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    Dojindo Labs dojindo laboratories cat
    Dojindo Laboratories Cat, supplied by Dojindo Labs, used in various techniques. Bioz Stars score: 99/100, based on 60040 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/dojindo+laboratories+cat/Cell+Counting+Kit-8/pm42013842-277-264-264
    Average 99 stars, based on 60040 article reviews
    dojindo laboratories cat - by Bioz Stars, 2026-10
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    CCK-8 Assay:

    Article Title: Senescence-induced endothelial-to-mesenchymal transition accelerates the subretinal fibrosis in neovascualr age-related macular degeneration
    Article Snippet: .. The Cell Counting Kit-8 (CCK-8; DOJINDO Laboratories, Cat. No. CK04-500T Japan) was used to assess cell viability. ..

    Article Title: MYC-mediated early glycolysis negatively regulates proinflammatory responses by controlling IRF4 in inflammatory macrophages
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Monoclonal rabbit anti-phosphorylated Akt antibody Cell Signaling RRID:AB_2315049 Polyclonal rabbit anti-A20 antibody Cell Signaling RRID:AB_2204524 Monoclonal rabbit anti-ATP-Citrate Lyase antibody Cell Signaling RRID:AB_2798203 Polyclonal rabbit anti-phosphorylated ATPCitrate Lyase antibody Cell Signaling RRID:AB_2257987 Monoclonal rabbit anti-phosphorylated p70 S6 Kinase antibody Cell Signaling RRID:AB_2269803 Monoclonal rabbit anti-p70 S6 Kinase Cell Signaling RRID:AB_390722 Polyclonal rabbit anti-phosphorylated 4EBP1 antibody Cell Signaling RRID:AB_330947 Monoclonal rabbit anti-4E-BP1 antibody Cell Signaling RRID:AB_2097841 Monoclonal rabbit anti-p65 antibody Cell Signaling RRID:AB_823578 Monoclonal mouse anti-a-tubulin antibody Sigma Aldrich RRID:AB_477593 Polyclonal anti-mouse IL-1 beta/IL-1F2 Biotinylated antibody R&D systems RRID:AB_356450 Bacterial and virus strains Listeria monocytogenes (wild-type strain 10403S) Serbina et al., 2003 N/A Biological samples Human Peripheral Blood New York Blood Center N/A Chemicals, peptides, and recombinant proteins Ultrapure LPS-EB (LPS from E. coli O111:B4) InvivoGen Cat#tlrl-3pelps LPS from Escherichia coli strain O55:B5 Sigma Aldrich Cat#L2880 Mouse recombinant IL-4 Miltenyi Biotec Cat#130-097-757 Pam3Cys EMC Microcollections Cat#L2000 Human recombinant M-CSF Peprotech Cat#300-25 L-(+)-Lactic acid Sigma Aldrich Cat#L6402 2-Deoxy-D-glucose (2-DG) Sigma Aldrich Cat#D8375 UK-5099 Sigma Aldrich Cat#PZ0160 Etomoxir Sigma Aldrich Cat#E1905 Pefabloc SC Sigma Aldrich Cat#76307 Deoxyribonuclease I Sigma Aldrich Cat#DN25 Collagenase, Type IV Thermo Fisher Scientific Cat#17104019 CHC Tocris Bioscience Cat#5029 FX11 EMD Millipore Cat#427218 Polybrene Santa Cruz Cat#sc-134220 Gentamycin Thermo Fisher Scientific Cat#15710064 FuGENE(R) HD Transfection Reagent Promega Cat#E2312 TransIT-TKO Transfection Reagent Mirus Bio Cat#MIR 2150 SYTO 24 green fluorescent nucleic acid stain Molecular Probes Cat#S7559 Brain Heart Infusion BD BioSciences Cat#BD 237500 Brilliant Stain Buffer BD BioSciences Cat#563794 PerCP/Cy5.5 Streptavidin Biolegend Cat#405214 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Thermo Fisher Scientific Cat#D1306 (Continued on next page) Cell Reports 35, 109264, June 15, 2021 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER eBioscience Fixable Viability Dye eFluor 455UV Thermo Fisher Scientific Cat#65-0868-18 CountBright Absolute Counting Beads, for flow cytometry Thermo Fisher Scientific Cat#C36950 UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-42 Streptavidin-HRP R&D systems Cat#DY998 Critical commercial assays First strand cDNA synthesis kit Fermentas Cat#K1622 RNeasy mini kit QIAGEN Cat#74104 Fast SYBR Green Master Mix Life Technologies Cat#4385618 Mouse Magnetic Luminex Assay R&D systems Custom made Lactate Dehydrogenase Assay Kit Abcam Cat#ab102526 Seahorse XF Glycolysis Stress Test Kit Agilent Cat#103020-100 Seahorse XF Mito Stress Test Kit Agilent Cat#103015-100 Cell Counting Kit-8 Dojindo Laboratories CatCK04-01 Experimental models: organisms/strains LysM Cre: B6.129P2-Lyz2tm1(cre)Ifo/J Jackson Laboratory RRID:IMSR_JAX:004781 Myc flox: B6.129S6-Myctm2Fwa/Mmjax Jackson Laboratory RRID:MMRRC_032046-JAX Hif1a flox: B6.129-Hif1atm3Rsjo/J Jackson Laboratory RRID:IMSR_JAX:007561 C57BL/6J Jackson Laboratory RRID:IMSR_JAX:000664 IRF4 KO A gift from Dr. Kelvin P. Lee; Utley et al., 2020 N/A Oligonucleotides See Table S2 Recombinant DNA pMXs-c-Myc Takahashi and Yamanaka, 2006 RRID:Addgene_13375 pMXs-gw Takahashi and Yamanaka, 2006 RRID:Addgene_18656 Deposited data RNA-seq This paper GEO: GSE164475 Software and algorithms Bowtie2 version 2.2.6 Langmead and Salzberg, 2012 https://www.bioinformatics.babraham .ac.uk/projects/fastqc STAR Aligner Dobin et al., 2013 https://github.com/alexdobin/STAR edgeR Robinson et al., 2010 https://www.bioconductor.org/ packages/release/bioc/html/ edgeR.html R https://www.R-project.org/ Cuffdiff2 Trapnell et al., 2013 http://cole-trapnell-lab.github.io/ cufflinks/cuffdiff/ Gene Set Enrichment Analysis (GSEA) Broad Institute, Inc. https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp MassHunter Quantitative Analysis (v. B.09.00) Agilent Technologies https://www.agilent.com/en/product/ software-informatics/ mass-spectrometry-software/ data-analysis/quantitative-analysis Mass Profiler Professional (v. 15.0) Agilent Technologies https://www.agilent.com/en/product/ software-informatics/ mass-spectrometry-software/ data-analysis/ mass-profiler-professional-software (Continued on next page) e3 Cell Reports 35, 109264, June 15, 2021 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Metaboanalyst Chong et al., 2019 https://www.metaboanalyst.ca Seahorse Wave Desktop Software Agilent Technologies https://www.agilent.com/en/ product/cell-analysis/real-timecell-metabolic-analysis/xfsoftware/seahorse-wavedesktop-software-740897 Flowjo (v10.7.1) BD Biosciences https://www.flowjo.com/ solutions/flowjo/downloads/ GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Article ll OPEN ACCESS

    Article Title: Cholesterol suppresses GOLM1-dependent selective autophagy of RTKs in hepatocellular carcinoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Flag Magnetic Beads Bimake Cat#B26101 Anti-Myc Magnetic Beads Bimake Cat#B26301 Protein A/G Magnetic Beads for IP Bimake Cat#B23201 Phosphatase Inhibitor Cocktail Bimake Cat#B15001 Protease Inhibitor Cocktail Bimake Cat#B14001 Critical commercial assays Amplex Red Cholesterol Assay Kit Invitrogen Cat#A12216 Cell Counting Kit-8 Dojindo Laboratories CatCK04 QuickMutation Site-directed Gene Mutagenesis Kit Beyotime Biotechnology Cat#D0206 Experimental models: Cell lines Human: HCCLM3 cells Liver Cancer Institute, Fudan University N/A Human: MHCC97-H cells Liver Cancer Institute, Fudan University N/A Human: PLC/PRF/5 cells Cell Resources Center, Chinese Academy of Sciences Cat#TCHu119; RRID:CVCL_0485 Human: Hep3B cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-5045; RRID:CVCL_0326 Human: HepG2 cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-510; RRID:CVCL_0027 Human: HuH-7 cells Cell Resources Center, Chinese Academy of Sciences Cat# SCSP-526; RRID:CVCL_0336 Human: HEK293T cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-502; RRID:CVCL_0063 Experimental models: Organisms/strains Mouse: BALBc nu/nu Shanghai Laboratory Animal Center, Chinese Academy of Science N/A Oligonucleotides qRT-PCR primers for MET/EGFR/GOLM1/ ATG5/ATG7, see Table S3 This paper N/A shRNA target sequences for GOLM1/ATG5/ ATG7/SLC38A9, see Table S4 This paper N/A PCR primers for GOLM1/MET/EGFR cDNA clone, see Table S5 This paper N/A Mutation primers for GOLM1, see Table S6 This paper N/A Recombinant DNA pCDH-CMV-MCS-EF1-Puro This paper N/A pLKO.1-TRC This paper N/A pMD2.G This paper N/A pSPAX2 This paper N/A pCDNA3.1-GFP-LC3 This paper N/A pcDNA3.1-mRFP-GFP-LC3 This paper N/A pcDNA3-c-5XMyc This paper N/A p3xFlag-CMV-14 This paper N/A Software and algorithms ImageJ (v1.53) NIH Image https://imagej.nih.gov/ij/index.html GraphPad Prism (v8.4.3) GraphPad Software http://www.graphpad-prism.cn ..

