experimental models: Organisms/strains fL Sanger Institute Mouse Genetics project RRID:IMSR_EM:07849 CSF1R Cre Jackson Lab RRID:IMSR_JAX:029206 Vav Cre Jackson Lab RRID:IMSR_JAX:008610 OT-II Jackson Lab RRID:IMSR_JAX:004194 OTI Jackson Lab RRID:IMSR_JAX:003831 SMARTA Jackson Lab RRID:IMSR_JAX:030450 P14 Jackson Lab RRID:MMRRC_037394-JAX Software and algorithms FlowJo 10 https://www.flowjo.com N/A GraphPad Prism v10 https://www.graphpad.com N/A Adobe Illustrator CC 2024 https://www.adobe.com/ N/A (Continued on next page) e2 iScience 29, 116052, June 19, 2026
Control:Article Title: Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-HA Roche Cat# 1186742300; RRID: AB_390918 Chicken anti-GFP Abcam Cat# Ab13970; RRID: AB_300798 Rabbit anti-NeuN Sigma Aldrich Cat# ABN78; RRID: AB_10807945 Mouse anti-Robo3 R&D Systems Cat# AF3155; RRID: AB_10644167 Mouse anti-GluN1 SySy Cat# 114011; RRID: AB_887750 Goat anti-rat Alexa 555 ThermoFisher Cat# A21434; RRID: AB_2535855 Goat anti-chicken Alexa 488 ThermoFisher Cat# A11039; RRID: AB_2534096 Goat anti-mouse Alexa 647 ThermoFisher Cat# A21235; RRID: AB_2535804 Streptavidin Alexa 647 ThermoFisher Cat# S32357 Bacterial and virus strains scAAV9-hSyn-iCre-HA Boston Children’s Hospital Viral Core N/A scAAV9-hSyn-DiCre-HA Boston Children’s Hospital Viral Core N/A AAV9-hSyn-DN-THR Boston Children’s Hospital Viral Core N/A AAV9-hSyn-WT-THR Boston Children’s Hospital Viral Core N/A AAV9-SIO-nEF-DN-Thrb Janelia Viral Tools N/A AAV9-SIO-nEF-WT-Thrb Janelia Viral Tools N/A AAV9-hSyn-FLEX-CoChR-GFP UNC GTC Vector Core N/A AAVretro-CAG-Cre UNC GTC Vector Core N/A AAV9-hSyn-CoChR-GFP UNC GTC Vector Core N/A pENN.AAV_PHPeB.hSyn.HI.eGFP-Cre.WPRE.SV40 Addgene Addgene 105540 AAV9-S5E2-ChR2-mCherry Addgene Addgene 135634 Chemicals, peptides, and recombinant proteins 3,3’,5-Triiodo-L-thyronine Sigma-Aldrich Cat# T6397 Sobetirome Thomas Scanlan N/A Kolliphor Sigma-Aldrich Cat# C5135 NMP Sigma-Aldrich Cat# 328634 0.15% PTU Diet Inotiv Cat# TD.95125 Control Diet Inotiv Cat# TD.97350 Trizol Life Technologies Cat# 15596018 RIPA buffer ThermoFisher Cat# 89900 cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail Roche Cat# 11836170001 Biocytin Sigma Aldrich Cat# B4261 Critical commercial assays Chromium Next GEM Single Cell 3’ Kit v3 10X Genomics Cat#1000268 RNEasy Micro Kit Qiagen Cat#74004 SuperScript IV VILO Master Mix Kit with ezDNAse enzyme ThermoFisher Cat#11766050 RNAscope Multiplex Fluorescent Reagent Kit v1 (discontinued) and v2 Advanced Cell Diagnostics Cat#323100 (Continued on next page) e1 Cell 187, 1–19.e1–e11, October 3, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data snRNA-seq datasets This paper GEO: GSE271421 snRNA-seq datasets This paper https://cellxgene.cziscience.com/ collections/c450e15d-321a-42d6986b-11409d04896d Moseq, electrophysiology, and 2ABT datasets This paper https://dataverse.harvard.edu/ dataverse/2024_hochbaum_thyroid Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat# 664; RRID:IMSR_JAX:000664 Mouse: Robo3 fl/fl: Robo3tm1.1Ache Alain Chédotal111 MGI:4441335 Oligonucleotides TaqMan probe for Hr: (Mm00498963_m1) ThermoFisher Cat# 4331182 TaqMan probe for Dio1: (Mm00839358_m1) ThermoFisher Cat# 4331182 TaqMan probe for Ier5: (Mm01295615_s1) ThermoFisher Cat# 4331182 TaqMan probe for Gapdh: (Mm99999915_g1) ThermoFisher Cat# 4351370 TaqMan probe for Cyp11a1: (Mm00490735_m1) ThermoFisher Cat# 4331182 FISH probe for Hr Advanced Cell Diagnostics Cat# 883311 FISH probe for Ier5 Advanced Cell Diagnostics Cat# 530401-C3 FISH probe for Robo3 Advanced Cell Diagnostics Cat# 558811-C2 4-plex positive probe Advanced Cell Diagnostics Cat# 321811 4-plex negative control probe Advanced Cell Diagnostics Cat# 321831 Recombinant DNA DRH001_scAAV-hSyn-iCre-HA This paper Addgene 225086 DRH002_scAAV-hSyn-DiCre-HA This paper Addgene 225087 DRH015_ AAV-hSyn-WT-THR This paper Addgene 225088 DRH016_ AAV-hSyn-DN-THR This paper Addgene 225089 DRH031_ AAV-SIO-nEF-WT-THR This paper Addgene 225090 DRH032_ AAV-SIO-nEF-DN-THR This paper Addgene 225091 Software and algorithms Custom software This paper https://github.com/bernardosabatinilab/ hochbaum_thyroid_2024 NeuroInfo MBF Bioscience https://www.mbfbioscience.com/ products/neuroinfo/; RRID:SCR_017346 MoSeq behavior analysis pipeline Lin et al.54 http://www.moseq4all.org/ ImageJ (Fiji) Schindelin et al.112 https://imagej.net/; RRID: SCR_003070 CellRanger v.5 pipeline 10x Genomics https://www.10xgenomics.com/support/ software/cell-ranger/latest Modified Seurat v.2 workflow Gazestani et al.113 N/A fGSEA package version 1.24.0 Korotkevich et al.114 N/A MATLAB version R2021b MathWorks https://www.mathworks.com/ products/matlab.html R version 4.2.2 R Foundation https://cran.r-project.org/bin/ windows/base/old/4.2.2/ Python version 3.9 Python Software Foundation https://www.python.org ll OPEN ACCESS Please cite this article in press as: Hochbaum et al., Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration, Cell (2024), https://doi.org/10.1016/j.cell.2024.07.041
Article Title: YY1 Lactylation in Microglia Promotes Angiogenesis Through Transcription Activation-Mediated Upregulation of FGF2
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal Anti-CD31 Abcam Cat# ab9498; RRID: AB_307284 Rabbit polyclonal Anti-SIRT1 Abcam Cat# ab7343; RRID: AB_305867 Rabbit monoclonal Anti-Ki67 Abcam Cat# ab16667; RRID: AB_302459 Rabbit polyclonal Anti-PCAF Abcam Cat# ab12188; RRID: AB_298918 Goat polyclonal Anti-Iba1 Abcam Cat# ab5076; RRID: AB_2224402 VeriBlot for IP Detection Reagent (HRP) Abcam Cat# 131366 Mouse monoclonal Anti-β-Actin Abcam Cat# ab8226, RRID: AB_306371 Mouse monoclonal Anti-YY1 Proteintech Cat# 66281-1-lg; RRID: AB_2737053 Mouse monoclonal Anti-HDAC6 Santa Cruz Biotechnology Cat# sc-28386; RRID: AB_627708 Mouse monoclonal Anti-FGF2 Santa Cruz Biotechnology Cat# sc-74412; RRID: AB_1122854 Mouse monoclonal Anti-p300 Santa Cruz Biotechnology Cat# sc-48343; RRID: AB_628075 Mouse monoclonal Anti-TIP60 Santa Cruz Biotechnology Cat# sc-166323; RRID: AB_2296327 Rabbit monoclonal Anti-Iba1 FUJIFILM Wako Shibayagi Cat# 019-19741; RRID: AB_839504 Rabbit Pan-Kla PTM BIO Cat# PTM-1401; RRID: AB_2868521 Rabbit (DA1E) mAb IgG XP Isotype Control antibody Cell Signaling Technology Cat# 3900; RRID: AB_1550038 Rabbit monoclonal Anti-YY1 Cell Signaling Technology Cat# 46395; RRID: AB_2799302 Goat Anti-Mouse Alexa Flour 488 Bioss Cat# bs-0368G-A488,RRID:AB_10892893 Goat Anti-Rabbit Alexa Flour 488 Bioss Cat# bs-0295G A488;RRID:AB_10893781 Donkey Anti-Goat Cy3 Bioss Cat# bs-0294D-Cy3;RRID:AB_10894752 Goat Anti-Mouse Cy3 Bioss Cat# bs-0296G-Cy3;RRID:AB_10892835 Goat Anti-Rabbit Cy3 Bioss Cat# bs-0295G-Cy3;RRID:AB_10892956 Chemicals, peptides, and recombinant proteins EMEM ATCC Cat# 30-2003 Complete Classic Medium with Serum & CultureBoost Cell Systems Cat# 4Z0-500 Trypsin-EDTA (0.05%) Gibco Cat# 25300054 FBS Gibco Cat# 10099141 Penicillin-Streptomycin-Glutam(100X) Gibco Cat# 10378016 DMSO Solarbio Cat# 67-68-5 TRIzol Thermofisher Cat# 15596026 DAPI Thermofisher Cat# 62248 RIPA buffer Thermofisher Cat# 89900 Rotenone Rhawn Cat# R006873 Sodium Dichloroacetate Rhawn Cat# R052025 PLX3397 MedChemExpress Cat# HY-16749 PEG-300 Sigma-Aldrich 90878-250ML-F Puromycin Sigma-Aldrich Cat#P8833 Tween 80 Sigma-Aldrich Cat# P1754 TritonX-100 Sigma-Aldrich Cat# 648466 Lipofectamine 2000 Invitrogen Cat#11668019 Critical commercial assays RT Master Mix for qPCR MedChemExpress Cat# HY-K0511 SYBR Green qPCR Master Mix MedChemExpress Cat# HY-K0522 This preprint research paper has not been peer reviewed. .. Electronic copy available at: https://ssrn.com/abstract=4044116 Pr pr in t n ot p ee r r ev ie we d Ultra High Sensitivity ECL Kit MedChemExpress Cat# HY-K1005 Immunoprecipitation kit Abcam Cat# ab206996 SimpleChIP Plus Enzymatic Chromatin IP Kit Cell Signaling Technology Cat# 9004S Dual-Luciferase Reporter Assay System Promega Cat# E2920 The LA Assay Kit Solarbio Cat# BC2235 4% paraformaldehyde Biosharp Cat# 143174 Goat serum Boster Cat# AR0009 Experimental models: Cell lines HMC3 cells ATCC Cat# CRL-3304 HRMECs Cell Systems Cat# ACBRI 181 Experimental models: Organisms/strains Mouse: C57BL/6J The Experimental Animal Center of Chongqing Medical University N/A Oligonucleotides Primers used for qRT-PCR, see Table S2 Shanghai Sangon Biotech N/A Primers used for ChIP-qPCR, see Table S2 Shanghai Sangon Biotech N/A Recombinant DNA Ubi-MCS(YY1 WT)-3FLAG-CBh-gcGFP-IRES-puromycin Shanghai Genechem Co, Ltd N/A Ubi-MCS(YY1 K183R)-3FLAG-CBh-gcGFP-IRESpuromycin Shanghai Genechem Co, Ltd N/A MCS-SV40-firefly_Luciferase-PloyA-Tk-Renilla_LuciferasePolyA (FGF2 promoter luciferase reporter) Shanghai Genechem Co, Ltd N/A CAS9-Easy-Lentivirus(SAM)(EP300): Lenti-dCAS9puro; U6-sgRNA-SV40-MS2-P65-HSF1-CMV-EGFP Shanghai Genechem Co, Ltd N/A Software and algorithms GraphPad Prism 8.0 https://www.graphpad.com N/A NIH ImageJ https://imagej.nih.gov/ij/ N/A cellSens Dimension https://www.olympuslifescience.com.cn/en/software/ cellsens/ N/A ZEN https://www.zeiss.com/microsc opy/int/ downloads.html N/A IBM.SPSS.V20. https://spssau.com/?10200000 0&b_scene_zt=1 N/A This preprint research paper has not been peer reviewed.