    Article Title: Senescence-induced endothelial-to-mesenchymal transition accelerates the subretinal fibrosis in neovascualr age-related macular degeneration.
    Article Snippet: .. 209 Cell viability 210 The Cell Counting Kit-8 (CCK-8; DOJINDO Laboratories, Cat. No. CK04-500T 211 Japan) was used to assess cell viability. ..

    Flow Cytometry:

    Article Title: MYC-mediated early glycolysis negatively regulates proinflammatory responses by controlling IRF4 in inflammatory macrophages
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Monoclonal rabbit anti-phosphorylated Akt antibody Cell Signaling RRID:AB_2315049 Polyclonal rabbit anti-A20 antibody Cell Signaling RRID:AB_2204524 Monoclonal rabbit anti-ATP-Citrate Lyase antibody Cell Signaling RRID:AB_2798203 Polyclonal rabbit anti-phosphorylated ATPCitrate Lyase antibody Cell Signaling RRID:AB_2257987 Monoclonal rabbit anti-phosphorylated p70 S6 Kinase antibody Cell Signaling RRID:AB_2269803 Monoclonal rabbit anti-p70 S6 Kinase Cell Signaling RRID:AB_390722 Polyclonal rabbit anti-phosphorylated 4EBP1 antibody Cell Signaling RRID:AB_330947 Monoclonal rabbit anti-4E-BP1 antibody Cell Signaling RRID:AB_2097841 Monoclonal rabbit anti-p65 antibody Cell Signaling RRID:AB_823578 Monoclonal mouse anti-a-tubulin antibody Sigma Aldrich RRID:AB_477593 Polyclonal anti-mouse IL-1 beta/IL-1F2 Biotinylated antibody R&D systems RRID:AB_356450 Bacterial and virus strains Listeria monocytogenes (wild-type strain 10403S) Serbina et al., 2003 N/A Biological samples Human Peripheral Blood New York Blood Center N/A Chemicals, peptides, and recombinant proteins Ultrapure LPS-EB (LPS from E. coli O111:B4) InvivoGen Cat#tlrl-3pelps LPS from Escherichia coli strain O55:B5 Sigma Aldrich Cat#L2880 Mouse recombinant IL-4 Miltenyi Biotec Cat#130-097-757 Pam3Cys EMC Microcollections Cat#L2000 Human recombinant M-CSF Peprotech Cat#300-25 L-(+)-Lactic acid Sigma Aldrich Cat#L6402 2-Deoxy-D-glucose (2-DG) Sigma Aldrich Cat#D8375 UK-5099 Sigma Aldrich Cat#PZ0160 Etomoxir Sigma Aldrich Cat#E1905 Pefabloc SC Sigma Aldrich Cat#76307 Deoxyribonuclease I Sigma Aldrich Cat#DN25 Collagenase, Type IV Thermo Fisher Scientific Cat#17104019 CHC Tocris Bioscience Cat#5029 FX11 EMD Millipore Cat#427218 Polybrene Santa Cruz Cat#sc-134220 Gentamycin Thermo Fisher Scientific Cat#15710064 FuGENE(R) HD Transfection Reagent Promega Cat#E2312 TransIT-TKO Transfection Reagent Mirus Bio Cat#MIR 2150 SYTO 24 green fluorescent nucleic acid stain Molecular Probes Cat#S7559 Brain Heart Infusion BD BioSciences Cat#BD 237500 Brilliant Stain Buffer BD BioSciences Cat#563794 PerCP/Cy5.5 Streptavidin Biolegend Cat#405214 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Thermo Fisher Scientific Cat#D1306 (Continued on next page) Cell Reports 35, 109264, June 15, 2021 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER eBioscience Fixable Viability Dye eFluor 455UV Thermo Fisher Scientific Cat#65-0868-18 CountBright Absolute Counting Beads, for flow cytometry Thermo Fisher Scientific Cat#C36950 UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-42 Streptavidin-HRP R&D systems Cat#DY998 Critical commercial assays First strand cDNA synthesis kit Fermentas Cat#K1622 RNeasy mini kit QIAGEN Cat#74104 Fast SYBR Green Master Mix Life Technologies Cat#4385618 Mouse Magnetic Luminex Assay R&D systems Custom made Lactate Dehydrogenase Assay Kit Abcam Cat#ab102526 Seahorse XF Glycolysis Stress Test Kit Agilent Cat#103020-100 Seahorse XF Mito Stress Test Kit Agilent Cat#103015-100 Cell Counting Kit-8 Dojindo Laboratories CatCK04-01 Experimental models: organisms/strains LysM Cre: B6.129P2-Lyz2tm1(cre)Ifo/J Jackson Laboratory RRID:IMSR_JAX:004781 Myc flox: B6.129S6-Myctm2Fwa/Mmjax Jackson Laboratory RRID:MMRRC_032046-JAX Hif1a flox: B6.129-Hif1atm3Rsjo/J Jackson Laboratory RRID:IMSR_JAX:007561 C57BL/6J Jackson Laboratory RRID:IMSR_JAX:000664 IRF4 KO A gift from Dr. Kelvin P. Lee; Utley et al., 2020 N/A Oligonucleotides See Table S2 Recombinant DNA pMXs-c-Myc Takahashi and Yamanaka, 2006 RRID:Addgene_13375 pMXs-gw Takahashi and Yamanaka, 2006 RRID:Addgene_18656 Deposited data RNA-seq This paper GEO: GSE164475 Software and algorithms Bowtie2 version 2.2.6 Langmead and Salzberg, 2012 https://www.bioinformatics.babraham .ac.uk/projects/fastqc STAR Aligner Dobin et al., 2013 https://github.com/alexdobin/STAR edgeR Robinson et al., 2010 https://www.bioconductor.org/ packages/release/bioc/html/ edgeR.html R https://www.R-project.org/ Cuffdiff2 Trapnell et al., 2013 http://cole-trapnell-lab.github.io/ cufflinks/cuffdiff/ Gene Set Enrichment Analysis (GSEA) Broad Institute, Inc. https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp MassHunter Quantitative Analysis (v. B.09.00) Agilent Technologies https://www.agilent.com/en/product/ software-informatics/ mass-spectrometry-software/ data-analysis/quantitative-analysis Mass Profiler Professional (v. 15.0) Agilent Technologies https://www.agilent.com/en/product/ software-informatics/ mass-spectrometry-software/ data-analysis/ mass-profiler-professional-software (Continued on next page) e3 Cell Reports 35, 109264, June 15, 2021 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Metaboanalyst Chong et al., 2019 https://www.metaboanalyst.ca Seahorse Wave Desktop Software Agilent Technologies https://www.agilent.com/en/ product/cell-analysis/real-timecell-metabolic-analysis/xfsoftware/seahorse-wavedesktop-software-740897 Flowjo (v10.7.1) BD Biosciences https://www.flowjo.com/ solutions/flowjo/downloads/ GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Article ll OPEN ACCESS

    cDNA Synthesis:

    Article Title: MYC-mediated early glycolysis negatively regulates proinflammatory responses by controlling IRF4 in inflammatory macrophages
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Monoclonal rabbit anti-phosphorylated Akt antibody Cell Signaling RRID:AB_2315049 Polyclonal rabbit anti-A20 antibody Cell Signaling RRID:AB_2204524 Monoclonal rabbit anti-ATP-Citrate Lyase antibody Cell Signaling RRID:AB_2798203 Polyclonal rabbit anti-phosphorylated ATPCitrate Lyase antibody Cell Signaling RRID:AB_2257987 Monoclonal rabbit anti-phosphorylated p70 S6 Kinase antibody Cell Signaling RRID:AB_2269803 Monoclonal rabbit anti-p70 S6 Kinase Cell Signaling RRID:AB_390722 Polyclonal rabbit anti-phosphorylated 4EBP1 antibody Cell Signaling RRID:AB_330947 Monoclonal rabbit anti-4E-BP1 antibody Cell Signaling RRID:AB_2097841 Monoclonal rabbit anti-p65 antibody Cell Signaling RRID:AB_823578 Monoclonal mouse anti-a-tubulin antibody Sigma Aldrich RRID:AB_477593 Polyclonal anti-mouse IL-1 beta/IL-1F2 Biotinylated antibody R&D systems RRID:AB_356450 Bacterial and virus strains Listeria monocytogenes (wild-type strain 10403S) Serbina et al., 2003 N/A Biological samples Human Peripheral Blood New York Blood Center N/A Chemicals, peptides, and recombinant proteins Ultrapure LPS-EB (LPS from E. coli O111:B4) InvivoGen Cat#tlrl-3pelps LPS from Escherichia coli strain O55:B5 Sigma Aldrich Cat#L2880 Mouse recombinant IL-4 Miltenyi Biotec Cat#130-097-757 Pam3Cys EMC Microcollections Cat#L2000 Human recombinant M-CSF Peprotech Cat#300-25 L-(+)-Lactic acid Sigma Aldrich Cat#L6402 2-Deoxy-D-glucose (2-DG) Sigma Aldrich Cat#D8375 UK-5099 Sigma Aldrich Cat#PZ0160 Etomoxir Sigma Aldrich Cat#E1905 Pefabloc SC Sigma Aldrich Cat#76307 Deoxyribonuclease I Sigma Aldrich Cat#DN25 Collagenase, Type IV Thermo Fisher Scientific Cat#17104019 CHC Tocris Bioscience Cat#5029 FX11 EMD Millipore Cat#427218 Polybrene Santa Cruz Cat#sc-134220 Gentamycin Thermo Fisher Scientific Cat#15710064 FuGENE(R) HD Transfection Reagent Promega Cat#E2312 TransIT-TKO Transfection Reagent Mirus Bio Cat#MIR 2150 SYTO 24 green fluorescent nucleic acid stain Molecular Probes Cat#S7559 Brain Heart Infusion BD BioSciences Cat#BD 237500 Brilliant Stain Buffer BD BioSciences Cat#563794 PerCP/Cy5.5 Streptavidin Biolegend Cat#405214 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Thermo Fisher Scientific Cat#D1306 (Continued on next page) Cell Reports 35, 109264, June 15, 2021 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER eBioscience Fixable Viability Dye eFluor 455UV Thermo Fisher Scientific Cat#65-0868-18 CountBright Absolute Counting Beads, for flow cytometry Thermo Fisher Scientific Cat#C36950 UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-42 Streptavidin-HRP R&D systems Cat#DY998 Critical commercial assays First strand cDNA synthesis kit Fermentas Cat#K1622 RNeasy mini kit QIAGEN Cat#74104 Fast SYBR Green Master Mix Life Technologies Cat#4385618 Mouse Magnetic Luminex Assay R&D systems Custom made Lactate Dehydrogenase Assay Kit Abcam Cat#ab102526 Seahorse XF Glycolysis Stress Test Kit Agilent Cat#103020-100 Seahorse XF Mito Stress Test Kit Agilent Cat#103015-100 Cell Counting Kit-8 Dojindo Laboratories CatCK04-01 Experimental models: organisms/strains LysM Cre: B6.129P2-Lyz2tm1(cre)Ifo/J Jackson Laboratory RRID:IMSR_JAX:004781 Myc flox: B6.129S6-Myctm2Fwa/Mmjax Jackson Laboratory RRID:MMRRC_032046-JAX Hif1a flox: B6.129-Hif1atm3Rsjo/J Jackson Laboratory RRID:IMSR_JAX:007561 C57BL/6J Jackson Laboratory RRID:IMSR_JAX:000664 IRF4 KO A gift from Dr. Kelvin P. Lee; Utley et al., 2020 N/A Oligonucleotides See Table S2 Recombinant DNA pMXs-c-Myc Takahashi and Yamanaka, 2006 RRID:Addgene_13375 pMXs-gw Takahashi and Yamanaka, 2006 RRID:Addgene_18656 Deposited data RNA-seq This paper GEO: GSE164475 Software and algorithms Bowtie2 version 2.2.6 Langmead and Salzberg, 2012 https://www.bioinformatics.babraham .ac.uk/projects/fastqc STAR Aligner Dobin et al., 2013 https://github.com/alexdobin/STAR edgeR Robinson et al., 2010 https://www.bioconductor.org/ packages/release/bioc/html/ edgeR.html R https://www.R-project.org/ Cuffdiff2 Trapnell et al., 2013 http://cole-trapnell-lab.github.io/ cufflinks/cuffdiff/ Gene Set Enrichment Analysis (GSEA) Broad Institute, Inc. https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp MassHunter Quantitative Analysis (v. B.09.00) Agilent Technologies https://www.agilent.com/en/product/ software-informatics/ mass-spectrometry-software/ data-analysis/quantitative-analysis Mass Profiler Professional (v. 15.0) Agilent Technologies https://www.agilent.com/en/product/ software-informatics/ mass-spectrometry-software/ data-analysis/ mass-profiler-professional-software (Continued on next page) e3 Cell Reports 35, 109264, June 15, 2021 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Metaboanalyst Chong et al., 2019 https://www.metaboanalyst.ca Seahorse Wave Desktop Software Agilent Technologies https://www.agilent.com/en/ product/cell-analysis/real-timecell-metabolic-analysis/xfsoftware/seahorse-wavedesktop-software-740897 Flowjo (v10.7.1) BD Biosciences https://www.flowjo.com/ solutions/flowjo/downloads/ GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Article ll OPEN ACCESS

    SYBR Green Assay:

    Article Title: MYC-mediated early glycolysis negatively regulates proinflammatory responses by controlling IRF4 in inflammatory macrophages
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Monoclonal rabbit anti-phosphorylated Akt antibody Cell Signaling RRID:AB_2315049 Polyclonal rabbit anti-A20 antibody Cell Signaling RRID:AB_2204524 Monoclonal rabbit anti-ATP-Citrate Lyase antibody Cell Signaling RRID:AB_2798203 Polyclonal rabbit anti-phosphorylated ATPCitrate Lyase antibody Cell Signaling RRID:AB_2257987 Monoclonal rabbit anti-phosphorylated p70 S6 Kinase antibody Cell Signaling RRID:AB_2269803 Monoclonal rabbit anti-p70 S6 Kinase Cell Signaling RRID:AB_390722 Polyclonal rabbit anti-phosphorylated 4EBP1 antibody Cell Signaling RRID:AB_330947 Monoclonal rabbit anti-4E-BP1 antibody Cell Signaling RRID:AB_2097841 Monoclonal rabbit anti-p65 antibody Cell Signaling RRID:AB_823578 Monoclonal mouse anti-a-tubulin antibody Sigma Aldrich RRID:AB_477593 Polyclonal anti-mouse IL-1 beta/IL-1F2 Biotinylated antibody R&D systems RRID:AB_356450 Bacterial and virus strains Listeria monocytogenes (wild-type strain 10403S) Serbina et al., 2003 N/A Biological samples Human Peripheral Blood New York Blood Center N/A Chemicals, peptides, and recombinant proteins Ultrapure LPS-EB (LPS from E. coli O111:B4) InvivoGen Cat#tlrl-3pelps LPS from Escherichia coli strain O55:B5 Sigma Aldrich Cat#L2880 Mouse recombinant IL-4 Miltenyi Biotec Cat#130-097-757 Pam3Cys EMC Microcollections Cat#L2000 Human recombinant M-CSF Peprotech Cat#300-25 L-(+)-Lactic acid Sigma Aldrich Cat#L6402 2-Deoxy-D-glucose (2-DG) Sigma Aldrich Cat#D8375 UK-5099 Sigma Aldrich Cat#PZ0160 Etomoxir Sigma Aldrich Cat#E1905 Pefabloc SC Sigma Aldrich Cat#76307 Deoxyribonuclease I Sigma Aldrich Cat#DN25 Collagenase, Type IV Thermo Fisher Scientific Cat#17104019 CHC Tocris Bioscience Cat#5029 FX11 EMD Millipore Cat#427218 Polybrene Santa Cruz Cat#sc-134220 Gentamycin Thermo Fisher Scientific Cat#15710064 FuGENE(R) HD Transfection Reagent Promega Cat#E2312 TransIT-TKO Transfection Reagent Mirus Bio Cat#MIR 2150 SYTO 24 green fluorescent nucleic acid stain Molecular Probes Cat#S7559 Brain Heart Infusion BD BioSciences Cat#BD 237500 Brilliant Stain Buffer BD BioSciences Cat#563794 PerCP/Cy5.5 Streptavidin Biolegend Cat#405214 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Thermo Fisher Scientific Cat#D1306 (Continued on next page) Cell Reports 35, 109264, June 15, 2021 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER eBioscience Fixable Viability Dye eFluor 455UV Thermo Fisher Scientific Cat#65-0868-18 CountBright Absolute Counting Beads, for flow cytometry Thermo Fisher Scientific Cat#C36950 UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-42 Streptavidin-HRP R&D systems Cat#DY998 Critical commercial assays First strand cDNA synthesis kit Fermentas Cat#K1622 RNeasy mini kit QIAGEN Cat#74104 Fast SYBR Green Master Mix Life Technologies Cat#4385618 Mouse Magnetic Luminex Assay R&D systems Custom made Lactate Dehydrogenase Assay Kit Abcam Cat#ab102526 Seahorse XF Glycolysis Stress Test Kit Agilent Cat#103020-100 Seahorse XF Mito Stress Test Kit Agilent Cat#103015-100 Cell Counting Kit-8 Dojindo Laboratories CatCK04-01 Experimental models: organisms/strains LysM Cre: B6.129P2-Lyz2tm1(cre)Ifo/J Jackson Laboratory RRID:IMSR_JAX:004781 Myc flox: B6.129S6-Myctm2Fwa/Mmjax Jackson Laboratory RRID:MMRRC_032046-JAX Hif1a flox: B6.129-Hif1atm3Rsjo/J Jackson Laboratory RRID:IMSR_JAX:007561 C57BL/6J Jackson Laboratory RRID:IMSR_JAX:000664 IRF4 KO A gift from Dr. Kelvin P. Lee; Utley et al., 2020 N/A Oligonucleotides See Table S2 Recombinant DNA pMXs-c-Myc Takahashi and Yamanaka, 2006 RRID:Addgene_13375 pMXs-gw Takahashi and Yamanaka, 2006 RRID:Addgene_18656 Deposited data RNA-seq This paper GEO: GSE164475 Software and algorithms Bowtie2 version 2.2.6 Langmead and Salzberg, 2012 https://www.bioinformatics.babraham .ac.uk/projects/fastqc STAR Aligner Dobin et al., 2013 https://github.com/alexdobin/STAR edgeR Robinson et al., 2010 https://www.bioconductor.org/ packages/release/bioc/html/ edgeR.html R https://www.R-project.org/ Cuffdiff2 Trapnell et al., 2013 http://cole-trapnell-lab.github.io/ cufflinks/cuffdiff/ Gene Set Enrichment Analysis (GSEA) Broad Institute, Inc. https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp MassHunter Quantitative Analysis (v. B.09.00) Agilent Technologies https://www.agilent.com/en/product/ software-informatics/ mass-spectrometry-software/ data-analysis/quantitative-analysis Mass Profiler Professional (v. 15.0) Agilent Technologies https://www.agilent.com/en/product/ software-informatics/ mass-spectrometry-software/ data-analysis/ mass-profiler-professional-software (Continued on next page) e3 Cell Reports 35, 109264, June 15, 2021 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Metaboanalyst Chong et al., 2019 https://www.metaboanalyst.ca Seahorse Wave Desktop Software Agilent Technologies https://www.agilent.com/en/ product/cell-analysis/real-timecell-metabolic-analysis/xfsoftware/seahorse-wavedesktop-software-740897 Flowjo (v10.7.1) BD Biosciences https://www.flowjo.com/ solutions/flowjo/downloads/ GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Article ll OPEN ACCESS