Protease Inhibitor:Article Title: Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-HA Roche Cat# 1186742300; RRID: AB_390918 Chicken anti-GFP Abcam Cat# Ab13970; RRID: AB_300798 Rabbit anti-NeuN Sigma Aldrich Cat# ABN78; RRID: AB_10807945 Mouse anti-Robo3 R&D Systems Cat# AF3155; RRID: AB_10644167 Mouse anti-GluN1 SySy Cat# 114011; RRID: AB_887750 Goat anti-rat Alexa 555 ThermoFisher Cat# A21434; RRID: AB_2535855 Goat anti-chicken Alexa 488 ThermoFisher Cat# A11039; RRID: AB_2534096 Goat anti-mouse Alexa 647 ThermoFisher Cat# A21235; RRID: AB_2535804 Streptavidin Alexa 647 ThermoFisher Cat# S32357 Bacterial and virus strains scAAV9-hSyn-iCre-HA Boston Children’s Hospital Viral Core N/A scAAV9-hSyn-DiCre-HA Boston Children’s Hospital Viral Core N/A AAV9-hSyn-DN-THR Boston Children’s Hospital Viral Core N/A AAV9-hSyn-WT-THR Boston Children’s Hospital Viral Core N/A AAV9-SIO-nEF-DN-Thrb Janelia Viral Tools N/A AAV9-SIO-nEF-WT-Thrb Janelia Viral Tools N/A AAV9-hSyn-FLEX-CoChR-GFP UNC GTC Vector Core N/A AAVretro-CAG-Cre UNC GTC Vector Core N/A AAV9-hSyn-CoChR-GFP UNC GTC Vector Core N/A pENN.AAV_PHPeB.hSyn.HI.eGFP-Cre.WPRE.SV40 Addgene Addgene 105540 AAV9-S5E2-ChR2-mCherry Addgene Addgene 135634 Chemicals, peptides, and recombinant proteins 3,3’,5-Triiodo-L-thyronine Sigma-Aldrich Cat# T6397 Sobetirome Thomas Scanlan N/A Kolliphor Sigma-Aldrich Cat# C5135 NMP Sigma-Aldrich Cat# 328634 0.15% PTU Diet Inotiv Cat# TD.95125 Control Diet Inotiv Cat# TD.97350 Trizol Life Technologies Cat# 15596018 RIPA buffer ThermoFisher Cat# 89900 cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail Roche Cat# 11836170001 Biocytin Sigma Aldrich Cat# B4261 Critical commercial assays Chromium Next GEM Single Cell 3’ Kit v3 10X Genomics Cat#1000268 RNEasy Micro Kit Qiagen Cat#74004 SuperScript IV VILO Master Mix Kit with ezDNAse enzyme ThermoFisher Cat#11766050 RNAscope Multiplex Fluorescent Reagent Kit v1 (discontinued) and v2 Advanced Cell Diagnostics Cat#323100 (Continued on next page) e1 Cell 187, 1–19.e1–e11, October 3, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data snRNA-seq datasets This paper GEO: GSE271421 snRNA-seq datasets This paper https://cellxgene.cziscience.com/ collections/c450e15d-321a-42d6986b-11409d04896d Moseq, electrophysiology, and 2ABT datasets This paper https://dataverse.harvard.edu/ dataverse/2024_hochbaum_thyroid Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat# 664; RRID:IMSR_JAX:000664 Mouse: Robo3 fl/fl: Robo3tm1.1Ache Alain Chédotal111 MGI:4441335 Oligonucleotides TaqMan probe for Hr: (Mm00498963_m1) ThermoFisher Cat# 4331182 TaqMan probe for Dio1: (Mm00839358_m1) ThermoFisher Cat# 4331182 TaqMan probe for Ier5: (Mm01295615_s1) ThermoFisher Cat# 4331182 TaqMan probe for Gapdh: (Mm99999915_g1) ThermoFisher Cat# 4351370 TaqMan probe for Cyp11a1: (Mm00490735_m1) ThermoFisher Cat# 4331182 FISH probe for Hr Advanced Cell Diagnostics Cat# 883311 FISH probe for Ier5 Advanced Cell Diagnostics Cat# 530401-C3 FISH probe for Robo3 Advanced Cell Diagnostics Cat# 558811-C2 4-plex positive probe Advanced Cell Diagnostics Cat# 321811 4-plex negative control probe Advanced Cell Diagnostics Cat# 321831 Recombinant DNA DRH001_scAAV-hSyn-iCre-HA This paper Addgene 225086 DRH002_scAAV-hSyn-DiCre-HA This paper Addgene 225087 DRH015_ AAV-hSyn-WT-THR This paper Addgene 225088 DRH016_ AAV-hSyn-DN-THR This paper Addgene 225089 DRH031_ AAV-SIO-nEF-WT-THR This paper Addgene 225090 DRH032_ AAV-SIO-nEF-DN-THR This paper Addgene 225091 Software and algorithms Custom software This paper https://github.com/bernardosabatinilab/ hochbaum_thyroid_2024 NeuroInfo MBF Bioscience https://www.mbfbioscience.com/ products/neuroinfo/; RRID:SCR_017346 MoSeq behavior analysis pipeline Lin et al.54 http://www.moseq4all.org/ ImageJ (Fiji) Schindelin et al.112 https://imagej.net/; RRID: SCR_003070 CellRanger v.5 pipeline 10x Genomics https://www.10xgenomics.com/support/ software/cell-ranger/latest Modified Seurat v.2 workflow Gazestani et al.113 N/A fGSEA package version 1.24.0 Korotkevich et al.114 N/A MATLAB version R2021b MathWorks https://www.mathworks.com/ products/matlab.html R version 4.2.2 R Foundation https://cran.r-project.org/bin/ windows/base/old/4.2.2/ Python version 3.9 Python Software Foundation https://www.python.org ll OPEN ACCESS Please cite this article in press as: Hochbaum et al., Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration, Cell (2024), https://doi.org/10.1016/j.cell.2024.07.041
Article Title: VPS33B regulates MHC class II antigen presentation in dendritic cells to drive CD4 T cell immunity
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Fc shield CD16/CD32 Tonbo biosciences Cat#70-0161-U500; RRID:AB_2621487 anti-CD90.2 biotin BioLegend 105304; RRID:AB_313175 anti-NK1.1 biotin BioLegend Cat#108703; RRID:AB_313390 anti-Ly6G biotin BioLegend Cat#127603; RRID:AB_1186105 anti-Ter119 biotin BioLegend Cat#116203; RRID:AB_313704 anti-F4/80 biotin BioLegend Cat#123105; RRID:AB_893499 anti-CD317 biotin BioLegend Cat#127006; RRID:AB_2028466 anti-CD19 biotin BioLegend Cat#115503; RRID:AB_313638 anti-CD11b (BV785) BioLegend Cat#101243; RRID:AB_2561373 anti-CD11c (BV650) BioLegend Cat#117339; RRID:AB_2562414 anti-CD45.1(PE) BioLegend Cat#110707; RRID:AB_313496 anti-CD45.2 (AF700) BioLegend Cat#109821; RRID:AB_493730 anti-CD90.2 (BV785) BioLegend Cat#105331; RRID:AB_2562900 anti-CD8α (APC/Cyanine7) BioLegend Cat#100713; RRID:AB_312752 anti-CD4 (PE) BioLegend Cat#100511; RRID:AB_312714 anti-15G4 (PE) Santa Cruz Cat#sc-53946 PE; RRID:AB_831549 anti-CD44 (APC) BioLegend Cat#103011; RRID:AB_312962 anti-MHCII (AF700) BioLegend Cat#107622; RRID:493727 anti-MHCI (FITC) BioLegend Cat#114605; RRID:AB_313596 anti-CD86 (PE) BioLegend Cat#105106; RRID:AB_313159 anti-XCR1 (BV421) BioLegend Cat#148216; RRID:AB_2565230 anti-SIRPα (PE/Cyanine7) Invitrogen Cat#251721-82; RRID: AB_2762640 anti-Tbet (PE/Cyanine7) BioLegend Cat#644824; RRID:AB_2561761 anti-GranzymeB (FITC) BioLegend Cat#515403; RRID:AB_2114575 anti-TCR Vα2 BioLegnd Cat#127810; RRID:AB_1089250 anti-TNFα (APC) BioLegend Cat#506307; RRID:AB_315428 Anti-IFNγ (PE/Cyanine7) BioLegend Cat#505825; RRID:AB_1595591 anti-IL-12/IL-23 p40 (AF700) BioLegend Cat#505213; RRID:AB_2894642 anti-H3 Cell Signaling Cat#5192S; RRID:AB_1950410 anti-VPS33B Gift from Helmut Kramer UTSW Medical Center – anti-IFNγ capture antibody BioLegend Cat#505701; RRID:AB_315389 Biotinylated anti-IFNγ detection antibody BioLegend 505803; RRID:AB_315397 Biotinylated anti-CD19 antibody BioLegend Cat#115504; RRID:313639 YAe biotin Invitrogen Cat#13-5741-82; RRID:AB_657821 Streptavidin (BV421) BioLegend Cat#405226; RRID:AB_3662382 Streptavidin nanobeads BioLegend Cat#480015 Anti-biotin MicroBeads Miltenyi Biotec Cat#130-097-046 Bacterial and virus strains LCMV Armstrong Gift from Koichi Araki Lab CCHMC Araki et al.70 Chemicals, peptides, and recombinant proteins Zombie Yellow BioLegend Cat#423104 RIPA buffer ThermoFisher Cat89901 Protease inhibitor Cocktail Tablets Roche Cat#1169748001 (Continued on next page) iScience 29, 116052, June 19, 2026 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Phosphatase inhibitor Cocktail Tablets Roche Cat#4906845001 Dynabeads Protein G Invitrogen Cat#10003D NuPAGE LDS buffer Invitrogen Cat#NP0007 Fetal calf serum (FCS) Sigma-Aldrich Cat#F0926 DNAse I Sigma-Aldrich Cat#D8515 Recombinant GM-CSF BioLegend Cat#576306 2-Mercaptoethanol (BME) Sigma-Aldrich Cat#M6250 Paraformaldehyde aqueous solution ThermoFischer Cat#15710 Fluorescein isothiocyanate (FITC) isomer I Sigma-Aldrich Cat#F7250 Dibutyl Phthalate Sigma-Aldrich Cat#524980 Acetone Sigma-Aldrich Cat#179124 PBS ThermoFisher Cat#14190250 Hyclone RPMI-1640 with L-Glutamine Cytiva Cat#SH3002701 Bovine Serum Albumin (BSA) Sigma-Aldrich Cat#A7906 Phosphatase inhibitor Roche Cat#4906845001 Collagenase IV Worthington Cat#LS004188 DNase I Roche Cat#10104159001 TRIzol Reagent Invitrogen Cat#15596026 DMEM, high glucose ThermoFisher Cat#11965118 Gibco HEPES ThermoFisher Cat#15630080 OPD Sigma-Aldrich Cat#P1526 EDTA Sigma-Aldrich Cat#E9884 RBC lysis buffer Sigma-Aldrich Cat#R7757 IL-2 BioLegend Cat#575402 PMA Invivogen Cat#tlrl-pma Ionomycin Invivogen Cat#inh-ion Brefeldin A BioLegend Cat#420601 CD4 T cell isolation kit BioLegend Cat#480039 CD8 T cell isolation kit BioLegend Cat#480043 Cell Trace Violet Invitrogen Cat#C34557 EndoFitTM OVA Invivogen Cat#vac-pova DQ-OVA Invitrogen Cat#D12053 OVA 323-339 Invivogen Cat#vac-isq Lipopolysaccharide Sigma-Aldrich Cat#L288 CpG-B Invivogen Cat#Tlrl-1668 Experimental models: Organisms/strains fL Sanger Institute Mouse Genetics project RRID:IMSR_EM:07849 CSF1R Cre Jackson Lab RRID:IMSR_JAX:029206 Vav Cre Jackson Lab RRID:IMSR_JAX:008610 OT-II Jackson Lab RRID:IMSR_JAX:004194 OTI Jackson Lab RRID:IMSR_JAX:003831 SMARTA Jackson Lab RRID:IMSR_JAX:030450 P14 Jackson Lab RRID:MMRRC_037394-JAX Software and algorithms FlowJo 10 https://www.flowjo.com N/A GraphPad Prism v10 https://www.graphpad.com N/A Adobe Illustrator CC 2024 https://www.adobe.com/ N/A (Continued on next page) e2 iScience 29, 116052, June 19, 2026
Single Cell:Article Title: Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-HA Roche Cat# 1186742300; RRID: AB_390918 Chicken anti-GFP Abcam Cat# Ab13970; RRID: AB_300798 Rabbit anti-NeuN Sigma Aldrich Cat# ABN78; RRID: AB_10807945 Mouse anti-Robo3 R&D Systems Cat# AF3155; RRID: AB_10644167 Mouse anti-GluN1 SySy Cat# 114011; RRID: AB_887750 Goat anti-rat Alexa 555 ThermoFisher Cat# A21434; RRID: AB_2535855 Goat anti-chicken Alexa 488 ThermoFisher Cat# A11039; RRID: AB_2534096 Goat anti-mouse Alexa 647 ThermoFisher Cat# A21235; RRID: AB_2535804 Streptavidin Alexa 647 ThermoFisher Cat# S32357 Bacterial and virus strains scAAV9-hSyn-iCre-HA Boston Children’s Hospital Viral Core N/A scAAV9-hSyn-DiCre-HA Boston Children’s Hospital Viral Core N/A AAV9-hSyn-DN-THR Boston Children’s Hospital Viral Core N/A AAV9-hSyn-WT-THR Boston Children’s Hospital Viral Core N/A AAV9-SIO-nEF-DN-Thrb Janelia Viral Tools N/A AAV9-SIO-nEF-WT-Thrb Janelia Viral Tools N/A AAV9-hSyn-FLEX-CoChR-GFP UNC GTC Vector Core N/A AAVretro-CAG-Cre UNC GTC Vector Core N/A AAV9-hSyn-CoChR-GFP UNC GTC Vector Core N/A pENN.AAV_PHPeB.hSyn.HI.eGFP-Cre.WPRE.SV40 Addgene Addgene 105540 AAV9-S5E2-ChR2-mCherry Addgene Addgene 135634 Chemicals, peptides, and recombinant proteins 3,3’,5-Triiodo-L-thyronine Sigma-Aldrich Cat# T6397 Sobetirome Thomas Scanlan N/A Kolliphor Sigma-Aldrich Cat# C5135 NMP Sigma-Aldrich Cat# 328634 0.15% PTU Diet Inotiv Cat# TD.95125 Control Diet Inotiv Cat# TD.97350 Trizol Life Technologies Cat# 15596018 RIPA buffer ThermoFisher Cat# 89900 cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail Roche Cat# 11836170001 Biocytin Sigma Aldrich Cat# B4261 Critical commercial assays Chromium Next GEM Single Cell 3’ Kit v3 10X Genomics Cat#1000268 RNEasy Micro Kit Qiagen Cat#74004 SuperScript IV VILO Master Mix Kit with ezDNAse enzyme ThermoFisher Cat#11766050 RNAscope Multiplex Fluorescent Reagent Kit v1 (discontinued) and v2 Advanced Cell Diagnostics Cat#323100 (Continued on next page) e1 Cell 187, 1–19.e1–e11, October 3, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data snRNA-seq datasets This paper GEO: GSE271421 snRNA-seq datasets This paper https://cellxgene.cziscience.com/ collections/c450e15d-321a-42d6986b-11409d04896d Moseq, electrophysiology, and 2ABT datasets This paper https://dataverse.harvard.edu/ dataverse/2024_hochbaum_thyroid Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat# 664; RRID:IMSR_JAX:000664 Mouse: Robo3 fl/fl: Robo3tm1.1Ache Alain Chédotal111 MGI:4441335 Oligonucleotides TaqMan probe for Hr: (Mm00498963_m1) ThermoFisher Cat# 4331182 TaqMan probe for Dio1: (Mm00839358_m1) ThermoFisher Cat# 4331182 TaqMan probe for Ier5: (Mm01295615_s1) ThermoFisher Cat# 4331182 TaqMan probe for Gapdh: (Mm99999915_g1) ThermoFisher Cat# 4351370 TaqMan probe for Cyp11a1: (Mm00490735_m1) ThermoFisher Cat# 4331182 FISH probe for Hr Advanced Cell Diagnostics Cat# 883311 FISH probe for Ier5 Advanced Cell Diagnostics Cat# 530401-C3 FISH probe for Robo3 Advanced Cell Diagnostics Cat# 558811-C2 4-plex positive probe Advanced Cell Diagnostics Cat# 321811 4-plex negative control probe Advanced Cell Diagnostics Cat# 321831 Recombinant DNA DRH001_scAAV-hSyn-iCre-HA This paper Addgene 225086 DRH002_scAAV-hSyn-DiCre-HA This paper Addgene 225087 DRH015_ AAV-hSyn-WT-THR This paper Addgene 225088 DRH016_ AAV-hSyn-DN-THR This paper Addgene 225089 DRH031_ AAV-SIO-nEF-WT-THR This paper Addgene 225090 DRH032_ AAV-SIO-nEF-DN-THR This paper Addgene 225091 Software and algorithms Custom software This paper https://github.com/bernardosabatinilab/ hochbaum_thyroid_2024 NeuroInfo MBF Bioscience https://www.mbfbioscience.com/ products/neuroinfo/; RRID:SCR_017346 MoSeq behavior analysis pipeline Lin et al.54 http://www.moseq4all.org/ ImageJ (Fiji) Schindelin et al.112 https://imagej.net/; RRID: SCR_003070 CellRanger v.5 pipeline 10x Genomics https://www.10xgenomics.com/support/ software/cell-ranger/latest Modified Seurat v.2 workflow Gazestani et al.113 N/A fGSEA package version 1.24.0 Korotkevich et al.114 N/A MATLAB version R2021b MathWorks https://www.mathworks.com/ products/matlab.html R version 4.2.2 R Foundation https://cran.r-project.org/bin/ windows/base/old/4.2.2/ Python version 3.9 Python Software Foundation https://www.python.org ll OPEN ACCESS Please cite this article in press as: Hochbaum et al., Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration, Cell (2024), https://doi.org/10.1016/j.cell.2024.07.041