    Luminex:

    Article Title: MYC-mediated early glycolysis negatively regulates proinflammatory responses by controlling IRF4 in inflammatory macrophages
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Monoclonal rabbit anti-phosphorylated Akt antibody Cell Signaling RRID:AB_2315049 Polyclonal rabbit anti-A20 antibody Cell Signaling RRID:AB_2204524 Monoclonal rabbit anti-ATP-Citrate Lyase antibody Cell Signaling RRID:AB_2798203 Polyclonal rabbit anti-phosphorylated ATPCitrate Lyase antibody Cell Signaling RRID:AB_2257987 Monoclonal rabbit anti-phosphorylated p70 S6 Kinase antibody Cell Signaling RRID:AB_2269803 Monoclonal rabbit anti-p70 S6 Kinase Cell Signaling RRID:AB_390722 Polyclonal rabbit anti-phosphorylated 4EBP1 antibody Cell Signaling RRID:AB_330947 Monoclonal rabbit anti-4E-BP1 antibody Cell Signaling RRID:AB_2097841 Monoclonal rabbit anti-p65 antibody Cell Signaling RRID:AB_823578 Monoclonal mouse anti-a-tubulin antibody Sigma Aldrich RRID:AB_477593 Polyclonal anti-mouse IL-1 beta/IL-1F2 Biotinylated antibody R&D systems RRID:AB_356450 Bacterial and virus strains Listeria monocytogenes (wild-type strain 10403S) Serbina et al., 2003 N/A Biological samples Human Peripheral Blood New York Blood Center N/A Chemicals, peptides, and recombinant proteins Ultrapure LPS-EB (LPS from E. coli O111:B4) InvivoGen Cat#tlrl-3pelps LPS from Escherichia coli strain O55:B5 Sigma Aldrich Cat#L2880 Mouse recombinant IL-4 Miltenyi Biotec Cat#130-097-757 Pam3Cys EMC Microcollections Cat#L2000 Human recombinant M-CSF Peprotech Cat#300-25 L-(+)-Lactic acid Sigma Aldrich Cat#L6402 2-Deoxy-D-glucose (2-DG) Sigma Aldrich Cat#D8375 UK-5099 Sigma Aldrich Cat#PZ0160 Etomoxir Sigma Aldrich Cat#E1905 Pefabloc SC Sigma Aldrich Cat#76307 Deoxyribonuclease I Sigma Aldrich Cat#DN25 Collagenase, Type IV Thermo Fisher Scientific Cat#17104019 CHC Tocris Bioscience Cat#5029 FX11 EMD Millipore Cat#427218 Polybrene Santa Cruz Cat#sc-134220 Gentamycin Thermo Fisher Scientific Cat#15710064 FuGENE(R) HD Transfection Reagent Promega Cat#E2312 TransIT-TKO Transfection Reagent Mirus Bio Cat#MIR 2150 SYTO 24 green fluorescent nucleic acid stain Molecular Probes Cat#S7559 Brain Heart Infusion BD BioSciences Cat#BD 237500 Brilliant Stain Buffer BD BioSciences Cat#563794 PerCP/Cy5.5 Streptavidin Biolegend Cat#405214 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Thermo Fisher Scientific Cat#D1306 (Continued on next page) Cell Reports 35, 109264, June 15, 2021 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER eBioscience Fixable Viability Dye eFluor 455UV Thermo Fisher Scientific Cat#65-0868-18 CountBright Absolute Counting Beads, for flow cytometry Thermo Fisher Scientific Cat#C36950 UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-42 Streptavidin-HRP R&D systems Cat#DY998 Critical commercial assays First strand cDNA synthesis kit Fermentas Cat#K1622 RNeasy mini kit QIAGEN Cat#74104 Fast SYBR Green Master Mix Life Technologies Cat#4385618 Mouse Magnetic Luminex Assay R&D systems Custom made Lactate Dehydrogenase Assay Kit Abcam Cat#ab102526 Seahorse XF Glycolysis Stress Test Kit Agilent Cat#103020-100 Seahorse XF Mito Stress Test Kit Agilent Cat#103015-100 Cell Counting Kit-8 Dojindo Laboratories CatCK04-01 Experimental models: organisms/strains LysM Cre: B6.129P2-Lyz2tm1(cre)Ifo/J Jackson Laboratory RRID:IMSR_JAX:004781 Myc flox: B6.129S6-Myctm2Fwa/Mmjax Jackson Laboratory RRID:MMRRC_032046-JAX Hif1a flox: B6.129-Hif1atm3Rsjo/J Jackson Laboratory RRID:IMSR_JAX:007561 C57BL/6J Jackson Laboratory RRID:IMSR_JAX:000664 IRF4 KO A gift from Dr. Kelvin P. Lee; Utley et al., 2020 N/A Oligonucleotides See Table S2 Recombinant DNA pMXs-c-Myc Takahashi and Yamanaka, 2006 RRID:Addgene_13375 pMXs-gw Takahashi and Yamanaka, 2006 RRID:Addgene_18656 Deposited data RNA-seq This paper GEO: GSE164475 Software and algorithms Bowtie2 version 2.2.6 Langmead and Salzberg, 2012 https://www.bioinformatics.babraham .ac.uk/projects/fastqc STAR Aligner Dobin et al., 2013 https://github.com/alexdobin/STAR edgeR Robinson et al., 2010 https://www.bioconductor.org/ packages/release/bioc/html/ edgeR.html R https://www.R-project.org/ Cuffdiff2 Trapnell et al., 2013 http://cole-trapnell-lab.github.io/ cufflinks/cuffdiff/ Gene Set Enrichment Analysis (GSEA) Broad Institute, Inc. https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp MassHunter Quantitative Analysis (v. B.09.00) Agilent Technologies https://www.agilent.com/en/product/ software-informatics/ mass-spectrometry-software/ data-analysis/quantitative-analysis Mass Profiler Professional (v. 15.0) Agilent Technologies https://www.agilent.com/en/product/ software-informatics/ mass-spectrometry-software/ data-analysis/ mass-profiler-professional-software (Continued on next page) e3 Cell Reports 35, 109264, June 15, 2021 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Metaboanalyst Chong et al., 2019 https://www.metaboanalyst.ca Seahorse Wave Desktop Software Agilent Technologies https://www.agilent.com/en/ product/cell-analysis/real-timecell-metabolic-analysis/xfsoftware/seahorse-wavedesktop-software-740897 Flowjo (v10.7.1) BD Biosciences https://www.flowjo.com/ solutions/flowjo/downloads/ GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Article ll OPEN ACCESS

    Lactate Dehydrogenase Assay:

    Article Title: MYC-mediated early glycolysis negatively regulates proinflammatory responses by controlling IRF4 in inflammatory macrophages
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Monoclonal rabbit anti-phosphorylated Akt antibody Cell Signaling RRID:AB_2315049 Polyclonal rabbit anti-A20 antibody Cell Signaling RRID:AB_2204524 Monoclonal rabbit anti-ATP-Citrate Lyase antibody Cell Signaling RRID:AB_2798203 Polyclonal rabbit anti-phosphorylated ATPCitrate Lyase antibody Cell Signaling RRID:AB_2257987 Monoclonal rabbit anti-phosphorylated p70 S6 Kinase antibody Cell Signaling RRID:AB_2269803 Monoclonal rabbit anti-p70 S6 Kinase Cell Signaling RRID:AB_390722 Polyclonal rabbit anti-phosphorylated 4EBP1 antibody Cell Signaling RRID:AB_330947 Monoclonal rabbit anti-4E-BP1 antibody Cell Signaling RRID:AB_2097841 Monoclonal rabbit anti-p65 antibody Cell Signaling RRID:AB_823578 Monoclonal mouse anti-a-tubulin antibody Sigma Aldrich RRID:AB_477593 Polyclonal anti-mouse IL-1 beta/IL-1F2 Biotinylated antibody R&D systems RRID:AB_356450 Bacterial and virus strains Listeria monocytogenes (wild-type strain 10403S) Serbina et al., 2003 N/A Biological samples Human Peripheral Blood New York Blood Center N/A Chemicals, peptides, and recombinant proteins Ultrapure LPS-EB (LPS from E. coli O111:B4) InvivoGen Cat#tlrl-3pelps LPS from Escherichia coli strain O55:B5 Sigma Aldrich Cat#L2880 Mouse recombinant IL-4 Miltenyi Biotec Cat#130-097-757 Pam3Cys EMC Microcollections Cat#L2000 Human recombinant M-CSF Peprotech Cat#300-25 L-(+)-Lactic acid Sigma Aldrich Cat#L6402 2-Deoxy-D-glucose (2-DG) Sigma Aldrich Cat#D8375 UK-5099 Sigma Aldrich Cat#PZ0160 Etomoxir Sigma Aldrich Cat#E1905 Pefabloc SC Sigma Aldrich Cat#76307 Deoxyribonuclease I Sigma Aldrich Cat#DN25 Collagenase, Type IV Thermo Fisher Scientific Cat#17104019 CHC Tocris Bioscience Cat#5029 FX11 EMD Millipore Cat#427218 Polybrene Santa Cruz Cat#sc-134220 Gentamycin Thermo Fisher Scientific Cat#15710064 FuGENE(R) HD Transfection Reagent Promega Cat#E2312 TransIT-TKO Transfection Reagent Mirus Bio Cat#MIR 2150 SYTO 24 green fluorescent nucleic acid stain Molecular Probes Cat#S7559 Brain Heart Infusion BD BioSciences Cat#BD 237500 Brilliant Stain Buffer BD BioSciences Cat#563794 PerCP/Cy5.5 Streptavidin Biolegend Cat#405214 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Thermo Fisher Scientific Cat#D1306 (Continued on next page) Cell Reports 35, 109264, June 15, 2021 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER eBioscience Fixable Viability Dye eFluor 455UV Thermo Fisher Scientific Cat#65-0868-18 CountBright Absolute Counting Beads, for flow cytometry Thermo Fisher Scientific Cat#C36950 UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-42 Streptavidin-HRP R&D systems Cat#DY998 Critical commercial assays First strand cDNA synthesis kit Fermentas Cat#K1622 RNeasy mini kit QIAGEN Cat#74104 Fast SYBR Green Master Mix Life Technologies Cat#4385618 Mouse Magnetic Luminex Assay R&D systems Custom made Lactate Dehydrogenase Assay Kit Abcam Cat#ab102526 Seahorse XF Glycolysis Stress Test Kit Agilent Cat#103020-100 Seahorse XF Mito Stress Test Kit Agilent Cat#103015-100 Cell Counting Kit-8 Dojindo Laboratories CatCK04-01 Experimental models: organisms/strains LysM Cre: B6.129P2-Lyz2tm1(cre)Ifo/J Jackson Laboratory RRID:IMSR_JAX:004781 Myc flox: B6.129S6-Myctm2Fwa/Mmjax Jackson Laboratory RRID:MMRRC_032046-JAX Hif1a flox: B6.129-Hif1atm3Rsjo/J Jackson Laboratory RRID:IMSR_JAX:007561 C57BL/6J Jackson Laboratory RRID:IMSR_JAX:000664 IRF4 KO A gift from Dr. Kelvin P. Lee; Utley et al., 2020 N/A Oligonucleotides See Table S2 Recombinant DNA pMXs-c-Myc Takahashi and Yamanaka, 2006 RRID:Addgene_13375 pMXs-gw Takahashi and Yamanaka, 2006 RRID:Addgene_18656 Deposited data RNA-seq This paper GEO: GSE164475 Software and algorithms Bowtie2 version 2.2.6 Langmead and Salzberg, 2012 https://www.bioinformatics.babraham .ac.uk/projects/fastqc STAR Aligner Dobin et al., 2013 https://github.com/alexdobin/STAR edgeR Robinson et al., 2010 https://www.bioconductor.org/ packages/release/bioc/html/ edgeR.html R https://www.R-project.org/ Cuffdiff2 Trapnell et al., 2013 http://cole-trapnell-lab.github.io/ cufflinks/cuffdiff/ Gene Set Enrichment Analysis (GSEA) Broad Institute, Inc. https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp MassHunter Quantitative Analysis (v. B.09.00) Agilent Technologies https://www.agilent.com/en/product/ software-informatics/ mass-spectrometry-software/ data-analysis/quantitative-analysis Mass Profiler Professional (v. 15.0) Agilent Technologies https://www.agilent.com/en/product/ software-informatics/ mass-spectrometry-software/ data-analysis/ mass-profiler-professional-software (Continued on next page) e3 Cell Reports 35, 109264, June 15, 2021 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Metaboanalyst Chong et al., 2019 https://www.metaboanalyst.ca Seahorse Wave Desktop Software Agilent Technologies https://www.agilent.com/en/ product/cell-analysis/real-timecell-metabolic-analysis/xfsoftware/seahorse-wavedesktop-software-740897 Flowjo (v10.7.1) BD Biosciences https://www.flowjo.com/ solutions/flowjo/downloads/ GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Article ll OPEN ACCESS

    Recombinant:

    Article Title: MYC-mediated early glycolysis negatively regulates proinflammatory responses by controlling IRF4 in inflammatory macrophages
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Monoclonal rabbit anti-phosphorylated Akt antibody Cell Signaling RRID:AB_2315049 Polyclonal rabbit anti-A20 antibody Cell Signaling RRID:AB_2204524 Monoclonal rabbit anti-ATP-Citrate Lyase antibody Cell Signaling RRID:AB_2798203 Polyclonal rabbit anti-phosphorylated ATPCitrate Lyase antibody Cell Signaling RRID:AB_2257987 Monoclonal rabbit anti-phosphorylated p70 S6 Kinase antibody Cell Signaling RRID:AB_2269803 Monoclonal rabbit anti-p70 S6 Kinase Cell Signaling RRID:AB_390722 Polyclonal rabbit anti-phosphorylated 4EBP1 antibody Cell Signaling RRID:AB_330947 Monoclonal rabbit anti-4E-BP1 antibody Cell Signaling RRID:AB_2097841 Monoclonal rabbit anti-p65 antibody Cell Signaling RRID:AB_823578 Monoclonal mouse anti-a-tubulin antibody Sigma Aldrich RRID:AB_477593 Polyclonal anti-mouse IL-1 beta/IL-1F2 Biotinylated antibody R&D systems RRID:AB_356450 Bacterial and virus strains Listeria monocytogenes (wild-type strain 10403S) Serbina et al., 2003 N/A Biological samples Human Peripheral Blood New York Blood Center N/A Chemicals, peptides, and recombinant proteins Ultrapure LPS-EB (LPS from E. coli O111:B4) InvivoGen Cat#tlrl-3pelps LPS from Escherichia coli strain O55:B5 Sigma Aldrich Cat#L2880 Mouse recombinant IL-4 Miltenyi Biotec Cat#130-097-757 Pam3Cys EMC Microcollections Cat#L2000 Human recombinant M-CSF Peprotech Cat#300-25 L-(+)-Lactic acid Sigma Aldrich Cat#L6402 2-Deoxy-D-glucose (2-DG) Sigma Aldrich Cat#D8375 UK-5099 Sigma Aldrich Cat#PZ0160 Etomoxir Sigma Aldrich Cat#E1905 Pefabloc SC Sigma Aldrich Cat#76307 Deoxyribonuclease I Sigma Aldrich Cat#DN25 Collagenase, Type IV Thermo Fisher Scientific Cat#17104019 CHC Tocris Bioscience Cat#5029 FX11 EMD Millipore Cat#427218 Polybrene Santa Cruz Cat#sc-134220 Gentamycin Thermo Fisher Scientific Cat#15710064 FuGENE(R) HD Transfection Reagent Promega Cat#E2312 TransIT-TKO Transfection Reagent Mirus Bio Cat#MIR 2150 SYTO 24 green fluorescent nucleic acid stain Molecular Probes Cat#S7559 Brain Heart Infusion BD BioSciences Cat#BD 237500 Brilliant Stain Buffer BD BioSciences Cat#563794 PerCP/Cy5.5 Streptavidin Biolegend Cat#405214 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Thermo Fisher Scientific Cat#D1306 (Continued on next page) Cell Reports 35, 109264, June 15, 2021 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER eBioscience Fixable Viability Dye eFluor 455UV Thermo Fisher Scientific Cat#65-0868-18 CountBright Absolute Counting Beads, for flow cytometry Thermo Fisher Scientific Cat#C36950 UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-42 Streptavidin-HRP R&D systems Cat#DY998 Critical commercial assays First strand cDNA synthesis kit Fermentas Cat#K1622 RNeasy mini kit QIAGEN Cat#74104 Fast SYBR Green Master Mix Life Technologies Cat#4385618 Mouse Magnetic Luminex Assay R&D systems Custom made Lactate Dehydrogenase Assay Kit Abcam Cat#ab102526 Seahorse XF Glycolysis Stress Test Kit Agilent Cat#103020-100 Seahorse XF Mito Stress Test Kit Agilent Cat#103015-100 Cell Counting Kit-8 Dojindo Laboratories CatCK04-01 Experimental models: organisms/strains LysM Cre: B6.129P2-Lyz2tm1(cre)Ifo/J Jackson Laboratory RRID:IMSR_JAX:004781 Myc flox: B6.129S6-Myctm2Fwa/Mmjax Jackson Laboratory RRID:MMRRC_032046-JAX Hif1a flox: B6.129-Hif1atm3Rsjo/J Jackson Laboratory RRID:IMSR_JAX:007561 C57BL/6J Jackson Laboratory RRID:IMSR_JAX:000664 IRF4 KO A gift from Dr. Kelvin P. Lee; Utley et al., 2020 N/A Oligonucleotides See Table S2 Recombinant DNA pMXs-c-Myc Takahashi and Yamanaka, 2006 RRID:Addgene_13375 pMXs-gw Takahashi and Yamanaka, 2006 RRID:Addgene_18656 Deposited data RNA-seq This paper GEO: GSE164475 Software and algorithms Bowtie2 version 2.2.6 Langmead and Salzberg, 2012 https://www.bioinformatics.babraham .ac.uk/projects/fastqc STAR Aligner Dobin et al., 2013 https://github.com/alexdobin/STAR edgeR Robinson et al., 2010 https://www.bioconductor.org/ packages/release/bioc/html/ edgeR.html R https://www.R-project.org/ Cuffdiff2 Trapnell et al., 2013 http://cole-trapnell-lab.github.io/ cufflinks/cuffdiff/ Gene Set Enrichment Analysis (GSEA) Broad Institute, Inc. https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp MassHunter Quantitative Analysis (v. B.09.00) Agilent Technologies https://www.agilent.com/en/product/ software-informatics/ mass-spectrometry-software/ data-analysis/quantitative-analysis Mass Profiler Professional (v. 15.0) Agilent Technologies https://www.agilent.com/en/product/ software-informatics/ mass-spectrometry-software/ data-analysis/ mass-profiler-professional-software (Continued on next page) e3 Cell Reports 35, 109264, June 15, 2021 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Metaboanalyst Chong et al., 2019 https://www.metaboanalyst.ca Seahorse Wave Desktop Software Agilent Technologies https://www.agilent.com/en/ product/cell-analysis/real-timecell-metabolic-analysis/xfsoftware/seahorse-wavedesktop-software-740897 Flowjo (v10.7.1) BD Biosciences https://www.flowjo.com/ solutions/flowjo/downloads/ GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Article ll OPEN ACCESS