RNAscope:Article Title: Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-HA Roche Cat# 1186742300; RRID: AB_390918 Chicken anti-GFP Abcam Cat# Ab13970; RRID: AB_300798 Rabbit anti-NeuN Sigma Aldrich Cat# ABN78; RRID: AB_10807945 Mouse anti-Robo3 R&D Systems Cat# AF3155; RRID: AB_10644167 Mouse anti-GluN1 SySy Cat# 114011; RRID: AB_887750 Goat anti-rat Alexa 555 ThermoFisher Cat# A21434; RRID: AB_2535855 Goat anti-chicken Alexa 488 ThermoFisher Cat# A11039; RRID: AB_2534096 Goat anti-mouse Alexa 647 ThermoFisher Cat# A21235; RRID: AB_2535804 Streptavidin Alexa 647 ThermoFisher Cat# S32357 Bacterial and virus strains scAAV9-hSyn-iCre-HA Boston Children’s Hospital Viral Core N/A scAAV9-hSyn-DiCre-HA Boston Children’s Hospital Viral Core N/A AAV9-hSyn-DN-THR Boston Children’s Hospital Viral Core N/A AAV9-hSyn-WT-THR Boston Children’s Hospital Viral Core N/A AAV9-SIO-nEF-DN-Thrb Janelia Viral Tools N/A AAV9-SIO-nEF-WT-Thrb Janelia Viral Tools N/A AAV9-hSyn-FLEX-CoChR-GFP UNC GTC Vector Core N/A AAVretro-CAG-Cre UNC GTC Vector Core N/A AAV9-hSyn-CoChR-GFP UNC GTC Vector Core N/A pENN.AAV_PHPeB.hSyn.HI.eGFP-Cre.WPRE.SV40 Addgene Addgene 105540 AAV9-S5E2-ChR2-mCherry Addgene Addgene 135634 Chemicals, peptides, and recombinant proteins 3,3’,5-Triiodo-L-thyronine Sigma-Aldrich Cat# T6397 Sobetirome Thomas Scanlan N/A Kolliphor Sigma-Aldrich Cat# C5135 NMP Sigma-Aldrich Cat# 328634 0.15% PTU Diet Inotiv Cat# TD.95125 Control Diet Inotiv Cat# TD.97350 Trizol Life Technologies Cat# 15596018 RIPA buffer ThermoFisher Cat# 89900 cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail Roche Cat# 11836170001 Biocytin Sigma Aldrich Cat# B4261 Critical commercial assays Chromium Next GEM Single Cell 3’ Kit v3 10X Genomics Cat#1000268 RNEasy Micro Kit Qiagen Cat#74004 SuperScript IV VILO Master Mix Kit with ezDNAse enzyme ThermoFisher Cat#11766050 RNAscope Multiplex Fluorescent Reagent Kit v1 (discontinued) and v2 Advanced Cell Diagnostics Cat#323100 (Continued on next page) e1 Cell 187, 1–19.e1–e11, October 3, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data snRNA-seq datasets This paper GEO: GSE271421 snRNA-seq datasets This paper https://cellxgene.cziscience.com/ collections/c450e15d-321a-42d6986b-11409d04896d Moseq, electrophysiology, and 2ABT datasets This paper https://dataverse.harvard.edu/ dataverse/2024_hochbaum_thyroid Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat# 664; RRID:IMSR_JAX:000664 Mouse: Robo3 fl/fl: Robo3tm1.1Ache Alain Chédotal111 MGI:4441335 Oligonucleotides TaqMan probe for Hr: (Mm00498963_m1) ThermoFisher Cat# 4331182 TaqMan probe for Dio1: (Mm00839358_m1) ThermoFisher Cat# 4331182 TaqMan probe for Ier5: (Mm01295615_s1) ThermoFisher Cat# 4331182 TaqMan probe for Gapdh: (Mm99999915_g1) ThermoFisher Cat# 4351370 TaqMan probe for Cyp11a1: (Mm00490735_m1) ThermoFisher Cat# 4331182 FISH probe for Hr Advanced Cell Diagnostics Cat# 883311 FISH probe for Ier5 Advanced Cell Diagnostics Cat# 530401-C3 FISH probe for Robo3 Advanced Cell Diagnostics Cat# 558811-C2 4-plex positive probe Advanced Cell Diagnostics Cat# 321811 4-plex negative control probe Advanced Cell Diagnostics Cat# 321831 Recombinant DNA DRH001_scAAV-hSyn-iCre-HA This paper Addgene 225086 DRH002_scAAV-hSyn-DiCre-HA This paper Addgene 225087 DRH015_ AAV-hSyn-WT-THR This paper Addgene 225088 DRH016_ AAV-hSyn-DN-THR This paper Addgene 225089 DRH031_ AAV-SIO-nEF-WT-THR This paper Addgene 225090 DRH032_ AAV-SIO-nEF-DN-THR This paper Addgene 225091 Software and algorithms Custom software This paper https://github.com/bernardosabatinilab/ hochbaum_thyroid_2024 NeuroInfo MBF Bioscience https://www.mbfbioscience.com/ products/neuroinfo/; RRID:SCR_017346 MoSeq behavior analysis pipeline Lin et al.54 http://www.moseq4all.org/ ImageJ (Fiji) Schindelin et al.112 https://imagej.net/; RRID: SCR_003070 CellRanger v.5 pipeline 10x Genomics https://www.10xgenomics.com/support/ software/cell-ranger/latest Modified Seurat v.2 workflow Gazestani et al.113 N/A fGSEA package version 1.24.0 Korotkevich et al.114 N/A MATLAB version R2021b MathWorks https://www.mathworks.com/ products/matlab.html R version 4.2.2 R Foundation https://cran.r-project.org/bin/ windows/base/old/4.2.2/ Python version 3.9 Python Software Foundation https://www.python.org ll OPEN ACCESS Please cite this article in press as: Hochbaum et al., Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration, Cell (2024), https://doi.org/10.1016/j.cell.2024.07.041
Multiplex Assay:Article Title: Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rat anti-HA Roche Cat# 1186742300; RRID: AB_390918 Chicken anti-GFP Abcam Cat# Ab13970; RRID: AB_300798 Rabbit anti-NeuN Sigma Aldrich Cat# ABN78; RRID: AB_10807945 Mouse anti-Robo3 R&D Systems Cat# AF3155; RRID: AB_10644167 Mouse anti-GluN1 SySy Cat# 114011; RRID: AB_887750 Goat anti-rat Alexa 555 ThermoFisher Cat# A21434; RRID: AB_2535855 Goat anti-chicken Alexa 488 ThermoFisher Cat# A11039; RRID: AB_2534096 Goat anti-mouse Alexa 647 ThermoFisher Cat# A21235; RRID: AB_2535804 Streptavidin Alexa 647 ThermoFisher Cat# S32357 Bacterial and virus strains scAAV9-hSyn-iCre-HA Boston Children’s Hospital Viral Core N/A scAAV9-hSyn-DiCre-HA Boston Children’s Hospital Viral Core N/A AAV9-hSyn-DN-THR Boston Children’s Hospital Viral Core N/A AAV9-hSyn-WT-THR Boston Children’s Hospital Viral Core N/A AAV9-SIO-nEF-DN-Thrb Janelia Viral Tools N/A AAV9-SIO-nEF-WT-Thrb Janelia Viral Tools N/A AAV9-hSyn-FLEX-CoChR-GFP UNC GTC Vector Core N/A AAVretro-CAG-Cre UNC GTC Vector Core N/A AAV9-hSyn-CoChR-GFP UNC GTC Vector Core N/A pENN.AAV_PHPeB.hSyn.HI.eGFP-Cre.WPRE.SV40 Addgene Addgene 105540 AAV9-S5E2-ChR2-mCherry Addgene Addgene 135634 Chemicals, peptides, and recombinant proteins 3,3’,5-Triiodo-L-thyronine Sigma-Aldrich Cat# T6397 Sobetirome Thomas Scanlan N/A Kolliphor Sigma-Aldrich Cat# C5135 NMP Sigma-Aldrich Cat# 328634 0.15% PTU Diet Inotiv Cat# TD.95125 Control Diet Inotiv Cat# TD.97350 Trizol Life Technologies Cat# 15596018 RIPA buffer ThermoFisher Cat# 89900 cOmplete, Mini, EDTA-free Protease Inhibitor Cocktail Roche Cat# 11836170001 Biocytin Sigma Aldrich Cat# B4261 Critical commercial assays Chromium Next GEM Single Cell 3’ Kit v3 10X Genomics Cat#1000268 RNEasy Micro Kit Qiagen Cat#74004 SuperScript IV VILO Master Mix Kit with ezDNAse enzyme ThermoFisher Cat#11766050 RNAscope Multiplex Fluorescent Reagent Kit v1 (discontinued) and v2 Advanced Cell Diagnostics Cat#323100 (Continued on next page) e1 Cell 187, 1–19.e1–e11, October 3, 2024 .. REAGENT or RESOURCE SOURCE IDENTIFIER Deposited data snRNA-seq datasets This paper GEO: GSE271421 snRNA-seq datasets This paper https://cellxgene.cziscience.com/ collections/c450e15d-321a-42d6986b-11409d04896d Moseq, electrophysiology, and 2ABT datasets This paper https://dataverse.harvard.edu/ dataverse/2024_hochbaum_thyroid Experimental models: Organisms/strains Mouse: C57BL/6J The Jackson Laboratory Cat# 664; RRID:IMSR_JAX:000664 Mouse: Robo3 fl/fl: Robo3tm1.1Ache Alain Chédotal111 MGI:4441335 Oligonucleotides TaqMan probe for Hr: (Mm00498963_m1) ThermoFisher Cat# 4331182 TaqMan probe for Dio1: (Mm00839358_m1) ThermoFisher Cat# 4331182 TaqMan probe for Ier5: (Mm01295615_s1) ThermoFisher Cat# 4331182 TaqMan probe for Gapdh: (Mm99999915_g1) ThermoFisher Cat# 4351370 TaqMan probe for Cyp11a1: (Mm00490735_m1) ThermoFisher Cat# 4331182 FISH probe for Hr Advanced Cell Diagnostics Cat# 883311 FISH probe for Ier5 Advanced Cell Diagnostics Cat# 530401-C3 FISH probe for Robo3 Advanced Cell Diagnostics Cat# 558811-C2 4-plex positive probe Advanced Cell Diagnostics Cat# 321811 4-plex negative control probe Advanced Cell Diagnostics Cat# 321831 Recombinant DNA DRH001_scAAV-hSyn-iCre-HA This paper Addgene 225086 DRH002_scAAV-hSyn-DiCre-HA This paper Addgene 225087 DRH015_ AAV-hSyn-WT-THR This paper Addgene 225088 DRH016_ AAV-hSyn-DN-THR This paper Addgene 225089 DRH031_ AAV-SIO-nEF-WT-THR This paper Addgene 225090 DRH032_ AAV-SIO-nEF-DN-THR This paper Addgene 225091 Software and algorithms Custom software This paper https://github.com/bernardosabatinilab/ hochbaum_thyroid_2024 NeuroInfo MBF Bioscience https://www.mbfbioscience.com/ products/neuroinfo/; RRID:SCR_017346 MoSeq behavior analysis pipeline Lin et al.54 http://www.moseq4all.org/ ImageJ (Fiji) Schindelin et al.112 https://imagej.net/; RRID: SCR_003070 CellRanger v.5 pipeline 10x Genomics https://www.10xgenomics.com/support/ software/cell-ranger/latest Modified Seurat v.2 workflow Gazestani et al.113 N/A fGSEA package version 1.24.0 Korotkevich et al.114 N/A MATLAB version R2021b MathWorks https://www.mathworks.com/ products/matlab.html R version 4.2.2 R Foundation https://cran.r-project.org/bin/ windows/base/old/4.2.2/ Python version 3.9 Python Software Foundation https://www.python.org ll OPEN ACCESS Please cite this article in press as: Hochbaum et al., Thyroid hormone remodels cortex to coordinate body-wide metabolism and exploration, Cell (2024), https://doi.org/10.1016/j.cell.2024.07.041
Isolation:Article Title: AMPK activation protects against prostate cancer by inducing a catabolic cellular state.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies ACC (Rabbit polyclonal) Cell Signaling Technology Cat#3661 ACC (Mouse monoclonal) Millipore Cat#05–1098; Clone 7D2.2 AKT (Pan) (Mouse monoclonal) Cell Signaling Technology Cat#2920; Clone 20D4 AMPK alpha 1/2 (Mouse monoclonal) Cell Signaling Technology Cat#2793; Clone F6 AMPK beta1/2 (Rabbit monoclonal) Cell Signaling Technology Cat#4150; Clone 57C12 Cleaved-caspase 3 (Rabbit polyclonal) Cell Signaling Technology Cat#9661 FBP1 (Rabbit monoclonal) Abcam Cat#109020; Clone EPR4619 FLAG (Rabbit polyclonal) Sigma-Aldrich Cat#F7425 Ki-67 (Rabbit monoclonal) Abcam Cat#ab16667; Clone SP6 NF-kB p65 (D14E12) (Rabbit monoclonal) Cell Signaling Technology Cat#8242 pAKTSer473 (Rabbit monoclonal) Cell Signaling Technology Cat#4060; Clone D9E pAMPKaThr172 (Rabbit monoclonal) Cell Signaling Technology Cat#2535; Clone 40H9 PGC1a (Rabbit polyclonal) Novus Cat#NP1-04676 SNAI1 (Rabbit monoclonal) Cell Signaling Technology Cat#3879; Clone C15D3 TOMM20 (Rabbit monoclonal) Abcam Cat#ab186735; Clone EPR15581-54 Total OXPHOS antibody cocktail Abcam Cat#ab110413 Vinculin (Mouse monoclonal) Sigma-Aldrich Cat#V9131; Clone hVIN-1 Anti-mouse EpCAM APC BioLegend Cat#118214 Anti-mouse E-Cadherin PerCP-Efluor710 eBiosciences Cat#46-3249-82 Goat Anti-Rabbit IgG, Biotinylated Vector Laboratories Cat#BA-1000-1.5 Goat Anti-Mouse IgG, HRP conjugate Cell Signaling Technology Cat#91196 Goat Anti-Rabbit IgG, HRP conjugate Cell Signaling Technology Cat#7074 IRDye 680RD Goat anti-Mouse IgG LI-COR Biosciences Cat#926-68070 IRDye 680RD Goat anti-Rabbit IgG LI-COR Biosciences Cat#926-68071 IRDye 800CW Goat anti-Mouse IgG LI-COR Biosciences Cat#926-32210 IRDye 800CW Goat anti-Rabbit IgG LI-COR Biosciences Cat#926-32211 Chemicals, peptides, and recombinant proteins Acetic acid Sigma-Aldrich Cat#A6283 Antimycin A Sigma-Aldrich Cat#A8674 BI9774 Dr. Jon Read, AstraZeneca N/A Chloroform ThermoFisher Cat#022920.K2 Collagenase/hyaluronidase solution (10x) STEMCELL Technologies Cat#07912 Crystal violet sln Sigma-Aldrich Cat#V5265 DHT Sigma-Aldrich Cat#A8380 Dispase STEMCELL Technologies Cat#07913 DMEM/F-12 Gibco Cat#10565 DNaseI STEMCELL Technologies Cat#07900 DPX mountant VWR Cat#06522 Etomoxir Cambridge Bioscience 11969-10mg-CAY EquiSPLASHTM LIPIDOMIX Quantitative MS Internal Standard Avanti Polar Lipids Cat#330731 FBS Sigma-Aldrich Cat#F9665 FBS (Charcoal stripped) Gibco Cat#12676 Gill Hematoxylin Sigma-Aldrich Cat#GHS132-1L (Continued on next page) Cell Reports 42, 112396, April 25, 2023 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Glutamax (100x) Gibco Cat#35050 Glygen C18 spin tips Glygen Corp Cat#TT2C18.96 HBSS STEMCELL Technologies Cat#37150 Hydrogen peroxide Sigma-Aldrich Cat#H1009 Lipofectamine 3000 ThermoFisher Cat#L3000015 LysC Wako Cat#125-05061 Matrigel (Organoid culture) Corning Cat#354234 Matrigel (Xenografts) Corning 354248 NEBNext Ultra II Directional RNA Library Prep Kit NEB Cat#E7760 NEBNext Poly(A) mRNA Magnetic Isolation Module NEB Cat#E7490 Normal goat serum ThermoFisher Cat#16-210-064 Penicillin-Streptomycin ThermoFisher Cat#15140122 Paraformaldehyde Sigma-Aldrich Cat#158127 Poly-L-lysine Sigma-Aldrich Cat#P4707 QubitTM dsDNA HS Assay Kit ThermoFisher Cat#Q32851 RIPA buffer ThermoFisher Cat89900 ROCK inhibitor Y-27632 STEMCELL Technologies Cat#07171 Rotenone Sigma-Aldrich Cat#R8875 RPMI-1640 Gibco Cat#61870036 Sulphobutylether-b-cyclodextrin MedChemExpress Cat#HY-17031 TRIzol reagent ThermoFisher Cat#15596018 Trypsin/EDTA STEMCELL Technologies Cat#07901 Trypsin Gold Promega Cat#V5280 Tween 20 VWR Cat#0777-1L Xylene Sigma-Aldrich Cat#534056-4L Critical commercial assays alamarBlue Cell Viability Reagent ThermoFisher Cat#DAL1100 BCA Protein Assay ThermoFisher Cat#23225 CellTiter Glo 2.0 Cell Viability Promega Cat#G9242 DAB Substrate Kit Vector Laboratories Cat#SK-4100 VECTASTAIN ELITE ABC-HRP KIT Vector Laboratories Cat#PK-6100 PowerUp SYBR Green Master Mix Life Technologies Cat#A25742 RNeasy Mini Kit Qiagen Qiagen Cat#74106 Seahorse FluxPaks Agilent Cat#102416-100 Seahorse XF DMEM Medium pH7.4 Agilent Cat#103575-100 Seahorse XF 1.0m Glucose Solution Agilent Cat#103577-100 Seahorse XF 200 mm glutamine solution Agilent Cat#103579-100 Seahorse XF Palmitate-BSA FAO Substrate Kit Agilent Cat#102720-100 SuperScript II Reverse Transcriptase ThermoFisher Cat#18064014 RTCA CIM-plates (migration) Agilent Cat#5665825001 RTCA E-plates (proliferation) Agilent Cat#5469813001 Deposited data Lipidomics datasets This study MassIVE: MSV000091405 Proteomics datasets This study PRIDE: PXD040731 RNAsequencing This study GEO: GSE214601 TCGA PRAD dataset Cancer Genome Atlas Research Network25 N/A (Continued on next page) 16 Cell Reports 42, 112396, April 25, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Primary and metastatic PCa Taylor et al.26 GEO: GSE21034 CRPC dataset Grasso et al.48 GEO: GSE35988 Primary and metastatic PCa Cai et al.49 GEO: GSE32269 Experimental models: Cell lines C4-2 ATCC Cat#CRL-3314 C4-2b Prof. Ian Mills, Oxford N/A Experimental models: Organisms/strains Mouse: Male C57BL/6J Pbsn-cre4+; Pten; Ampkg1(D316A) This study N/A Mouse: Male C57BL/6J Pbsn-cre4+; Pten; Ampkg1(WT) This study N/A Mouse: Male NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) Charles River (UK) Cat#005557 Oligonucleotides Primers for qPCR.