    Article Title: Cholesterol suppresses GOLM1-dependent selective autophagy of RTKs in hepatocellular carcinoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Flag Magnetic Beads Bimake Cat#B26101 Anti-Myc Magnetic Beads Bimake Cat#B26301 Protein A/G Magnetic Beads for IP Bimake Cat#B23201 Phosphatase Inhibitor Cocktail Bimake Cat#B15001 Protease Inhibitor Cocktail Bimake Cat#B14001 Critical commercial assays Amplex Red Cholesterol Assay Kit Invitrogen Cat#A12216 Cell Counting Kit-8 Dojindo Laboratories CatCK04 QuickMutation Site-directed Gene Mutagenesis Kit Beyotime Biotechnology Cat#D0206 Experimental models: Cell lines Human: HCCLM3 cells Liver Cancer Institute, Fudan University N/A Human: MHCC97-H cells Liver Cancer Institute, Fudan University N/A Human: PLC/PRF/5 cells Cell Resources Center, Chinese Academy of Sciences Cat#TCHu119; RRID:CVCL_0485 Human: Hep3B cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-5045; RRID:CVCL_0326 Human: HepG2 cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-510; RRID:CVCL_0027 Human: HuH-7 cells Cell Resources Center, Chinese Academy of Sciences Cat# SCSP-526; RRID:CVCL_0336 Human: HEK293T cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-502; RRID:CVCL_0063 Experimental models: Organisms/strains Mouse: BALBc nu/nu Shanghai Laboratory Animal Center, Chinese Academy of Science N/A Oligonucleotides qRT-PCR primers for MET/EGFR/GOLM1/ ATG5/ATG7, see Table S3 This paper N/A shRNA target sequences for GOLM1/ATG5/ ATG7/SLC38A9, see Table S4 This paper N/A PCR primers for GOLM1/MET/EGFR cDNA clone, see Table S5 This paper N/A Mutation primers for GOLM1, see Table S6 This paper N/A Recombinant DNA pCDH-CMV-MCS-EF1-Puro This paper N/A pLKO.1-TRC This paper N/A pMD2.G This paper N/A pSPAX2 This paper N/A pCDNA3.1-GFP-LC3 This paper N/A pcDNA3.1-mRFP-GFP-LC3 This paper N/A pcDNA3-c-5XMyc This paper N/A p3xFlag-CMV-14 This paper N/A Software and algorithms ImageJ (v1.53) NIH Image https://imagej.nih.gov/ij/index.html GraphPad Prism (v8.4.3) GraphPad Software http://www.graphpad-prism.cn ..

    RNA Sequencing:

    Article Title: MYC-mediated early glycolysis negatively regulates proinflammatory responses by controlling IRF4 in inflammatory macrophages
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Monoclonal rabbit anti-phosphorylated Akt antibody Cell Signaling RRID:AB_2315049 Polyclonal rabbit anti-A20 antibody Cell Signaling RRID:AB_2204524 Monoclonal rabbit anti-ATP-Citrate Lyase antibody Cell Signaling RRID:AB_2798203 Polyclonal rabbit anti-phosphorylated ATPCitrate Lyase antibody Cell Signaling RRID:AB_2257987 Monoclonal rabbit anti-phosphorylated p70 S6 Kinase antibody Cell Signaling RRID:AB_2269803 Monoclonal rabbit anti-p70 S6 Kinase Cell Signaling RRID:AB_390722 Polyclonal rabbit anti-phosphorylated 4EBP1 antibody Cell Signaling RRID:AB_330947 Monoclonal rabbit anti-4E-BP1 antibody Cell Signaling RRID:AB_2097841 Monoclonal rabbit anti-p65 antibody Cell Signaling RRID:AB_823578 Monoclonal mouse anti-a-tubulin antibody Sigma Aldrich RRID:AB_477593 Polyclonal anti-mouse IL-1 beta/IL-1F2 Biotinylated antibody R&D systems RRID:AB_356450 Bacterial and virus strains Listeria monocytogenes (wild-type strain 10403S) Serbina et al., 2003 N/A Biological samples Human Peripheral Blood New York Blood Center N/A Chemicals, peptides, and recombinant proteins Ultrapure LPS-EB (LPS from E. coli O111:B4) InvivoGen Cat#tlrl-3pelps LPS from Escherichia coli strain O55:B5 Sigma Aldrich Cat#L2880 Mouse recombinant IL-4 Miltenyi Biotec Cat#130-097-757 Pam3Cys EMC Microcollections Cat#L2000 Human recombinant M-CSF Peprotech Cat#300-25 L-(+)-Lactic acid Sigma Aldrich Cat#L6402 2-Deoxy-D-glucose (2-DG) Sigma Aldrich Cat#D8375 UK-5099 Sigma Aldrich Cat#PZ0160 Etomoxir Sigma Aldrich Cat#E1905 Pefabloc SC Sigma Aldrich Cat#76307 Deoxyribonuclease I Sigma Aldrich Cat#DN25 Collagenase, Type IV Thermo Fisher Scientific Cat#17104019 CHC Tocris Bioscience Cat#5029 FX11 EMD Millipore Cat#427218 Polybrene Santa Cruz Cat#sc-134220 Gentamycin Thermo Fisher Scientific Cat#15710064 FuGENE(R) HD Transfection Reagent Promega Cat#E2312 TransIT-TKO Transfection Reagent Mirus Bio Cat#MIR 2150 SYTO 24 green fluorescent nucleic acid stain Molecular Probes Cat#S7559 Brain Heart Infusion BD BioSciences Cat#BD 237500 Brilliant Stain Buffer BD BioSciences Cat#563794 PerCP/Cy5.5 Streptavidin Biolegend Cat#405214 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Thermo Fisher Scientific Cat#D1306 (Continued on next page) Cell Reports 35, 109264, June 15, 2021 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER eBioscience Fixable Viability Dye eFluor 455UV Thermo Fisher Scientific Cat#65-0868-18 CountBright Absolute Counting Beads, for flow cytometry Thermo Fisher Scientific Cat#C36950 UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-42 Streptavidin-HRP R&D systems Cat#DY998 Critical commercial assays First strand cDNA synthesis kit Fermentas Cat#K1622 RNeasy mini kit QIAGEN Cat#74104 Fast SYBR Green Master Mix Life Technologies Cat#4385618 Mouse Magnetic Luminex Assay R&D systems Custom made Lactate Dehydrogenase Assay Kit Abcam Cat#ab102526 Seahorse XF Glycolysis Stress Test Kit Agilent Cat#103020-100 Seahorse XF Mito Stress Test Kit Agilent Cat#103015-100 Cell Counting Kit-8 Dojindo Laboratories CatCK04-01 Experimental models: organisms/strains LysM Cre: B6.129P2-Lyz2tm1(cre)Ifo/J Jackson Laboratory RRID:IMSR_JAX:004781 Myc flox: B6.129S6-Myctm2Fwa/Mmjax Jackson Laboratory RRID:MMRRC_032046-JAX Hif1a flox: B6.129-Hif1atm3Rsjo/J Jackson Laboratory RRID:IMSR_JAX:007561 C57BL/6J Jackson Laboratory RRID:IMSR_JAX:000664 IRF4 KO A gift from Dr. Kelvin P. Lee; Utley et al., 2020 N/A Oligonucleotides See Table S2 Recombinant DNA pMXs-c-Myc Takahashi and Yamanaka, 2006 RRID:Addgene_13375 pMXs-gw Takahashi and Yamanaka, 2006 RRID:Addgene_18656 Deposited data RNA-seq This paper GEO: GSE164475 Software and algorithms Bowtie2 version 2.2.6 Langmead and Salzberg, 2012 https://www.bioinformatics.babraham .ac.uk/projects/fastqc STAR Aligner Dobin et al., 2013 https://github.com/alexdobin/STAR edgeR Robinson et al., 2010 https://www.bioconductor.org/ packages/release/bioc/html/ edgeR.html R https://www.R-project.org/ Cuffdiff2 Trapnell et al., 2013 http://cole-trapnell-lab.github.io/ cufflinks/cuffdiff/ Gene Set Enrichment Analysis (GSEA) Broad Institute, Inc. https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp MassHunter Quantitative Analysis (v. B.09.00) Agilent Technologies https://www.agilent.com/en/product/ software-informatics/ mass-spectrometry-software/ data-analysis/quantitative-analysis Mass Profiler Professional (v. 15.0) Agilent Technologies https://www.agilent.com/en/product/ software-informatics/ mass-spectrometry-software/ data-analysis/ mass-profiler-professional-software (Continued on next page) e3 Cell Reports 35, 109264, June 15, 2021 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Metaboanalyst Chong et al., 2019 https://www.metaboanalyst.ca Seahorse Wave Desktop Software Agilent Technologies https://www.agilent.com/en/ product/cell-analysis/real-timecell-metabolic-analysis/xfsoftware/seahorse-wavedesktop-software-740897 Flowjo (v10.7.1) BD Biosciences https://www.flowjo.com/ solutions/flowjo/downloads/ GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Article ll OPEN ACCESS

    Software:

    Article Title: MYC-mediated early glycolysis negatively regulates proinflammatory responses by controlling IRF4 in inflammatory macrophages
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Monoclonal rabbit anti-phosphorylated Akt antibody Cell Signaling RRID:AB_2315049 Polyclonal rabbit anti-A20 antibody Cell Signaling RRID:AB_2204524 Monoclonal rabbit anti-ATP-Citrate Lyase antibody Cell Signaling RRID:AB_2798203 Polyclonal rabbit anti-phosphorylated ATPCitrate Lyase antibody Cell Signaling RRID:AB_2257987 Monoclonal rabbit anti-phosphorylated p70 S6 Kinase antibody Cell Signaling RRID:AB_2269803 Monoclonal rabbit anti-p70 S6 Kinase Cell Signaling RRID:AB_390722 Polyclonal rabbit anti-phosphorylated 4EBP1 antibody Cell Signaling RRID:AB_330947 Monoclonal rabbit anti-4E-BP1 antibody Cell Signaling RRID:AB_2097841 Monoclonal rabbit anti-p65 antibody Cell Signaling RRID:AB_823578 Monoclonal mouse anti-a-tubulin antibody Sigma Aldrich RRID:AB_477593 Polyclonal anti-mouse IL-1 beta/IL-1F2 Biotinylated antibody R&D systems RRID:AB_356450 Bacterial and virus strains Listeria monocytogenes (wild-type strain 10403S) Serbina et al., 2003 N/A Biological samples Human Peripheral Blood New York Blood Center N/A Chemicals, peptides, and recombinant proteins Ultrapure LPS-EB (LPS from E. coli O111:B4) InvivoGen Cat#tlrl-3pelps LPS from Escherichia coli strain O55:B5 Sigma Aldrich Cat#L2880 Mouse recombinant IL-4 Miltenyi Biotec Cat#130-097-757 Pam3Cys EMC Microcollections Cat#L2000 Human recombinant M-CSF Peprotech Cat#300-25 L-(+)-Lactic acid Sigma Aldrich Cat#L6402 2-Deoxy-D-glucose (2-DG) Sigma Aldrich Cat#D8375 UK-5099 Sigma Aldrich Cat#PZ0160 Etomoxir Sigma Aldrich Cat#E1905 Pefabloc SC Sigma Aldrich Cat#76307 Deoxyribonuclease I Sigma Aldrich Cat#DN25 Collagenase, Type IV Thermo Fisher Scientific Cat#17104019 CHC Tocris Bioscience Cat#5029 FX11 EMD Millipore Cat#427218 Polybrene Santa Cruz Cat#sc-134220 Gentamycin Thermo Fisher Scientific Cat#15710064 FuGENE(R) HD Transfection Reagent Promega Cat#E2312 TransIT-TKO Transfection Reagent Mirus Bio Cat#MIR 2150 SYTO 24 green fluorescent nucleic acid stain Molecular Probes Cat#S7559 Brain Heart Infusion BD BioSciences Cat#BD 237500 Brilliant Stain Buffer BD BioSciences Cat#563794 PerCP/Cy5.5 Streptavidin Biolegend Cat#405214 DAPI (4’,6-Diamidino-2-Phenylindole, Dihydrochloride) Thermo Fisher Scientific Cat#D1306 (Continued on next page) Cell Reports 35, 109264, June 15, 2021 e2 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER eBioscience Fixable Viability Dye eFluor 455UV Thermo Fisher Scientific Cat#65-0868-18 CountBright Absolute Counting Beads, for flow cytometry Thermo Fisher Scientific Cat#C36950 UltraComp eBeads Compensation Beads Thermo Fisher Scientific Cat#01-2222-42 Streptavidin-HRP R&D systems Cat#DY998 Critical commercial assays First strand cDNA synthesis kit Fermentas Cat#K1622 RNeasy mini kit QIAGEN Cat#74104 Fast SYBR Green Master Mix Life Technologies Cat#4385618 Mouse Magnetic Luminex Assay R&D systems Custom made Lactate Dehydrogenase Assay Kit Abcam Cat#ab102526 Seahorse XF Glycolysis Stress Test Kit Agilent Cat#103020-100 Seahorse XF Mito Stress Test Kit Agilent Cat#103015-100 Cell Counting Kit-8 Dojindo Laboratories CatCK04-01 Experimental models: organisms/strains LysM Cre: B6.129P2-Lyz2tm1(cre)Ifo/J Jackson Laboratory RRID:IMSR_JAX:004781 Myc flox: B6.129S6-Myctm2Fwa/Mmjax Jackson Laboratory RRID:MMRRC_032046-JAX Hif1a flox: B6.129-Hif1atm3Rsjo/J Jackson Laboratory RRID:IMSR_JAX:007561 C57BL/6J Jackson Laboratory RRID:IMSR_JAX:000664 IRF4 KO A gift from Dr. Kelvin P. Lee; Utley et al., 2020 N/A Oligonucleotides See Table S2 Recombinant DNA pMXs-c-Myc Takahashi and Yamanaka, 2006 RRID:Addgene_13375 pMXs-gw Takahashi and Yamanaka, 2006 RRID:Addgene_18656 Deposited data RNA-seq This paper GEO: GSE164475 Software and algorithms Bowtie2 version 2.2.6 Langmead and Salzberg, 2012 https://www.bioinformatics.babraham .ac.uk/projects/fastqc STAR Aligner Dobin et al., 2013 https://github.com/alexdobin/STAR edgeR Robinson et al., 2010 https://www.bioconductor.org/ packages/release/bioc/html/ edgeR.html R https://www.R-project.org/ Cuffdiff2 Trapnell et al., 2013 http://cole-trapnell-lab.github.io/ cufflinks/cuffdiff/ Gene Set Enrichment Analysis (GSEA) Broad Institute, Inc. https://www.gsea-msigdb.org/gsea/ msigdb/index.jsp MassHunter Quantitative Analysis (v. B.09.00) Agilent Technologies https://www.agilent.com/en/product/ software-informatics/ mass-spectrometry-software/ data-analysis/quantitative-analysis Mass Profiler Professional (v. 15.0) Agilent Technologies https://www.agilent.com/en/product/ software-informatics/ mass-spectrometry-software/ data-analysis/ mass-profiler-professional-software (Continued on next page) e3 Cell Reports 35, 109264, June 15, 2021 Article ll OPEN ACCESS .. REAGENT or RESOURCE SOURCE IDENTIFIER Metaboanalyst Chong et al., 2019 https://www.metaboanalyst.ca Seahorse Wave Desktop Software Agilent Technologies https://www.agilent.com/en/ product/cell-analysis/real-timecell-metabolic-analysis/xfsoftware/seahorse-wavedesktop-software-740897 Flowjo (v10.7.1) BD Biosciences https://www.flowjo.com/ solutions/flowjo/downloads/ GraphPad Prism 8 GraphPad Software https://www.graphpad.com/ scientific-software/prism/ Article ll OPEN ACCESS