Bicinchoninic Acid Protein Assay:Article Title: AMPK activation protects against prostate cancer by inducing a catabolic cellular state.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies ACC (Rabbit polyclonal) Cell Signaling Technology Cat#3661 ACC (Mouse monoclonal) Millipore Cat#05–1098; Clone 7D2.2 AKT (Pan) (Mouse monoclonal) Cell Signaling Technology Cat#2920; Clone 20D4 AMPK alpha 1/2 (Mouse monoclonal) Cell Signaling Technology Cat#2793; Clone F6 AMPK beta1/2 (Rabbit monoclonal) Cell Signaling Technology Cat#4150; Clone 57C12 Cleaved-caspase 3 (Rabbit polyclonal) Cell Signaling Technology Cat#9661 FBP1 (Rabbit monoclonal) Abcam Cat#109020; Clone EPR4619 FLAG (Rabbit polyclonal) Sigma-Aldrich Cat#F7425 Ki-67 (Rabbit monoclonal) Abcam Cat#ab16667; Clone SP6 NF-kB p65 (D14E12) (Rabbit monoclonal) Cell Signaling Technology Cat#8242 pAKTSer473 (Rabbit monoclonal) Cell Signaling Technology Cat#4060; Clone D9E pAMPKaThr172 (Rabbit monoclonal) Cell Signaling Technology Cat#2535; Clone 40H9 PGC1a (Rabbit polyclonal) Novus Cat#NP1-04676 SNAI1 (Rabbit monoclonal) Cell Signaling Technology Cat#3879; Clone C15D3 TOMM20 (Rabbit monoclonal) Abcam Cat#ab186735; Clone EPR15581-54 Total OXPHOS antibody cocktail Abcam Cat#ab110413 Vinculin (Mouse monoclonal) Sigma-Aldrich Cat#V9131; Clone hVIN-1 Anti-mouse EpCAM APC BioLegend Cat#118214 Anti-mouse E-Cadherin PerCP-Efluor710 eBiosciences Cat#46-3249-82 Goat Anti-Rabbit IgG, Biotinylated Vector Laboratories Cat#BA-1000-1.5 Goat Anti-Mouse IgG, HRP conjugate Cell Signaling Technology Cat#91196 Goat Anti-Rabbit IgG, HRP conjugate Cell Signaling Technology Cat#7074 IRDye 680RD Goat anti-Mouse IgG LI-COR Biosciences Cat#926-68070 IRDye 680RD Goat anti-Rabbit IgG LI-COR Biosciences Cat#926-68071 IRDye 800CW Goat anti-Mouse IgG LI-COR Biosciences Cat#926-32210 IRDye 800CW Goat anti-Rabbit IgG LI-COR Biosciences Cat#926-32211 Chemicals, peptides, and recombinant proteins Acetic acid Sigma-Aldrich Cat#A6283 Antimycin A Sigma-Aldrich Cat#A8674 BI9774 Dr. Jon Read, AstraZeneca N/A Chloroform ThermoFisher Cat#022920.K2 Collagenase/hyaluronidase solution (10x) STEMCELL Technologies Cat#07912 Crystal violet sln Sigma-Aldrich Cat#V5265 DHT Sigma-Aldrich Cat#A8380 Dispase STEMCELL Technologies Cat#07913 DMEM/F-12 Gibco Cat#10565 DNaseI STEMCELL Technologies Cat#07900 DPX mountant VWR Cat#06522 Etomoxir Cambridge Bioscience 11969-10mg-CAY EquiSPLASHTM LIPIDOMIX Quantitative MS Internal Standard Avanti Polar Lipids Cat#330731 FBS Sigma-Aldrich Cat#F9665 FBS (Charcoal stripped) Gibco Cat#12676 Gill Hematoxylin Sigma-Aldrich Cat#GHS132-1L (Continued on next page) Cell Reports 42, 112396, April 25, 2023 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Glutamax (100x) Gibco Cat#35050 Glygen C18 spin tips Glygen Corp Cat#TT2C18.96 HBSS STEMCELL Technologies Cat#37150 Hydrogen peroxide Sigma-Aldrich Cat#H1009 Lipofectamine 3000 ThermoFisher Cat#L3000015 LysC Wako Cat#125-05061 Matrigel (Organoid culture) Corning Cat#354234 Matrigel (Xenografts) Corning 354248 NEBNext Ultra II Directional RNA Library Prep Kit NEB Cat#E7760 NEBNext Poly(A) mRNA Magnetic Isolation Module NEB Cat#E7490 Normal goat serum ThermoFisher Cat#16-210-064 Penicillin-Streptomycin ThermoFisher Cat#15140122 Paraformaldehyde Sigma-Aldrich Cat#158127 Poly-L-lysine Sigma-Aldrich Cat#P4707 QubitTM dsDNA HS Assay Kit ThermoFisher Cat#Q32851 RIPA buffer ThermoFisher Cat89900 ROCK inhibitor Y-27632 STEMCELL Technologies Cat#07171 Rotenone Sigma-Aldrich Cat#R8875 RPMI-1640 Gibco Cat#61870036 Sulphobutylether-b-cyclodextrin MedChemExpress Cat#HY-17031 TRIzol reagent ThermoFisher Cat#15596018 Trypsin/EDTA STEMCELL Technologies Cat#07901 Trypsin Gold Promega Cat#V5280 Tween 20 VWR Cat#0777-1L Xylene Sigma-Aldrich Cat#534056-4L Critical commercial assays alamarBlue Cell Viability Reagent ThermoFisher Cat#DAL1100 BCA Protein Assay ThermoFisher Cat#23225 CellTiter Glo 2.0 Cell Viability Promega Cat#G9242 DAB Substrate Kit Vector Laboratories Cat#SK-4100 VECTASTAIN ELITE ABC-HRP KIT Vector Laboratories Cat#PK-6100 PowerUp SYBR Green Master Mix Life Technologies Cat#A25742 RNeasy Mini Kit Qiagen Qiagen Cat#74106 Seahorse FluxPaks Agilent Cat#102416-100 Seahorse XF DMEM Medium pH7.4 Agilent Cat#103575-100 Seahorse XF 1.0m Glucose Solution Agilent Cat#103577-100 Seahorse XF 200 mm glutamine solution Agilent Cat#103579-100 Seahorse XF Palmitate-BSA FAO Substrate Kit Agilent Cat#102720-100 SuperScript II Reverse Transcriptase ThermoFisher Cat#18064014 RTCA CIM-plates (migration) Agilent Cat#5665825001 RTCA E-plates (proliferation) Agilent Cat#5469813001 Deposited data Lipidomics datasets This study MassIVE: MSV000091405 Proteomics datasets This study PRIDE: PXD040731 RNAsequencing This study GEO: GSE214601 TCGA PRAD dataset Cancer Genome Atlas Research Network25 N/A (Continued on next page) 16 Cell Reports 42, 112396, April 25, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Primary and metastatic PCa Taylor et al.26 GEO: GSE21034 CRPC dataset Grasso et al.48 GEO: GSE35988 Primary and metastatic PCa Cai et al.49 GEO: GSE32269 Experimental models: Cell lines C4-2 ATCC Cat#CRL-3314 C4-2b Prof. Ian Mills, Oxford N/A Experimental models: Organisms/strains Mouse: Male C57BL/6J Pbsn-cre4+; Pten; Ampkg1(D316A) This study N/A Mouse: Male C57BL/6J Pbsn-cre4+; Pten; Ampkg1(WT) This study N/A Mouse: Male NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) Charles River (UK) Cat#005557 Oligonucleotides Primers for qPCR.
Article Title: Glutamine Links Obesity to Inflammation in Human White Adipose Tissue.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Glucose Solution ThermoFisher Cat#A2494001 DMEM ThermoFisher Cat#21700-026 Ham’s F-12 Nutrient Mix ThermoFisher Cat#11765054 RIPA buffer ThermoFisher Cat#89901 Dynabeads protein G ThermoFisher Cat#1004D SYTOX Blue ThermoFisher Cat#S34857 CountBright Absolute Counting Beads ThermoFisher Cat#C36950 Pierce Protein A/G magnetic beads ThermoFisher Cat#88802 RIPA buffer ThermoFisher Cat#89901 Collagenase Sigma-Aldrich Cat#C6885 2-deoxy-D-glucose Sigma-Aldrich Cat#D6134-1G PUGNAc Sigma-Aldrich Cat#A7229 GalNAc-O-bn Sigma-Aldrich Cat#B4894 FGF2, Fibroblast Growth Factor-Basic human, bFGF Sigma-Aldrich Cat#F0291-4X25UG HyClone FBS, EU approved South American Origin Hyclone, GE Cat#SV30160-03 Critical Commercial Assays Seahorse XF Glycolysis Stress Test Agilent Cat#103020-100 Seahorse XFp Mito Fuel Flex Test Agilent Cat#103070-100 iSript cDNA Synthesis kit Bio-Rad Cat#170-8891 Insulin ELISA Kit Crystal Chem Cat#90080 EZ-Magna ChIP HiSens Chromatin Immunoprecipitation Kit Merck Cat#17-10461 V-plex Plus Human IL-1b kit Mesoscale Discovery Cat#K151QP NEBnext chip-seq library Prep master mix set New England Biolabs Cat#E6240L EZBlue Gel Staining Reagent Sigma-Aldrich Cat#G1041 Pierce BCA Protein Assay Kit ThermoFisher Cat#23227 20-plex Human panel ThermoFisher EXP200-12185-901 MCP-1/CCL2 Human ELISA Kit ThermoFisher Cat#88-7399-22 IL-6 Human ELISA Kit ThermoFisher Cat#KHC0061 RNeasy Lipid Tissue Mini Kit QIAGEN Cat#74804 NucleoSpin RNA Macherey-Nagel Cat#740955.250 Deposited Data Human gene expression data (gene microarray) This paper GEO: GSE59034 Human in vitro differentiated adipocytes incubated in high and low glutamine (gene microarray) This paper GEO: GSE140426 SP1 RNAi in human in vitro differentiated adipocytes (gene microarray) This paper GEO: GSE140426 O-GlcNAc ChIPseq (sequencing data) This paper GEO: GSE140426 Experimental Models: Organisms/Strains Mouse C57/BL/6J Charles River N/A Oligonucleotides TaqMan probe human LRP10 Applied Biosystems Hs00204094_m1 TaqMan probe human PPIA Applied Biosystems Hs04194521_s1 TaqMan probe human OGN Applied Biosystems Hs00247901_m1 TaqMan probe human CCL2 Applied Biosystems Hs00234140_m1 TaqMan probe human IL1B Applied Biosystems Hs01555410_m1 TaqMan probe human IL6 Applied Biosystems Hs00985639_m1 TaqMan probe human ADIPOQ Applied Biosystems Hs00605917_m1 TaqMan probe human PLIN1 Applied Biosystems Hs00193510_m1 TaqMan probe human PNPLA2 Applied Biosystems Hs00386101_m1 TaqMan probe human PPARG Applied Biosystems Hs01115513_m1 (Continued on next page) e2 Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3
SYBR Green Assay:Article Title: AMPK activation protects against prostate cancer by inducing a catabolic cellular state.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies ACC (Rabbit polyclonal) Cell Signaling Technology Cat#3661 ACC (Mouse monoclonal) Millipore Cat#05–1098; Clone 7D2.2 AKT (Pan) (Mouse monoclonal) Cell Signaling Technology Cat#2920; Clone 20D4 AMPK alpha 1/2 (Mouse monoclonal) Cell Signaling Technology Cat#2793; Clone F6 AMPK beta1/2 (Rabbit monoclonal) Cell Signaling Technology Cat#4150; Clone 57C12 Cleaved-caspase 3 (Rabbit polyclonal) Cell Signaling Technology Cat#9661 FBP1 (Rabbit monoclonal) Abcam Cat#109020; Clone EPR4619 FLAG (Rabbit polyclonal) Sigma-Aldrich Cat#F7425 Ki-67 (Rabbit monoclonal) Abcam Cat#ab16667; Clone SP6 NF-kB p65 (D14E12) (Rabbit monoclonal) Cell Signaling Technology Cat#8242 pAKTSer473 (Rabbit monoclonal) Cell Signaling Technology Cat#4060; Clone D9E pAMPKaThr172 (Rabbit monoclonal) Cell Signaling Technology Cat#2535; Clone 40H9 PGC1a (Rabbit polyclonal) Novus Cat#NP1-04676 SNAI1 (Rabbit monoclonal) Cell Signaling Technology Cat#3879; Clone C15D3 TOMM20 (Rabbit monoclonal) Abcam Cat#ab186735; Clone EPR15581-54 Total OXPHOS antibody cocktail Abcam Cat#ab110413 Vinculin (Mouse monoclonal) Sigma-Aldrich Cat#V9131; Clone hVIN-1 Anti-mouse EpCAM APC BioLegend Cat#118214 Anti-mouse E-Cadherin PerCP-Efluor710 eBiosciences Cat#46-3249-82 Goat Anti-Rabbit IgG, Biotinylated Vector Laboratories Cat#BA-1000-1.5 Goat Anti-Mouse IgG, HRP conjugate Cell Signaling Technology Cat#91196 Goat Anti-Rabbit IgG, HRP conjugate Cell Signaling Technology Cat#7074 IRDye 680RD Goat anti-Mouse IgG LI-COR Biosciences Cat#926-68070 IRDye 680RD Goat anti-Rabbit IgG LI-COR Biosciences Cat#926-68071 IRDye 800CW Goat anti-Mouse IgG LI-COR Biosciences Cat#926-32210 IRDye 800CW Goat anti-Rabbit IgG LI-COR Biosciences Cat#926-32211 Chemicals, peptides, and recombinant proteins Acetic acid Sigma-Aldrich Cat#A6283 Antimycin A Sigma-Aldrich Cat#A8674 BI9774 Dr. Jon Read, AstraZeneca N/A Chloroform ThermoFisher Cat#022920.K2 Collagenase/hyaluronidase solution (10x) STEMCELL Technologies Cat#07912 Crystal violet sln Sigma-Aldrich Cat#V5265 DHT Sigma-Aldrich Cat#A8380 Dispase STEMCELL Technologies Cat#07913 DMEM/F-12 Gibco Cat#10565 DNaseI STEMCELL Technologies Cat#07900 DPX mountant VWR Cat#06522 Etomoxir Cambridge Bioscience 11969-10mg-CAY EquiSPLASHTM LIPIDOMIX Quantitative MS Internal Standard Avanti Polar Lipids Cat#330731 FBS Sigma-Aldrich Cat#F9665 FBS (Charcoal stripped) Gibco Cat#12676 Gill Hematoxylin Sigma-Aldrich Cat#GHS132-1L (Continued on next page) Cell Reports 42, 112396, April 25, 2023 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Glutamax (100x) Gibco Cat#35050 Glygen C18 spin tips Glygen Corp Cat#TT2C18.96 HBSS STEMCELL Technologies Cat#37150 Hydrogen peroxide Sigma-Aldrich Cat#H1009 Lipofectamine 3000 ThermoFisher Cat#L3000015 LysC Wako Cat#125-05061 Matrigel (Organoid culture) Corning Cat#354234 Matrigel (Xenografts) Corning 354248 NEBNext Ultra II Directional RNA Library Prep Kit NEB Cat#E7760 NEBNext Poly(A) mRNA Magnetic Isolation Module NEB Cat#E7490 Normal goat serum ThermoFisher Cat#16-210-064 Penicillin-Streptomycin ThermoFisher Cat#15140122 Paraformaldehyde Sigma-Aldrich Cat#158127 Poly-L-lysine Sigma-Aldrich Cat#P4707 QubitTM dsDNA HS Assay Kit ThermoFisher Cat#Q32851 RIPA buffer ThermoFisher Cat89900 ROCK inhibitor Y-27632 STEMCELL Technologies Cat#07171 Rotenone Sigma-Aldrich Cat#R8875 RPMI-1640 Gibco Cat#61870036 Sulphobutylether-b-cyclodextrin MedChemExpress Cat#HY-17031 TRIzol reagent ThermoFisher Cat#15596018 Trypsin/EDTA STEMCELL Technologies Cat#07901 Trypsin Gold Promega Cat#V5280 Tween 20 VWR Cat#0777-1L Xylene Sigma-Aldrich Cat#534056-4L Critical commercial assays alamarBlue Cell Viability Reagent ThermoFisher Cat#DAL1100 BCA Protein Assay ThermoFisher Cat#23225 CellTiter Glo 2.0 Cell Viability Promega Cat#G9242 DAB Substrate Kit Vector Laboratories Cat#SK-4100 VECTASTAIN ELITE ABC-HRP KIT Vector Laboratories Cat#PK-6100 PowerUp SYBR Green Master Mix Life Technologies Cat#A25742 RNeasy Mini Kit Qiagen Qiagen Cat#74106 Seahorse FluxPaks Agilent Cat#102416-100 Seahorse XF DMEM Medium pH7.4 Agilent Cat#103575-100 Seahorse XF 1.0m Glucose Solution Agilent Cat#103577-100 Seahorse XF 200 mm glutamine solution Agilent Cat#103579-100 Seahorse XF Palmitate-BSA FAO Substrate Kit Agilent Cat#102720-100 SuperScript II Reverse Transcriptase ThermoFisher Cat#18064014 RTCA CIM-plates (migration) Agilent Cat#5665825001 RTCA E-plates (proliferation) Agilent Cat#5469813001 Deposited data Lipidomics datasets This study MassIVE: MSV000091405 Proteomics datasets This study PRIDE: PXD040731 RNAsequencing This study GEO: GSE214601 TCGA PRAD dataset Cancer Genome Atlas Research Network25 N/A (Continued on next page) 16 Cell Reports 42, 112396, April 25, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Primary and metastatic PCa Taylor et al.26 GEO: GSE21034 CRPC dataset Grasso et al.48 GEO: GSE35988 Primary and metastatic PCa Cai et al.49 GEO: GSE32269 Experimental models: Cell lines C4-2 ATCC Cat#CRL-3314 C4-2b Prof. Ian Mills, Oxford N/A Experimental models: Organisms/strains Mouse: Male C57BL/6J Pbsn-cre4+; Pten; Ampkg1(D316A) This study N/A Mouse: Male C57BL/6J Pbsn-cre4+; Pten; Ampkg1(WT) This study N/A Mouse: Male NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) Charles River (UK) Cat#005557 Oligonucleotides Primers for qPCR.
Article Title: YY1 Lactylation in Microglia Promotes Angiogenesis Through Transcription Activation-Mediated Upregulation of FGF2
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal Anti-CD31 Abcam Cat# ab9498; RRID: AB_307284 Rabbit polyclonal Anti-SIRT1 Abcam Cat# ab7343; RRID: AB_305867 Rabbit monoclonal Anti-Ki67 Abcam Cat# ab16667; RRID: AB_302459 Rabbit polyclonal Anti-PCAF Abcam Cat# ab12188; RRID: AB_298918 Goat polyclonal Anti-Iba1 Abcam Cat# ab5076; RRID: AB_2224402 VeriBlot for IP Detection Reagent (HRP) Abcam Cat# 131366 Mouse monoclonal Anti-β-Actin Abcam Cat# ab8226, RRID: AB_306371 Mouse monoclonal Anti-YY1 Proteintech Cat# 66281-1-lg; RRID: AB_2737053 Mouse monoclonal Anti-HDAC6 Santa Cruz Biotechnology Cat# sc-28386; RRID: AB_627708 Mouse monoclonal Anti-FGF2 Santa Cruz Biotechnology Cat# sc-74412; RRID: AB_1122854 Mouse monoclonal Anti-p300 Santa Cruz Biotechnology Cat# sc-48343; RRID: AB_628075 Mouse monoclonal Anti-TIP60 Santa Cruz Biotechnology Cat# sc-166323; RRID: AB_2296327 Rabbit monoclonal Anti-Iba1 FUJIFILM Wako Shibayagi Cat# 019-19741; RRID: AB_839504 Rabbit Pan-Kla PTM BIO Cat# PTM-1401; RRID: AB_2868521 Rabbit (DA1E) mAb IgG XP Isotype Control antibody Cell Signaling Technology Cat# 3900; RRID: AB_1550038 Rabbit monoclonal Anti-YY1 Cell Signaling Technology Cat# 46395; RRID: AB_2799302 Goat Anti-Mouse Alexa Flour 488 Bioss Cat# bs-0368G-A488,RRID:AB_10892893 Goat Anti-Rabbit Alexa Flour 488 Bioss Cat# bs-0295G A488;RRID:AB_10893781 Donkey Anti-Goat Cy3 Bioss Cat# bs-0294D-Cy3;RRID:AB_10894752 Goat Anti-Mouse Cy3 Bioss Cat# bs-0296G-Cy3;RRID:AB_10892835 Goat Anti-Rabbit Cy3 Bioss Cat# bs-0295G-Cy3;RRID:AB_10892956 Chemicals, peptides, and recombinant proteins EMEM ATCC Cat# 30-2003 Complete Classic Medium with Serum & CultureBoost Cell Systems Cat# 4Z0-500 Trypsin-EDTA (0.05%) Gibco Cat# 25300054 FBS Gibco Cat# 10099141 Penicillin-Streptomycin-Glutam(100X) Gibco Cat# 10378016 DMSO Solarbio Cat# 67-68-5 TRIzol Thermofisher Cat# 15596026 DAPI Thermofisher Cat# 62248 RIPA buffer Thermofisher Cat# 89900 Rotenone Rhawn Cat# R006873 Sodium Dichloroacetate Rhawn Cat# R052025 PLX3397 MedChemExpress Cat# HY-16749 PEG-300 Sigma-Aldrich 90878-250ML-F Puromycin Sigma-Aldrich Cat#P8833 Tween 80 Sigma-Aldrich Cat# P1754 TritonX-100 Sigma-Aldrich Cat# 648466 Lipofectamine 2000 Invitrogen Cat#11668019 Critical commercial assays RT Master Mix for qPCR MedChemExpress Cat# HY-K0511 SYBR Green qPCR Master Mix MedChemExpress Cat# HY-K0522 This preprint research paper has not been peer reviewed. .. Electronic copy available at: https://ssrn.com/abstract=4044116 Pr pr in t n ot p ee r r ev ie we d Ultra High Sensitivity ECL Kit MedChemExpress Cat# HY-K1005 Immunoprecipitation kit Abcam Cat# ab206996 SimpleChIP Plus Enzymatic Chromatin IP Kit Cell Signaling Technology Cat# 9004S Dual-Luciferase Reporter Assay System Promega Cat# E2920 The LA Assay Kit Solarbio Cat# BC2235 4% paraformaldehyde Biosharp Cat# 143174 Goat serum Boster Cat# AR0009 Experimental models: Cell lines HMC3 cells ATCC Cat# CRL-3304 HRMECs Cell Systems Cat# ACBRI 181 Experimental models: Organisms/strains Mouse: C57BL/6J The Experimental Animal Center of Chongqing Medical University N/A Oligonucleotides Primers used for qRT-PCR, see Table S2 Shanghai Sangon Biotech N/A Primers used for ChIP-qPCR, see Table S2 Shanghai Sangon Biotech N/A Recombinant DNA Ubi-MCS(YY1 WT)-3FLAG-CBh-gcGFP-IRES-puromycin Shanghai Genechem Co, Ltd N/A Ubi-MCS(YY1 K183R)-3FLAG-CBh-gcGFP-IRESpuromycin Shanghai Genechem Co, Ltd N/A MCS-SV40-firefly_Luciferase-PloyA-Tk-Renilla_LuciferasePolyA (FGF2 promoter luciferase reporter) Shanghai Genechem Co, Ltd N/A CAS9-Easy-Lentivirus(SAM)(EP300): Lenti-dCAS9puro; U6-sgRNA-SV40-MS2-P65-HSF1-CMV-EGFP Shanghai Genechem Co, Ltd N/A Software and algorithms GraphPad Prism 8.0 https://www.graphpad.com N/A NIH ImageJ https://imagej.nih.gov/ij/ N/A cellSens Dimension https://www.olympuslifescience.com.cn/en/software/ cellsens/ N/A ZEN https://www.zeiss.com/microsc opy/int/ downloads.html N/A IBM.SPSS.V20. https://spssau.com/?10200000 0&b_scene_zt=1 N/A This preprint research paper has not been peer reviewed.
Reverse Transcription:Article Title: AMPK activation protects against prostate cancer by inducing a catabolic cellular state.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies ACC (Rabbit polyclonal) Cell Signaling Technology Cat#3661 ACC (Mouse monoclonal) Millipore Cat#05–1098; Clone 7D2.2 AKT (Pan) (Mouse monoclonal) Cell Signaling Technology Cat#2920; Clone 20D4 AMPK alpha 1/2 (Mouse monoclonal) Cell Signaling Technology Cat#2793; Clone F6 AMPK beta1/2 (Rabbit monoclonal) Cell Signaling Technology Cat#4150; Clone 57C12 Cleaved-caspase 3 (Rabbit polyclonal) Cell Signaling Technology Cat#9661 FBP1 (Rabbit monoclonal) Abcam Cat#109020; Clone EPR4619 FLAG (Rabbit polyclonal) Sigma-Aldrich Cat#F7425 Ki-67 (Rabbit monoclonal) Abcam Cat#ab16667; Clone SP6 NF-kB p65 (D14E12) (Rabbit monoclonal) Cell Signaling Technology Cat#8242 pAKTSer473 (Rabbit monoclonal) Cell Signaling Technology Cat#4060; Clone D9E pAMPKaThr172 (Rabbit monoclonal) Cell Signaling Technology Cat#2535; Clone 40H9 PGC1a (Rabbit polyclonal) Novus Cat#NP1-04676 SNAI1 (Rabbit monoclonal) Cell Signaling Technology Cat#3879; Clone C15D3 TOMM20 (Rabbit monoclonal) Abcam Cat#ab186735; Clone EPR15581-54 Total OXPHOS antibody cocktail Abcam Cat#ab110413 Vinculin (Mouse monoclonal) Sigma-Aldrich Cat#V9131; Clone hVIN-1 Anti-mouse EpCAM APC BioLegend Cat#118214 Anti-mouse E-Cadherin PerCP-Efluor710 eBiosciences Cat#46-3249-82 Goat Anti-Rabbit IgG, Biotinylated Vector Laboratories Cat#BA-1000-1.5 Goat Anti-Mouse IgG, HRP conjugate Cell Signaling Technology Cat#91196 Goat Anti-Rabbit IgG, HRP conjugate Cell Signaling Technology Cat#7074 IRDye 680RD Goat anti-Mouse IgG LI-COR Biosciences Cat#926-68070 IRDye 680RD Goat anti-Rabbit IgG LI-COR Biosciences Cat#926-68071 IRDye 800CW Goat anti-Mouse IgG LI-COR Biosciences Cat#926-32210 IRDye 800CW Goat anti-Rabbit IgG LI-COR Biosciences Cat#926-32211 Chemicals, peptides, and recombinant proteins Acetic acid Sigma-Aldrich Cat#A6283 Antimycin A Sigma-Aldrich Cat#A8674 BI9774 Dr. Jon Read, AstraZeneca N/A Chloroform ThermoFisher Cat#022920.K2 Collagenase/hyaluronidase solution (10x) STEMCELL Technologies Cat#07912 Crystal violet sln Sigma-Aldrich Cat#V5265 DHT Sigma-Aldrich Cat#A8380 Dispase STEMCELL Technologies Cat#07913 DMEM/F-12 Gibco Cat#10565 DNaseI STEMCELL Technologies Cat#07900 DPX mountant VWR Cat#06522 Etomoxir Cambridge Bioscience 11969-10mg-CAY EquiSPLASHTM LIPIDOMIX Quantitative MS Internal Standard Avanti Polar Lipids Cat#330731 FBS Sigma-Aldrich Cat#F9665 FBS (Charcoal stripped) Gibco Cat#12676 Gill Hematoxylin Sigma-Aldrich Cat#GHS132-1L (Continued on next page) Cell Reports 42, 112396, April 25, 2023 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Glutamax (100x) Gibco Cat#35050 Glygen C18 spin tips Glygen Corp Cat#TT2C18.96 HBSS STEMCELL Technologies Cat#37150 Hydrogen peroxide Sigma-Aldrich Cat#H1009 Lipofectamine 3000 ThermoFisher Cat#L3000015 LysC Wako Cat#125-05061 Matrigel (Organoid culture) Corning Cat#354234 Matrigel (Xenografts) Corning 354248 NEBNext Ultra II Directional RNA Library Prep Kit NEB Cat#E7760 NEBNext Poly(A) mRNA Magnetic Isolation Module NEB Cat#E7490 Normal goat serum ThermoFisher Cat#16-210-064 Penicillin-Streptomycin ThermoFisher Cat#15140122 Paraformaldehyde Sigma-Aldrich Cat#158127 Poly-L-lysine Sigma-Aldrich Cat#P4707 QubitTM dsDNA HS Assay Kit ThermoFisher Cat#Q32851 RIPA buffer ThermoFisher Cat89900 ROCK inhibitor Y-27632 STEMCELL Technologies Cat#07171 Rotenone Sigma-Aldrich Cat#R8875 RPMI-1640 Gibco Cat#61870036 Sulphobutylether-b-cyclodextrin MedChemExpress Cat#HY-17031 TRIzol reagent ThermoFisher Cat#15596018 Trypsin/EDTA STEMCELL Technologies Cat#07901 Trypsin Gold Promega Cat#V5280 Tween 20 VWR Cat#0777-1L Xylene Sigma-Aldrich Cat#534056-4L Critical commercial assays alamarBlue Cell Viability Reagent ThermoFisher Cat#DAL1100 BCA Protein Assay ThermoFisher Cat#23225 CellTiter Glo 2.0 Cell Viability Promega Cat#G9242 DAB Substrate Kit Vector Laboratories Cat#SK-4100 VECTASTAIN ELITE ABC-HRP KIT Vector Laboratories Cat#PK-6100 PowerUp SYBR Green Master Mix Life Technologies Cat#A25742 RNeasy Mini Kit Qiagen Qiagen Cat#74106 Seahorse FluxPaks Agilent Cat#102416-100 Seahorse XF DMEM Medium pH7.4 Agilent Cat#103575-100 Seahorse XF 1.0m Glucose Solution Agilent Cat#103577-100 Seahorse XF 200 mm glutamine solution Agilent Cat#103579-100 Seahorse XF Palmitate-BSA FAO Substrate Kit Agilent Cat#102720-100 SuperScript II Reverse Transcriptase ThermoFisher Cat#18064014 RTCA CIM-plates (migration) Agilent Cat#5665825001 RTCA E-plates (proliferation) Agilent Cat#5469813001 Deposited data Lipidomics datasets This study MassIVE: MSV000091405 Proteomics datasets This study PRIDE: PXD040731 RNAsequencing This study GEO: GSE214601 TCGA PRAD dataset Cancer Genome Atlas Research Network25 N/A (Continued on next page) 16 Cell Reports 42, 112396, April 25, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Primary and metastatic PCa Taylor et al.26 GEO: GSE21034 CRPC dataset Grasso et al.48 GEO: GSE35988 Primary and metastatic PCa Cai et al.49 GEO: GSE32269 Experimental models: Cell lines C4-2 ATCC Cat#CRL-3314 C4-2b Prof. Ian Mills, Oxford N/A Experimental models: Organisms/strains Mouse: Male C57BL/6J Pbsn-cre4+; Pten; Ampkg1(D316A) This study N/A Mouse: Male C57BL/6J Pbsn-cre4+; Pten; Ampkg1(WT) This study N/A Mouse: Male NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) Charles River (UK) Cat#005557 Oligonucleotides Primers for qPCR.
Migration:Article Title: AMPK activation protects against prostate cancer by inducing a catabolic cellular state.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies ACC (Rabbit polyclonal) Cell Signaling Technology Cat#3661 ACC (Mouse monoclonal) Millipore Cat#05–1098; Clone 7D2.2 AKT (Pan) (Mouse monoclonal) Cell Signaling Technology Cat#2920; Clone 20D4 AMPK alpha 1/2 (Mouse monoclonal) Cell Signaling Technology Cat#2793; Clone F6 AMPK beta1/2 (Rabbit monoclonal) Cell Signaling Technology Cat#4150; Clone 57C12 Cleaved-caspase 3 (Rabbit polyclonal) Cell Signaling Technology Cat#9661 FBP1 (Rabbit monoclonal) Abcam Cat#109020; Clone EPR4619 FLAG (Rabbit polyclonal) Sigma-Aldrich Cat#F7425 Ki-67 (Rabbit monoclonal) Abcam Cat#ab16667; Clone SP6 NF-kB p65 (D14E12) (Rabbit monoclonal) Cell Signaling Technology Cat#8242 pAKTSer473 (Rabbit monoclonal) Cell Signaling Technology Cat#4060; Clone D9E pAMPKaThr172 (Rabbit monoclonal) Cell Signaling Technology Cat#2535; Clone 40H9 PGC1a (Rabbit polyclonal) Novus Cat#NP1-04676 SNAI1 (Rabbit monoclonal) Cell Signaling Technology Cat#3879; Clone C15D3 TOMM20 (Rabbit monoclonal) Abcam Cat#ab186735; Clone EPR15581-54 Total OXPHOS antibody cocktail Abcam Cat#ab110413 Vinculin (Mouse monoclonal) Sigma-Aldrich Cat#V9131; Clone hVIN-1 Anti-mouse EpCAM APC BioLegend Cat#118214 Anti-mouse E-Cadherin PerCP-Efluor710 eBiosciences Cat#46-3249-82 Goat Anti-Rabbit IgG, Biotinylated Vector Laboratories Cat#BA-1000-1.5 Goat Anti-Mouse IgG, HRP conjugate Cell Signaling Technology Cat#91196 Goat Anti-Rabbit IgG, HRP conjugate Cell Signaling Technology Cat#7074 IRDye 680RD Goat anti-Mouse IgG LI-COR Biosciences Cat#926-68070 IRDye 680RD Goat anti-Rabbit IgG LI-COR Biosciences Cat#926-68071 IRDye 800CW Goat anti-Mouse IgG LI-COR Biosciences Cat#926-32210 IRDye 800CW Goat anti-Rabbit IgG LI-COR Biosciences Cat#926-32211 Chemicals, peptides, and recombinant proteins Acetic acid Sigma-Aldrich Cat#A6283 Antimycin A Sigma-Aldrich Cat#A8674 BI9774 Dr. Jon Read, AstraZeneca N/A Chloroform ThermoFisher Cat#022920.K2 Collagenase/hyaluronidase solution (10x) STEMCELL Technologies Cat#07912 Crystal violet sln Sigma-Aldrich Cat#V5265 DHT Sigma-Aldrich Cat#A8380 Dispase STEMCELL Technologies Cat#07913 DMEM/F-12 Gibco Cat#10565 DNaseI STEMCELL Technologies Cat#07900 DPX mountant VWR Cat#06522 Etomoxir Cambridge Bioscience 11969-10mg-CAY EquiSPLASHTM LIPIDOMIX Quantitative MS Internal Standard Avanti Polar Lipids Cat#330731 FBS Sigma-Aldrich Cat#F9665 FBS (Charcoal stripped) Gibco Cat#12676 Gill Hematoxylin Sigma-Aldrich Cat#GHS132-1L (Continued on next page) Cell Reports 42, 112396, April 25, 2023 15 .. REAGENT or RESOURCE SOURCE IDENTIFIER Glutamax (100x) Gibco Cat#35050 Glygen C18 spin tips Glygen Corp Cat#TT2C18.96 HBSS STEMCELL Technologies Cat#37150 Hydrogen peroxide Sigma-Aldrich Cat#H1009 Lipofectamine 3000 ThermoFisher Cat#L3000015 LysC Wako Cat#125-05061 Matrigel (Organoid culture) Corning Cat#354234 Matrigel (Xenografts) Corning 354248 NEBNext Ultra II Directional RNA Library Prep Kit NEB Cat#E7760 NEBNext Poly(A) mRNA Magnetic Isolation Module NEB Cat#E7490 Normal goat serum ThermoFisher Cat#16-210-064 Penicillin-Streptomycin ThermoFisher Cat#15140122 Paraformaldehyde Sigma-Aldrich Cat#158127 Poly-L-lysine Sigma-Aldrich Cat#P4707 QubitTM dsDNA HS Assay Kit ThermoFisher Cat#Q32851 RIPA buffer ThermoFisher Cat89900 ROCK inhibitor Y-27632 STEMCELL Technologies Cat#07171 Rotenone Sigma-Aldrich Cat#R8875 RPMI-1640 Gibco Cat#61870036 Sulphobutylether-b-cyclodextrin MedChemExpress Cat#HY-17031 TRIzol reagent ThermoFisher Cat#15596018 Trypsin/EDTA STEMCELL Technologies Cat#07901 Trypsin Gold Promega Cat#V5280 Tween 20 VWR Cat#0777-1L Xylene Sigma-Aldrich Cat#534056-4L Critical commercial assays alamarBlue Cell Viability Reagent ThermoFisher Cat#DAL1100 BCA Protein Assay ThermoFisher Cat#23225 CellTiter Glo 2.0 Cell Viability Promega Cat#G9242 DAB Substrate Kit Vector Laboratories Cat#SK-4100 VECTASTAIN ELITE ABC-HRP KIT Vector Laboratories Cat#PK-6100 PowerUp SYBR Green Master Mix Life Technologies Cat#A25742 RNeasy Mini Kit Qiagen Qiagen Cat#74106 Seahorse FluxPaks Agilent Cat#102416-100 Seahorse XF DMEM Medium pH7.4 Agilent Cat#103575-100 Seahorse XF 1.0m Glucose Solution Agilent Cat#103577-100 Seahorse XF 200 mm glutamine solution Agilent Cat#103579-100 Seahorse XF Palmitate-BSA FAO Substrate Kit Agilent Cat#102720-100 SuperScript II Reverse Transcriptase ThermoFisher Cat#18064014 RTCA CIM-plates (migration) Agilent Cat#5665825001 RTCA E-plates (proliferation) Agilent Cat#5469813001 Deposited data Lipidomics datasets This study MassIVE: MSV000091405 Proteomics datasets This study PRIDE: PXD040731 RNAsequencing This study GEO: GSE214601 TCGA PRAD dataset Cancer Genome Atlas Research Network25 N/A (Continued on next page) 16 Cell Reports 42, 112396, April 25, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER Primary and metastatic PCa Taylor et al.26 GEO: GSE21034 CRPC dataset Grasso et al.48 GEO: GSE35988 Primary and metastatic PCa Cai et al.49 GEO: GSE32269 Experimental models: Cell lines C4-2 ATCC Cat#CRL-3314 C4-2b Prof. Ian Mills, Oxford N/A Experimental models: Organisms/strains Mouse: Male C57BL/6J Pbsn-cre4+; Pten; Ampkg1(D316A) This study N/A Mouse: Male C57BL/6J Pbsn-cre4+; Pten; Ampkg1(WT) This study N/A Mouse: Male NOD.Cg-Prkdcscid Il2rgtm1Wjl/SzJ (NSG) Charles River (UK) Cat#005557 Oligonucleotides Primers for qPCR.
Magnetic Beads:Article Title: Glutamine Links Obesity to Inflammation in Human White Adipose Tissue.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Glucose Solution ThermoFisher Cat#A2494001 DMEM ThermoFisher Cat#21700-026 Ham’s F-12 Nutrient Mix ThermoFisher Cat#11765054 RIPA buffer ThermoFisher Cat#89901 Dynabeads protein G ThermoFisher Cat#1004D SYTOX Blue ThermoFisher Cat#S34857 CountBright Absolute Counting Beads ThermoFisher Cat#C36950 Pierce Protein A/G magnetic beads ThermoFisher Cat#88802 RIPA buffer ThermoFisher Cat#89901 Collagenase Sigma-Aldrich Cat#C6885 2-deoxy-D-glucose Sigma-Aldrich Cat#D6134-1G PUGNAc Sigma-Aldrich Cat#A7229 GalNAc-O-bn Sigma-Aldrich Cat#B4894 FGF2, Fibroblast Growth Factor-Basic human, bFGF Sigma-Aldrich Cat#F0291-4X25UG HyClone FBS, EU approved South American Origin Hyclone, GE Cat#SV30160-03 Critical Commercial Assays Seahorse XF Glycolysis Stress Test Agilent Cat#103020-100 Seahorse XFp Mito Fuel Flex Test Agilent Cat#103070-100 iSript cDNA Synthesis kit Bio-Rad Cat#170-8891 Insulin ELISA Kit Crystal Chem Cat#90080 EZ-Magna ChIP HiSens Chromatin Immunoprecipitation Kit Merck Cat#17-10461 V-plex Plus Human IL-1b kit Mesoscale Discovery Cat#K151QP NEBnext chip-seq library Prep master mix set New England Biolabs Cat#E6240L EZBlue Gel Staining Reagent Sigma-Aldrich Cat#G1041 Pierce BCA Protein Assay Kit ThermoFisher Cat#23227 20-plex Human panel ThermoFisher EXP200-12185-901 MCP-1/CCL2 Human ELISA Kit ThermoFisher Cat#88-7399-22 IL-6 Human ELISA Kit ThermoFisher Cat#KHC0061 RNeasy Lipid Tissue Mini Kit QIAGEN Cat#74804 NucleoSpin RNA Macherey-Nagel Cat#740955.250 Deposited Data Human gene expression data (gene microarray) This paper GEO: GSE59034 Human in vitro differentiated adipocytes incubated in high and low glutamine (gene microarray) This paper GEO: GSE140426 SP1 RNAi in human in vitro differentiated adipocytes (gene microarray) This paper GEO: GSE140426 O-GlcNAc ChIPseq (sequencing data) This paper GEO: GSE140426 Experimental Models: Organisms/Strains Mouse C57/BL/6J Charles River N/A Oligonucleotides TaqMan probe human LRP10 Applied Biosystems Hs00204094_m1 TaqMan probe human PPIA Applied Biosystems Hs04194521_s1 TaqMan probe human OGN Applied Biosystems Hs00247901_m1 TaqMan probe human CCL2 Applied Biosystems Hs00234140_m1 TaqMan probe human IL1B Applied Biosystems Hs01555410_m1 TaqMan probe human IL6 Applied Biosystems Hs00985639_m1 TaqMan probe human ADIPOQ Applied Biosystems Hs00605917_m1 TaqMan probe human PLIN1 Applied Biosystems Hs00193510_m1 TaqMan probe human PNPLA2 Applied Biosystems Hs00386101_m1 TaqMan probe human PPARG Applied Biosystems Hs01115513_m1 (Continued on next page) e2 Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3
cDNA Synthesis:Article Title: Glutamine Links Obesity to Inflammation in Human White Adipose Tissue.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Glucose Solution ThermoFisher Cat#A2494001 DMEM ThermoFisher Cat#21700-026 Ham’s F-12 Nutrient Mix ThermoFisher Cat#11765054 RIPA buffer ThermoFisher Cat#89901 Dynabeads protein G ThermoFisher Cat#1004D SYTOX Blue ThermoFisher Cat#S34857 CountBright Absolute Counting Beads ThermoFisher Cat#C36950 Pierce Protein A/G magnetic beads ThermoFisher Cat#88802 RIPA buffer ThermoFisher Cat#89901 Collagenase Sigma-Aldrich Cat#C6885 2-deoxy-D-glucose Sigma-Aldrich Cat#D6134-1G PUGNAc Sigma-Aldrich Cat#A7229 GalNAc-O-bn Sigma-Aldrich Cat#B4894 FGF2, Fibroblast Growth Factor-Basic human, bFGF Sigma-Aldrich Cat#F0291-4X25UG HyClone FBS, EU approved South American Origin Hyclone, GE Cat#SV30160-03 Critical Commercial Assays Seahorse XF Glycolysis Stress Test Agilent Cat#103020-100 Seahorse XFp Mito Fuel Flex Test Agilent Cat#103070-100 iSript cDNA Synthesis kit Bio-Rad Cat#170-8891 Insulin ELISA Kit Crystal Chem Cat#90080 EZ-Magna ChIP HiSens Chromatin Immunoprecipitation Kit Merck Cat#17-10461 V-plex Plus Human IL-1b kit Mesoscale Discovery Cat#K151QP NEBnext chip-seq library Prep master mix set New England Biolabs Cat#E6240L EZBlue Gel Staining Reagent Sigma-Aldrich Cat#G1041 Pierce BCA Protein Assay Kit ThermoFisher Cat#23227 20-plex Human panel ThermoFisher EXP200-12185-901 MCP-1/CCL2 Human ELISA Kit ThermoFisher Cat#88-7399-22 IL-6 Human ELISA Kit ThermoFisher Cat#KHC0061 RNeasy Lipid Tissue Mini Kit QIAGEN Cat#74804 NucleoSpin RNA Macherey-Nagel Cat#740955.250 Deposited Data Human gene expression data (gene microarray) This paper GEO: GSE59034 Human in vitro differentiated adipocytes incubated in high and low glutamine (gene microarray) This paper GEO: GSE140426 SP1 RNAi in human in vitro differentiated adipocytes (gene microarray) This paper GEO: GSE140426 O-GlcNAc ChIPseq (sequencing data) This paper GEO: GSE140426 Experimental Models: Organisms/Strains Mouse C57/BL/6J Charles River N/A Oligonucleotides TaqMan probe human LRP10 Applied Biosystems Hs00204094_m1 TaqMan probe human PPIA Applied Biosystems Hs04194521_s1 TaqMan probe human OGN Applied Biosystems Hs00247901_m1 TaqMan probe human CCL2 Applied Biosystems Hs00234140_m1 TaqMan probe human IL1B Applied Biosystems Hs01555410_m1 TaqMan probe human IL6 Applied Biosystems Hs00985639_m1 TaqMan probe human ADIPOQ Applied Biosystems Hs00605917_m1 TaqMan probe human PLIN1 Applied Biosystems Hs00193510_m1 TaqMan probe human PNPLA2 Applied Biosystems Hs00386101_m1 TaqMan probe human PPARG Applied Biosystems Hs01115513_m1 (Continued on next page) e2 Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3
Enzyme-linked Immunosorbent Assay:Article Title: Glutamine Links Obesity to Inflammation in Human White Adipose Tissue.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Glucose Solution ThermoFisher Cat#A2494001 DMEM ThermoFisher Cat#21700-026 Ham’s F-12 Nutrient Mix ThermoFisher Cat#11765054 RIPA buffer ThermoFisher Cat#89901 Dynabeads protein G ThermoFisher Cat#1004D SYTOX Blue ThermoFisher Cat#S34857 CountBright Absolute Counting Beads ThermoFisher Cat#C36950 Pierce Protein A/G magnetic beads ThermoFisher Cat#88802 RIPA buffer ThermoFisher Cat#89901 Collagenase Sigma-Aldrich Cat#C6885 2-deoxy-D-glucose Sigma-Aldrich Cat#D6134-1G PUGNAc Sigma-Aldrich Cat#A7229 GalNAc-O-bn Sigma-Aldrich Cat#B4894 FGF2, Fibroblast Growth Factor-Basic human, bFGF Sigma-Aldrich Cat#F0291-4X25UG HyClone FBS, EU approved South American Origin Hyclone, GE Cat#SV30160-03 Critical Commercial Assays Seahorse XF Glycolysis Stress Test Agilent Cat#103020-100 Seahorse XFp Mito Fuel Flex Test Agilent Cat#103070-100 iSript cDNA Synthesis kit Bio-Rad Cat#170-8891 Insulin ELISA Kit Crystal Chem Cat#90080 EZ-Magna ChIP HiSens Chromatin Immunoprecipitation Kit Merck Cat#17-10461 V-plex Plus Human IL-1b kit Mesoscale Discovery Cat#K151QP NEBnext chip-seq library Prep master mix set New England Biolabs Cat#E6240L EZBlue Gel Staining Reagent Sigma-Aldrich Cat#G1041 Pierce BCA Protein Assay Kit ThermoFisher Cat#23227 20-plex Human panel ThermoFisher EXP200-12185-901 MCP-1/CCL2 Human ELISA Kit ThermoFisher Cat#88-7399-22 IL-6 Human ELISA Kit ThermoFisher Cat#KHC0061 RNeasy Lipid Tissue Mini Kit QIAGEN Cat#74804 NucleoSpin RNA Macherey-Nagel Cat#740955.250 Deposited Data Human gene expression data (gene microarray) This paper GEO: GSE59034 Human in vitro differentiated adipocytes incubated in high and low glutamine (gene microarray) This paper GEO: GSE140426 SP1 RNAi in human in vitro differentiated adipocytes (gene microarray) This paper GEO: GSE140426 O-GlcNAc ChIPseq (sequencing data) This paper GEO: GSE140426 Experimental Models: Organisms/Strains Mouse C57/BL/6J Charles River N/A Oligonucleotides TaqMan probe human LRP10 Applied Biosystems Hs00204094_m1 TaqMan probe human PPIA Applied Biosystems Hs04194521_s1 TaqMan probe human OGN Applied Biosystems Hs00247901_m1 TaqMan probe human CCL2 Applied Biosystems Hs00234140_m1 TaqMan probe human IL1B Applied Biosystems Hs01555410_m1 TaqMan probe human IL6 Applied Biosystems Hs00985639_m1 TaqMan probe human ADIPOQ Applied Biosystems Hs00605917_m1 TaqMan probe human PLIN1 Applied Biosystems Hs00193510_m1 TaqMan probe human PNPLA2 Applied Biosystems Hs00386101_m1 TaqMan probe human PPARG Applied Biosystems Hs01115513_m1 (Continued on next page) e2 Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3
Chromatin Immunoprecipitation:Article Title: Glutamine Links Obesity to Inflammation in Human White Adipose Tissue.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Glucose Solution ThermoFisher Cat#A2494001 DMEM ThermoFisher Cat#21700-026 Ham’s F-12 Nutrient Mix ThermoFisher Cat#11765054 RIPA buffer ThermoFisher Cat#89901 Dynabeads protein G ThermoFisher Cat#1004D SYTOX Blue ThermoFisher Cat#S34857 CountBright Absolute Counting Beads ThermoFisher Cat#C36950 Pierce Protein A/G magnetic beads ThermoFisher Cat#88802 RIPA buffer ThermoFisher Cat#89901 Collagenase Sigma-Aldrich Cat#C6885 2-deoxy-D-glucose Sigma-Aldrich Cat#D6134-1G PUGNAc Sigma-Aldrich Cat#A7229 GalNAc-O-bn Sigma-Aldrich Cat#B4894 FGF2, Fibroblast Growth Factor-Basic human, bFGF Sigma-Aldrich Cat#F0291-4X25UG HyClone FBS, EU approved South American Origin Hyclone, GE Cat#SV30160-03 Critical Commercial Assays Seahorse XF Glycolysis Stress Test Agilent Cat#103020-100 Seahorse XFp Mito Fuel Flex Test Agilent Cat#103070-100 iSript cDNA Synthesis kit Bio-Rad Cat#170-8891 Insulin ELISA Kit Crystal Chem Cat#90080 EZ-Magna ChIP HiSens Chromatin Immunoprecipitation Kit Merck Cat#17-10461 V-plex Plus Human IL-1b kit Mesoscale Discovery Cat#K151QP NEBnext chip-seq library Prep master mix set New England Biolabs Cat#E6240L EZBlue Gel Staining Reagent Sigma-Aldrich Cat#G1041 Pierce BCA Protein Assay Kit ThermoFisher Cat#23227 20-plex Human panel ThermoFisher EXP200-12185-901 MCP-1/CCL2 Human ELISA Kit ThermoFisher Cat#88-7399-22 IL-6 Human ELISA Kit ThermoFisher Cat#KHC0061 RNeasy Lipid Tissue Mini Kit QIAGEN Cat#74804 NucleoSpin RNA Macherey-Nagel Cat#740955.250 Deposited Data Human gene expression data (gene microarray) This paper GEO: GSE59034 Human in vitro differentiated adipocytes incubated in high and low glutamine (gene microarray) This paper GEO: GSE140426 SP1 RNAi in human in vitro differentiated adipocytes (gene microarray) This paper GEO: GSE140426 O-GlcNAc ChIPseq (sequencing data) This paper GEO: GSE140426 Experimental Models: Organisms/Strains Mouse C57/BL/6J Charles River N/A Oligonucleotides TaqMan probe human LRP10 Applied Biosystems Hs00204094_m1 TaqMan probe human PPIA Applied Biosystems Hs04194521_s1 TaqMan probe human OGN Applied Biosystems Hs00247901_m1 TaqMan probe human CCL2 Applied Biosystems Hs00234140_m1 TaqMan probe human IL1B Applied Biosystems Hs01555410_m1 TaqMan probe human IL6 Applied Biosystems Hs00985639_m1 TaqMan probe human ADIPOQ Applied Biosystems Hs00605917_m1 TaqMan probe human PLIN1 Applied Biosystems Hs00193510_m1 TaqMan probe human PNPLA2 Applied Biosystems Hs00386101_m1 TaqMan probe human PPARG Applied Biosystems Hs01115513_m1 (Continued on next page) e2 Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3
Staining:Article Title: Glutamine Links Obesity to Inflammation in Human White Adipose Tissue.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Glucose Solution ThermoFisher Cat#A2494001 DMEM ThermoFisher Cat#21700-026 Ham’s F-12 Nutrient Mix ThermoFisher Cat#11765054 RIPA buffer ThermoFisher Cat#89901 Dynabeads protein G ThermoFisher Cat#1004D SYTOX Blue ThermoFisher Cat#S34857 CountBright Absolute Counting Beads ThermoFisher Cat#C36950 Pierce Protein A/G magnetic beads ThermoFisher Cat#88802 RIPA buffer ThermoFisher Cat#89901 Collagenase Sigma-Aldrich Cat#C6885 2-deoxy-D-glucose Sigma-Aldrich Cat#D6134-1G PUGNAc Sigma-Aldrich Cat#A7229 GalNAc-O-bn Sigma-Aldrich Cat#B4894 FGF2, Fibroblast Growth Factor-Basic human, bFGF Sigma-Aldrich Cat#F0291-4X25UG HyClone FBS, EU approved South American Origin Hyclone, GE Cat#SV30160-03 Critical Commercial Assays Seahorse XF Glycolysis Stress Test Agilent Cat#103020-100 Seahorse XFp Mito Fuel Flex Test Agilent Cat#103070-100 iSript cDNA Synthesis kit Bio-Rad Cat#170-8891 Insulin ELISA Kit Crystal Chem Cat#90080 EZ-Magna ChIP HiSens Chromatin Immunoprecipitation Kit Merck Cat#17-10461 V-plex Plus Human IL-1b kit Mesoscale Discovery Cat#K151QP NEBnext chip-seq library Prep master mix set New England Biolabs Cat#E6240L EZBlue Gel Staining Reagent Sigma-Aldrich Cat#G1041 Pierce BCA Protein Assay Kit ThermoFisher Cat#23227 20-plex Human panel ThermoFisher EXP200-12185-901 MCP-1/CCL2 Human ELISA Kit ThermoFisher Cat#88-7399-22 IL-6 Human ELISA Kit ThermoFisher Cat#KHC0061 RNeasy Lipid Tissue Mini Kit QIAGEN Cat#74804 NucleoSpin RNA Macherey-Nagel Cat#740955.250 Deposited Data Human gene expression data (gene microarray) This paper GEO: GSE59034 Human in vitro differentiated adipocytes incubated in high and low glutamine (gene microarray) This paper GEO: GSE140426 SP1 RNAi in human in vitro differentiated adipocytes (gene microarray) This paper GEO: GSE140426 O-GlcNAc ChIPseq (sequencing data) This paper GEO: GSE140426 Experimental Models: Organisms/Strains Mouse C57/BL/6J Charles River N/A Oligonucleotides TaqMan probe human LRP10 Applied Biosystems Hs00204094_m1 TaqMan probe human PPIA Applied Biosystems Hs04194521_s1 TaqMan probe human OGN Applied Biosystems Hs00247901_m1 TaqMan probe human CCL2 Applied Biosystems Hs00234140_m1 TaqMan probe human IL1B Applied Biosystems Hs01555410_m1 TaqMan probe human IL6 Applied Biosystems Hs00985639_m1 TaqMan probe human ADIPOQ Applied Biosystems Hs00605917_m1 TaqMan probe human PLIN1 Applied Biosystems Hs00193510_m1 TaqMan probe human PNPLA2 Applied Biosystems Hs00386101_m1 TaqMan probe human PPARG Applied Biosystems Hs01115513_m1 (Continued on next page) e2 Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3
Gene Expression:Article Title: Glutamine Links Obesity to Inflammation in Human White Adipose Tissue.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Glucose Solution ThermoFisher Cat#A2494001 DMEM ThermoFisher Cat#21700-026 Ham’s F-12 Nutrient Mix ThermoFisher Cat#11765054 RIPA buffer ThermoFisher Cat#89901 Dynabeads protein G ThermoFisher Cat#1004D SYTOX Blue ThermoFisher Cat#S34857 CountBright Absolute Counting Beads ThermoFisher Cat#C36950 Pierce Protein A/G magnetic beads ThermoFisher Cat#88802 RIPA buffer ThermoFisher Cat#89901 Collagenase Sigma-Aldrich Cat#C6885 2-deoxy-D-glucose Sigma-Aldrich Cat#D6134-1G PUGNAc Sigma-Aldrich Cat#A7229 GalNAc-O-bn Sigma-Aldrich Cat#B4894 FGF2, Fibroblast Growth Factor-Basic human, bFGF Sigma-Aldrich Cat#F0291-4X25UG HyClone FBS, EU approved South American Origin Hyclone, GE Cat#SV30160-03 Critical Commercial Assays Seahorse XF Glycolysis Stress Test Agilent Cat#103020-100 Seahorse XFp Mito Fuel Flex Test Agilent Cat#103070-100 iSript cDNA Synthesis kit Bio-Rad Cat#170-8891 Insulin ELISA Kit Crystal Chem Cat#90080 EZ-Magna ChIP HiSens Chromatin Immunoprecipitation Kit Merck Cat#17-10461 V-plex Plus Human IL-1b kit Mesoscale Discovery Cat#K151QP NEBnext chip-seq library Prep master mix set New England Biolabs Cat#E6240L EZBlue Gel Staining Reagent Sigma-Aldrich Cat#G1041 Pierce BCA Protein Assay Kit ThermoFisher Cat#23227 20-plex Human panel ThermoFisher EXP200-12185-901 MCP-1/CCL2 Human ELISA Kit ThermoFisher Cat#88-7399-22 IL-6 Human ELISA Kit ThermoFisher Cat#KHC0061 RNeasy Lipid Tissue Mini Kit QIAGEN Cat#74804 NucleoSpin RNA Macherey-Nagel Cat#740955.250 Deposited Data Human gene expression data (gene microarray) This paper GEO: GSE59034 Human in vitro differentiated adipocytes incubated in high and low glutamine (gene microarray) This paper GEO: GSE140426 SP1 RNAi in human in vitro differentiated adipocytes (gene microarray) This paper GEO: GSE140426 O-GlcNAc ChIPseq (sequencing data) This paper GEO: GSE140426 Experimental Models: Organisms/Strains Mouse C57/BL/6J Charles River N/A Oligonucleotides TaqMan probe human LRP10 Applied Biosystems Hs00204094_m1 TaqMan probe human PPIA Applied Biosystems Hs04194521_s1 TaqMan probe human OGN Applied Biosystems Hs00247901_m1 TaqMan probe human CCL2 Applied Biosystems Hs00234140_m1 TaqMan probe human IL1B Applied Biosystems Hs01555410_m1 TaqMan probe human IL6 Applied Biosystems Hs00985639_m1 TaqMan probe human ADIPOQ Applied Biosystems Hs00605917_m1 TaqMan probe human PLIN1 Applied Biosystems Hs00193510_m1 TaqMan probe human PNPLA2 Applied Biosystems Hs00386101_m1 TaqMan probe human PPARG Applied Biosystems Hs01115513_m1 (Continued on next page) e2 Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3
Microarray:Article Title: Glutamine Links Obesity to Inflammation in Human White Adipose Tissue.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Glucose Solution ThermoFisher Cat#A2494001 DMEM ThermoFisher Cat#21700-026 Ham’s F-12 Nutrient Mix ThermoFisher Cat#11765054 RIPA buffer ThermoFisher Cat#89901 Dynabeads protein G ThermoFisher Cat#1004D SYTOX Blue ThermoFisher Cat#S34857 CountBright Absolute Counting Beads ThermoFisher Cat#C36950 Pierce Protein A/G magnetic beads ThermoFisher Cat#88802 RIPA buffer ThermoFisher Cat#89901 Collagenase Sigma-Aldrich Cat#C6885 2-deoxy-D-glucose Sigma-Aldrich Cat#D6134-1G PUGNAc Sigma-Aldrich Cat#A7229 GalNAc-O-bn Sigma-Aldrich Cat#B4894 FGF2, Fibroblast Growth Factor-Basic human, bFGF Sigma-Aldrich Cat#F0291-4X25UG HyClone FBS, EU approved South American Origin Hyclone, GE Cat#SV30160-03 Critical Commercial Assays Seahorse XF Glycolysis Stress Test Agilent Cat#103020-100 Seahorse XFp Mito Fuel Flex Test Agilent Cat#103070-100 iSript cDNA Synthesis kit Bio-Rad Cat#170-8891 Insulin ELISA Kit Crystal Chem Cat#90080 EZ-Magna ChIP HiSens Chromatin Immunoprecipitation Kit Merck Cat#17-10461 V-plex Plus Human IL-1b kit Mesoscale Discovery Cat#K151QP NEBnext chip-seq library Prep master mix set New England Biolabs Cat#E6240L EZBlue Gel Staining Reagent Sigma-Aldrich Cat#G1041 Pierce BCA Protein Assay Kit ThermoFisher Cat#23227 20-plex Human panel ThermoFisher EXP200-12185-901 MCP-1/CCL2 Human ELISA Kit ThermoFisher Cat#88-7399-22 IL-6 Human ELISA Kit ThermoFisher Cat#KHC0061 RNeasy Lipid Tissue Mini Kit QIAGEN Cat#74804 NucleoSpin RNA Macherey-Nagel Cat#740955.250 Deposited Data Human gene expression data (gene microarray) This paper GEO: GSE59034 Human in vitro differentiated adipocytes incubated in high and low glutamine (gene microarray) This paper GEO: GSE140426 SP1 RNAi in human in vitro differentiated adipocytes (gene microarray) This paper GEO: GSE140426 O-GlcNAc ChIPseq (sequencing data) This paper GEO: GSE140426 Experimental Models: Organisms/Strains Mouse C57/BL/6J Charles River N/A Oligonucleotides TaqMan probe human LRP10 Applied Biosystems Hs00204094_m1 TaqMan probe human PPIA Applied Biosystems Hs04194521_s1 TaqMan probe human OGN Applied Biosystems Hs00247901_m1 TaqMan probe human CCL2 Applied Biosystems Hs00234140_m1 TaqMan probe human IL1B Applied Biosystems Hs01555410_m1 TaqMan probe human IL6 Applied Biosystems Hs00985639_m1 TaqMan probe human ADIPOQ Applied Biosystems Hs00605917_m1 TaqMan probe human PLIN1 Applied Biosystems Hs00193510_m1 TaqMan probe human PNPLA2 Applied Biosystems Hs00386101_m1 TaqMan probe human PPARG Applied Biosystems Hs01115513_m1 (Continued on next page) e2 Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3
In Vitro:Article Title: Glutamine Links Obesity to Inflammation in Human White Adipose Tissue.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Glucose Solution ThermoFisher Cat#A2494001 DMEM ThermoFisher Cat#21700-026 Ham’s F-12 Nutrient Mix ThermoFisher Cat#11765054 RIPA buffer ThermoFisher Cat#89901 Dynabeads protein G ThermoFisher Cat#1004D SYTOX Blue ThermoFisher Cat#S34857 CountBright Absolute Counting Beads ThermoFisher Cat#C36950 Pierce Protein A/G magnetic beads ThermoFisher Cat#88802 RIPA buffer ThermoFisher Cat#89901 Collagenase Sigma-Aldrich Cat#C6885 2-deoxy-D-glucose Sigma-Aldrich Cat#D6134-1G PUGNAc Sigma-Aldrich Cat#A7229 GalNAc-O-bn Sigma-Aldrich Cat#B4894 FGF2, Fibroblast Growth Factor-Basic human, bFGF Sigma-Aldrich Cat#F0291-4X25UG HyClone FBS, EU approved South American Origin Hyclone, GE Cat#SV30160-03 Critical Commercial Assays Seahorse XF Glycolysis Stress Test Agilent Cat#103020-100 Seahorse XFp Mito Fuel Flex Test Agilent Cat#103070-100 iSript cDNA Synthesis kit Bio-Rad Cat#170-8891 Insulin ELISA Kit Crystal Chem Cat#90080 EZ-Magna ChIP HiSens Chromatin Immunoprecipitation Kit Merck Cat#17-10461 V-plex Plus Human IL-1b kit Mesoscale Discovery Cat#K151QP NEBnext chip-seq library Prep master mix set New England Biolabs Cat#E6240L EZBlue Gel Staining Reagent Sigma-Aldrich Cat#G1041 Pierce BCA Protein Assay Kit ThermoFisher Cat#23227 20-plex Human panel ThermoFisher EXP200-12185-901 MCP-1/CCL2 Human ELISA Kit ThermoFisher Cat#88-7399-22 IL-6 Human ELISA Kit ThermoFisher Cat#KHC0061 RNeasy Lipid Tissue Mini Kit QIAGEN Cat#74804 NucleoSpin RNA Macherey-Nagel Cat#740955.250 Deposited Data Human gene expression data (gene microarray) This paper GEO: GSE59034 Human in vitro differentiated adipocytes incubated in high and low glutamine (gene microarray) This paper GEO: GSE140426 SP1 RNAi in human in vitro differentiated adipocytes (gene microarray) This paper GEO: GSE140426 O-GlcNAc ChIPseq (sequencing data) This paper GEO: GSE140426 Experimental Models: Organisms/Strains Mouse C57/BL/6J Charles River N/A Oligonucleotides TaqMan probe human LRP10 Applied Biosystems Hs00204094_m1 TaqMan probe human PPIA Applied Biosystems Hs04194521_s1 TaqMan probe human OGN Applied Biosystems Hs00247901_m1 TaqMan probe human CCL2 Applied Biosystems Hs00234140_m1 TaqMan probe human IL1B Applied Biosystems Hs01555410_m1 TaqMan probe human IL6 Applied Biosystems Hs00985639_m1 TaqMan probe human ADIPOQ Applied Biosystems Hs00605917_m1 TaqMan probe human PLIN1 Applied Biosystems Hs00193510_m1 TaqMan probe human PNPLA2 Applied Biosystems Hs00386101_m1 TaqMan probe human PPARG Applied Biosystems Hs01115513_m1 (Continued on next page) e2 Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3
Incubation:Article Title: Glutamine Links Obesity to Inflammation in Human White Adipose Tissue.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Glucose Solution ThermoFisher Cat#A2494001 DMEM ThermoFisher Cat#21700-026 Ham’s F-12 Nutrient Mix ThermoFisher Cat#11765054 RIPA buffer ThermoFisher Cat#89901 Dynabeads protein G ThermoFisher Cat#1004D SYTOX Blue ThermoFisher Cat#S34857 CountBright Absolute Counting Beads ThermoFisher Cat#C36950 Pierce Protein A/G magnetic beads ThermoFisher Cat#88802 RIPA buffer ThermoFisher Cat#89901 Collagenase Sigma-Aldrich Cat#C6885 2-deoxy-D-glucose Sigma-Aldrich Cat#D6134-1G PUGNAc Sigma-Aldrich Cat#A7229 GalNAc-O-bn Sigma-Aldrich Cat#B4894 FGF2, Fibroblast Growth Factor-Basic human, bFGF Sigma-Aldrich Cat#F0291-4X25UG HyClone FBS, EU approved South American Origin Hyclone, GE Cat#SV30160-03 Critical Commercial Assays Seahorse XF Glycolysis Stress Test Agilent Cat#103020-100 Seahorse XFp Mito Fuel Flex Test Agilent Cat#103070-100 iSript cDNA Synthesis kit Bio-Rad Cat#170-8891 Insulin ELISA Kit Crystal Chem Cat#90080 EZ-Magna ChIP HiSens Chromatin Immunoprecipitation Kit Merck Cat#17-10461 V-plex Plus Human IL-1b kit Mesoscale Discovery Cat#K151QP NEBnext chip-seq library Prep master mix set New England Biolabs Cat#E6240L EZBlue Gel Staining Reagent Sigma-Aldrich Cat#G1041 Pierce BCA Protein Assay Kit ThermoFisher Cat#23227 20-plex Human panel ThermoFisher EXP200-12185-901 MCP-1/CCL2 Human ELISA Kit ThermoFisher Cat#88-7399-22 IL-6 Human ELISA Kit ThermoFisher Cat#KHC0061 RNeasy Lipid Tissue Mini Kit QIAGEN Cat#74804 NucleoSpin RNA Macherey-Nagel Cat#740955.250 Deposited Data Human gene expression data (gene microarray) This paper GEO: GSE59034 Human in vitro differentiated adipocytes incubated in high and low glutamine (gene microarray) This paper GEO: GSE140426 SP1 RNAi in human in vitro differentiated adipocytes (gene microarray) This paper GEO: GSE140426 O-GlcNAc ChIPseq (sequencing data) This paper GEO: GSE140426 Experimental Models: Organisms/Strains Mouse C57/BL/6J Charles River N/A Oligonucleotides TaqMan probe human LRP10 Applied Biosystems Hs00204094_m1 TaqMan probe human PPIA Applied Biosystems Hs04194521_s1 TaqMan probe human OGN Applied Biosystems Hs00247901_m1 TaqMan probe human CCL2 Applied Biosystems Hs00234140_m1 TaqMan probe human IL1B Applied Biosystems Hs01555410_m1 TaqMan probe human IL6 Applied Biosystems Hs00985639_m1 TaqMan probe human ADIPOQ Applied Biosystems Hs00605917_m1 TaqMan probe human PLIN1 Applied Biosystems Hs00193510_m1 TaqMan probe human PNPLA2 Applied Biosystems Hs00386101_m1 TaqMan probe human PPARG Applied Biosystems Hs01115513_m1 (Continued on next page) e2 Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3
Sequencing:Article Title: Glutamine Links Obesity to Inflammation in Human White Adipose Tissue.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3 .. REAGENT or RESOURCE SOURCE IDENTIFIER Glucose Solution ThermoFisher Cat#A2494001 DMEM ThermoFisher Cat#21700-026 Ham’s F-12 Nutrient Mix ThermoFisher Cat#11765054 RIPA buffer ThermoFisher Cat#89901 Dynabeads protein G ThermoFisher Cat#1004D SYTOX Blue ThermoFisher Cat#S34857 CountBright Absolute Counting Beads ThermoFisher Cat#C36950 Pierce Protein A/G magnetic beads ThermoFisher Cat#88802 RIPA buffer ThermoFisher Cat#89901 Collagenase Sigma-Aldrich Cat#C6885 2-deoxy-D-glucose Sigma-Aldrich Cat#D6134-1G PUGNAc Sigma-Aldrich Cat#A7229 GalNAc-O-bn Sigma-Aldrich Cat#B4894 FGF2, Fibroblast Growth Factor-Basic human, bFGF Sigma-Aldrich Cat#F0291-4X25UG HyClone FBS, EU approved South American Origin Hyclone, GE Cat#SV30160-03 Critical Commercial Assays Seahorse XF Glycolysis Stress Test Agilent Cat#103020-100 Seahorse XFp Mito Fuel Flex Test Agilent Cat#103070-100 iSript cDNA Synthesis kit Bio-Rad Cat#170-8891 Insulin ELISA Kit Crystal Chem Cat#90080 EZ-Magna ChIP HiSens Chromatin Immunoprecipitation Kit Merck Cat#17-10461 V-plex Plus Human IL-1b kit Mesoscale Discovery Cat#K151QP NEBnext chip-seq library Prep master mix set New England Biolabs Cat#E6240L EZBlue Gel Staining Reagent Sigma-Aldrich Cat#G1041 Pierce BCA Protein Assay Kit ThermoFisher Cat#23227 20-plex Human panel ThermoFisher EXP200-12185-901 MCP-1/CCL2 Human ELISA Kit ThermoFisher Cat#88-7399-22 IL-6 Human ELISA Kit ThermoFisher Cat#KHC0061 RNeasy Lipid Tissue Mini Kit QIAGEN Cat#74804 NucleoSpin RNA Macherey-Nagel Cat#740955.250 Deposited Data Human gene expression data (gene microarray) This paper GEO: GSE59034 Human in vitro differentiated adipocytes incubated in high and low glutamine (gene microarray) This paper GEO: GSE140426 SP1 RNAi in human in vitro differentiated adipocytes (gene microarray) This paper GEO: GSE140426 O-GlcNAc ChIPseq (sequencing data) This paper GEO: GSE140426 Experimental Models: Organisms/Strains Mouse C57/BL/6J Charles River N/A Oligonucleotides TaqMan probe human LRP10 Applied Biosystems Hs00204094_m1 TaqMan probe human PPIA Applied Biosystems Hs04194521_s1 TaqMan probe human OGN Applied Biosystems Hs00247901_m1 TaqMan probe human CCL2 Applied Biosystems Hs00234140_m1 TaqMan probe human IL1B Applied Biosystems Hs01555410_m1 TaqMan probe human IL6 Applied Biosystems Hs00985639_m1 TaqMan probe human ADIPOQ Applied Biosystems Hs00605917_m1 TaqMan probe human PLIN1 Applied Biosystems Hs00193510_m1 TaqMan probe human PNPLA2 Applied Biosystems Hs00386101_m1 TaqMan probe human PPARG Applied Biosystems Hs01115513_m1 (Continued on next page) e2 Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 .. REAGENT or RESOURCE SOURCE IDENTIFIER TaqMan probe human GLUL Applied Biosystems Hs00365928_g1 TaqMan probe human CEBPA Applied Biosystems Hs00269972_s1 TaqMan probe human ENO1 Applied Biosystems Hs00361415_m1 TaqMan probe human HK2 Applied Biosystems Hs00606086_m1 TaqMan probe human PFKFB3 Applied Biosystems HS00998700_m1 TaqMan probe human RICTOR Applied Biosystems Hs00380903_m1 TaqMan probe human ETS1 Applied Biosystems Hs00901425_m1 TaqMan probe murine Adipoq Applied Biosystems Mm00456425_m1 TaqMan probe murine Ccl2 Applied Biosystems Mm00441242_m1 TaqMan probe murine ActB Applied Biosystems Mm00607939_s1 TaqMan probe murine Il6 Applied Biosystems Mm00446190_m1 TaqMan probe murine Gapdh Applied Biosystems Mm99999915_g1 TaqMan probe murine Tnf Applied Biosystems Mm00443258_m1 TaqMan probe murine Pparg Applied Biosystems Mm00440940_m1 SYBR green probe murine Emr1; Fw:TGACTCACCTTGTGGTCCTAA; Rv:CTTCCCAGAATCCAGTCTTTCC Sigma-Aldrich N/A SYBR green probe murine Cd68; Fw:TGTCTGATCTTGCTAGGACCG; Rv:GAGAGTAACGGCCTTTTTGTGA Sigma-Aldrich N/A SYBR green probe murine Glul; Fw:TTAGGGGAATTAAGGACAGG; Rv:GAAGGAAAGTAACAGTCTGC Sigma-Aldrich N/A SYBR green probe murine Il1b; Fw:CAACCACACTCTCCAGCTGCA; Rv:GATCCACACTCTCCAGCTGCA Sigma-Aldrich N/A SYBR green probe murine Col6a1; Fw:CTGCTGCTACAAGCCTGCT; Rv:CCCCATAAGGTTTCAGCCTCA Sigma-Aldrich N/A SYBR green probe human ETS1 ChIP-qPCR; Fw:CGCTCTCCCCTC CTCTTTAG; Rv:CAGCCCTTCCTTTCGCTTTG Sigma-Aldrich N/A SYBR green probe human RICTOR ChIP-qPCR; Fw:GTCACAACACC GGAAACCTC; Rv:CGAACTCCTTGCAGACCTTG Sigma-Aldrich N/A SYBR green probe human PFKFB3 ChIP-qPCR; Fw:AAGATGCCGTT GGAACTGAC; Rv:AAAGCCGCCCCACACAAT Sigma-Aldrich N/A siRNA anti human OGT (siGENOME) Dharmacon M-019111-00-0005 siRNA anti human HK2 (siGENOME) Dharmacon M-006735-01-0005 siRNA anti human ENO1 (siGENOME) Dharmacon M-004034-02-0005 siRNA Non-targeting #1 (siGENOME) Dharmacon D-001206-13-05 siRNA anti human SP1 (pool of 3 siRNA) QIAGEN siSP1.1#SI02648072, siSP1.2#SI02648065, siSP1.3#SI00150990 siRNA Non-targeting QIAGEN Cat#1027310 Software and Algorithms Image Lab Bio-Rad N/A GraphPad Prism 7.0 GraphPad Software N/A SPSS v24 IBM N/A FlowJo Tree Star https://www.flowjo.com/ DAVID NIAID/NIH https://david.ncifcrf.gov ImageJ 1.45 software NIH N/A HOMER N/A http://homer.ucsd.edu Other Standard chow diet (4% kcal from fat) Lantm€annen R34 High Fat Diet (HFD; 60% kcal fat) Research Diet D12492i Cell Metabolism 31, 1–16.e1–e11, February 4, 2020 e3
Real-time Polymerase Chain Reaction:Article Title: YY1 Lactylation in Microglia Promotes Angiogenesis Through Transcription Activation-Mediated Upregulation of FGF2
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Mouse monoclonal Anti-CD31 Abcam Cat# ab9498; RRID: AB_307284 Rabbit polyclonal Anti-SIRT1 Abcam Cat# ab7343; RRID: AB_305867 Rabbit monoclonal Anti-Ki67 Abcam Cat# ab16667; RRID: AB_302459 Rabbit polyclonal Anti-PCAF Abcam Cat# ab12188; RRID: AB_298918 Goat polyclonal Anti-Iba1 Abcam Cat# ab5076; RRID: AB_2224402 VeriBlot for IP Detection Reagent (HRP) Abcam Cat# 131366 Mouse monoclonal Anti-β-Actin Abcam Cat# ab8226, RRID: AB_306371 Mouse monoclonal Anti-YY1 Proteintech Cat# 66281-1-lg; RRID: AB_2737053 Mouse monoclonal Anti-HDAC6 Santa Cruz Biotechnology Cat# sc-28386; RRID: AB_627708 Mouse monoclonal Anti-FGF2 Santa Cruz Biotechnology Cat# sc-74412; RRID: AB_1122854 Mouse monoclonal Anti-p300 Santa Cruz Biotechnology Cat# sc-48343; RRID: AB_628075 Mouse monoclonal Anti-TIP60 Santa Cruz Biotechnology Cat# sc-166323; RRID: AB_2296327 Rabbit monoclonal Anti-Iba1 FUJIFILM Wako Shibayagi Cat# 019-19741; RRID: AB_839504 Rabbit Pan-Kla PTM BIO Cat# PTM-1401; RRID: AB_2868521 Rabbit (DA1E) mAb IgG XP Isotype Control antibody Cell Signaling Technology Cat# 3900; RRID: AB_1550038 Rabbit monoclonal Anti-YY1 Cell Signaling Technology Cat# 46395; RRID: AB_2799302 Goat Anti-Mouse Alexa Flour 488 Bioss Cat# bs-0368G-A488,RRID:AB_10892893 Goat Anti-Rabbit Alexa Flour 488 Bioss Cat# bs-0295G A488;RRID:AB_10893781 Donkey Anti-Goat Cy3 Bioss Cat# bs-0294D-Cy3;RRID:AB_10894752 Goat Anti-Mouse Cy3 Bioss Cat# bs-0296G-Cy3;RRID:AB_10892835 Goat Anti-Rabbit Cy3 Bioss Cat# bs-0295G-Cy3;RRID:AB_10892956 Chemicals, peptides, and recombinant proteins EMEM ATCC Cat# 30-2003 Complete Classic Medium with Serum & CultureBoost Cell Systems Cat# 4Z0-500 Trypsin-EDTA (0.05%) Gibco Cat# 25300054 FBS Gibco Cat# 10099141 Penicillin-Streptomycin-Glutam(100X) Gibco Cat# 10378016 DMSO Solarbio Cat# 67-68-5 TRIzol Thermofisher Cat# 15596026 DAPI Thermofisher Cat# 62248 RIPA buffer Thermofisher Cat# 89900 Rotenone Rhawn Cat# R006873 Sodium Dichloroacetate Rhawn Cat# R052025 PLX3397 MedChemExpress Cat# HY-16749 PEG-300 Sigma-Aldrich 90878-250ML-F Puromycin Sigma-Aldrich Cat#P8833 Tween 80 Sigma-Aldrich Cat# P1754 TritonX-100 Sigma-Aldrich Cat# 648466 Lipofectamine 2000 Invitrogen Cat#11668019 Critical commercial assays RT Master Mix for qPCR MedChemExpress Cat# HY-K0511 SYBR Green qPCR Master Mix MedChemExpress Cat# HY-K0522 This preprint research paper has not been peer reviewed. .. Electronic copy available at: https://ssrn.com/abstract=4044116 Pr pr in t n ot p ee r r ev ie we d Ultra High Sensitivity ECL Kit MedChemExpress Cat# HY-K1005 Immunoprecipitation kit Abcam Cat# ab206996 SimpleChIP Plus Enzymatic Chromatin IP Kit Cell Signaling Technology Cat# 9004S Dual-Luciferase Reporter Assay System Promega Cat# E2920 The LA Assay Kit Solarbio Cat# BC2235 4% paraformaldehyde Biosharp Cat# 143174 Goat serum Boster Cat# AR0009 Experimental models: Cell lines HMC3 cells ATCC Cat# CRL-3304 HRMECs Cell Systems Cat# ACBRI 181 Experimental models: Organisms/strains Mouse: C57BL/6J The Experimental Animal Center of Chongqing Medical University N/A Oligonucleotides Primers used for qRT-PCR, see Table S2 Shanghai Sangon Biotech N/A Primers used for ChIP-qPCR, see Table S2 Shanghai Sangon Biotech N/A Recombinant DNA Ubi-MCS(YY1 WT)-3FLAG-CBh-gcGFP-IRES-puromycin Shanghai Genechem Co, Ltd N/A Ubi-MCS(YY1 K183R)-3FLAG-CBh-gcGFP-IRESpuromycin Shanghai Genechem Co, Ltd N/A MCS-SV40-firefly_Luciferase-PloyA-Tk-Renilla_LuciferasePolyA (FGF2 promoter luciferase reporter) Shanghai Genechem Co, Ltd N/A CAS9-Easy-Lentivirus(SAM)(EP300): Lenti-dCAS9puro; U6-sgRNA-SV40-MS2-P65-HSF1-CMV-EGFP Shanghai Genechem Co, Ltd N/A Software and algorithms GraphPad Prism 8.0 https://www.graphpad.com N/A NIH ImageJ https://imagej.nih.gov/ij/ N/A cellSens Dimension https://www.olympuslifescience.com.cn/en/software/ cellsens/ N/A ZEN https://www.zeiss.com/microsc opy/int/ downloads.html N/A IBM.SPSS.V20. https://spssau.com/?10200000 0&b_scene_zt=1 N/A This preprint research paper has not been peer reviewed.
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