    Article Title: Cholesterol suppresses GOLM1-dependent selective autophagy of RTKs in hepatocellular carcinoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Flag Magnetic Beads Bimake Cat#B26101 Anti-Myc Magnetic Beads Bimake Cat#B26301 Protein A/G Magnetic Beads for IP Bimake Cat#B23201 Phosphatase Inhibitor Cocktail Bimake Cat#B15001 Protease Inhibitor Cocktail Bimake Cat#B14001 Critical commercial assays Amplex Red Cholesterol Assay Kit Invitrogen Cat#A12216 Cell Counting Kit-8 Dojindo Laboratories CatCK04 QuickMutation Site-directed Gene Mutagenesis Kit Beyotime Biotechnology Cat#D0206 Experimental models: Cell lines Human: HCCLM3 cells Liver Cancer Institute, Fudan University N/A Human: MHCC97-H cells Liver Cancer Institute, Fudan University N/A Human: PLC/PRF/5 cells Cell Resources Center, Chinese Academy of Sciences Cat#TCHu119; RRID:CVCL_0485 Human: Hep3B cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-5045; RRID:CVCL_0326 Human: HepG2 cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-510; RRID:CVCL_0027 Human: HuH-7 cells Cell Resources Center, Chinese Academy of Sciences Cat# SCSP-526; RRID:CVCL_0336 Human: HEK293T cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-502; RRID:CVCL_0063 Experimental models: Organisms/strains Mouse: BALBc nu/nu Shanghai Laboratory Animal Center, Chinese Academy of Science N/A Oligonucleotides qRT-PCR primers for MET/EGFR/GOLM1/ ATG5/ATG7, see Table S3 This paper N/A shRNA target sequences for GOLM1/ATG5/ ATG7/SLC38A9, see Table S4 This paper N/A PCR primers for GOLM1/MET/EGFR cDNA clone, see Table S5 This paper N/A Mutation primers for GOLM1, see Table S6 This paper N/A Recombinant DNA pCDH-CMV-MCS-EF1-Puro This paper N/A pLKO.1-TRC This paper N/A pMD2.G This paper N/A pSPAX2 This paper N/A pCDNA3.1-GFP-LC3 This paper N/A pcDNA3.1-mRFP-GFP-LC3 This paper N/A pcDNA3-c-5XMyc This paper N/A p3xFlag-CMV-14 This paper N/A Software and algorithms ImageJ (v1.53) NIH Image https://imagej.nih.gov/ij/index.html GraphPad Prism (v8.4.3) GraphPad Software http://www.graphpad-prism.cn ..

    Magnetic Beads:

    Article Title: Cholesterol suppresses GOLM1-dependent selective autophagy of RTKs in hepatocellular carcinoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Flag Magnetic Beads Bimake Cat#B26101 Anti-Myc Magnetic Beads Bimake Cat#B26301 Protein A/G Magnetic Beads for IP Bimake Cat#B23201 Phosphatase Inhibitor Cocktail Bimake Cat#B15001 Protease Inhibitor Cocktail Bimake Cat#B14001 Critical commercial assays Amplex Red Cholesterol Assay Kit Invitrogen Cat#A12216 Cell Counting Kit-8 Dojindo Laboratories CatCK04 QuickMutation Site-directed Gene Mutagenesis Kit Beyotime Biotechnology Cat#D0206 Experimental models: Cell lines Human: HCCLM3 cells Liver Cancer Institute, Fudan University N/A Human: MHCC97-H cells Liver Cancer Institute, Fudan University N/A Human: PLC/PRF/5 cells Cell Resources Center, Chinese Academy of Sciences Cat#TCHu119; RRID:CVCL_0485 Human: Hep3B cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-5045; RRID:CVCL_0326 Human: HepG2 cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-510; RRID:CVCL_0027 Human: HuH-7 cells Cell Resources Center, Chinese Academy of Sciences Cat# SCSP-526; RRID:CVCL_0336 Human: HEK293T cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-502; RRID:CVCL_0063 Experimental models: Organisms/strains Mouse: BALBc nu/nu Shanghai Laboratory Animal Center, Chinese Academy of Science N/A Oligonucleotides qRT-PCR primers for MET/EGFR/GOLM1/ ATG5/ATG7, see Table S3 This paper N/A shRNA target sequences for GOLM1/ATG5/ ATG7/SLC38A9, see Table S4 This paper N/A PCR primers for GOLM1/MET/EGFR cDNA clone, see Table S5 This paper N/A Mutation primers for GOLM1, see Table S6 This paper N/A Recombinant DNA pCDH-CMV-MCS-EF1-Puro This paper N/A pLKO.1-TRC This paper N/A pMD2.G This paper N/A pSPAX2 This paper N/A pCDNA3.1-GFP-LC3 This paper N/A pcDNA3.1-mRFP-GFP-LC3 This paper N/A pcDNA3-c-5XMyc This paper N/A p3xFlag-CMV-14 This paper N/A Software and algorithms ImageJ (v1.53) NIH Image https://imagej.nih.gov/ij/index.html GraphPad Prism (v8.4.3) GraphPad Software http://www.graphpad-prism.cn ..

    Protease Inhibitor:

    Article Title: Cholesterol suppresses GOLM1-dependent selective autophagy of RTKs in hepatocellular carcinoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Flag Magnetic Beads Bimake Cat#B26101 Anti-Myc Magnetic Beads Bimake Cat#B26301 Protein A/G Magnetic Beads for IP Bimake Cat#B23201 Phosphatase Inhibitor Cocktail Bimake Cat#B15001 Protease Inhibitor Cocktail Bimake Cat#B14001 Critical commercial assays Amplex Red Cholesterol Assay Kit Invitrogen Cat#A12216 Cell Counting Kit-8 Dojindo Laboratories CatCK04 QuickMutation Site-directed Gene Mutagenesis Kit Beyotime Biotechnology Cat#D0206 Experimental models: Cell lines Human: HCCLM3 cells Liver Cancer Institute, Fudan University N/A Human: MHCC97-H cells Liver Cancer Institute, Fudan University N/A Human: PLC/PRF/5 cells Cell Resources Center, Chinese Academy of Sciences Cat#TCHu119; RRID:CVCL_0485 Human: Hep3B cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-5045; RRID:CVCL_0326 Human: HepG2 cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-510; RRID:CVCL_0027 Human: HuH-7 cells Cell Resources Center, Chinese Academy of Sciences Cat# SCSP-526; RRID:CVCL_0336 Human: HEK293T cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-502; RRID:CVCL_0063 Experimental models: Organisms/strains Mouse: BALBc nu/nu Shanghai Laboratory Animal Center, Chinese Academy of Science N/A Oligonucleotides qRT-PCR primers for MET/EGFR/GOLM1/ ATG5/ATG7, see Table S3 This paper N/A shRNA target sequences for GOLM1/ATG5/ ATG7/SLC38A9, see Table S4 This paper N/A PCR primers for GOLM1/MET/EGFR cDNA clone, see Table S5 This paper N/A Mutation primers for GOLM1, see Table S6 This paper N/A Recombinant DNA pCDH-CMV-MCS-EF1-Puro This paper N/A pLKO.1-TRC This paper N/A pMD2.G This paper N/A pSPAX2 This paper N/A pCDNA3.1-GFP-LC3 This paper N/A pcDNA3.1-mRFP-GFP-LC3 This paper N/A pcDNA3-c-5XMyc This paper N/A p3xFlag-CMV-14 This paper N/A Software and algorithms ImageJ (v1.53) NIH Image https://imagej.nih.gov/ij/index.html GraphPad Prism (v8.4.3) GraphPad Software http://www.graphpad-prism.cn ..

    Amplex Red Cholesterol Assay:

    Article Title: Cholesterol suppresses GOLM1-dependent selective autophagy of RTKs in hepatocellular carcinoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Flag Magnetic Beads Bimake Cat#B26101 Anti-Myc Magnetic Beads Bimake Cat#B26301 Protein A/G Magnetic Beads for IP Bimake Cat#B23201 Phosphatase Inhibitor Cocktail Bimake Cat#B15001 Protease Inhibitor Cocktail Bimake Cat#B14001 Critical commercial assays Amplex Red Cholesterol Assay Kit Invitrogen Cat#A12216 Cell Counting Kit-8 Dojindo Laboratories CatCK04 QuickMutation Site-directed Gene Mutagenesis Kit Beyotime Biotechnology Cat#D0206 Experimental models: Cell lines Human: HCCLM3 cells Liver Cancer Institute, Fudan University N/A Human: MHCC97-H cells Liver Cancer Institute, Fudan University N/A Human: PLC/PRF/5 cells Cell Resources Center, Chinese Academy of Sciences Cat#TCHu119; RRID:CVCL_0485 Human: Hep3B cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-5045; RRID:CVCL_0326 Human: HepG2 cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-510; RRID:CVCL_0027 Human: HuH-7 cells Cell Resources Center, Chinese Academy of Sciences Cat# SCSP-526; RRID:CVCL_0336 Human: HEK293T cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-502; RRID:CVCL_0063 Experimental models: Organisms/strains Mouse: BALBc nu/nu Shanghai Laboratory Animal Center, Chinese Academy of Science N/A Oligonucleotides qRT-PCR primers for MET/EGFR/GOLM1/ ATG5/ATG7, see Table S3 This paper N/A shRNA target sequences for GOLM1/ATG5/ ATG7/SLC38A9, see Table S4 This paper N/A PCR primers for GOLM1/MET/EGFR cDNA clone, see Table S5 This paper N/A Mutation primers for GOLM1, see Table S6 This paper N/A Recombinant DNA pCDH-CMV-MCS-EF1-Puro This paper N/A pLKO.1-TRC This paper N/A pMD2.G This paper N/A pSPAX2 This paper N/A pCDNA3.1-GFP-LC3 This paper N/A pcDNA3.1-mRFP-GFP-LC3 This paper N/A pcDNA3-c-5XMyc This paper N/A p3xFlag-CMV-14 This paper N/A Software and algorithms ImageJ (v1.53) NIH Image https://imagej.nih.gov/ij/index.html GraphPad Prism (v8.4.3) GraphPad Software http://www.graphpad-prism.cn ..

    Mutagenesis:

    Article Title: Cholesterol suppresses GOLM1-dependent selective autophagy of RTKs in hepatocellular carcinoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Flag Magnetic Beads Bimake Cat#B26101 Anti-Myc Magnetic Beads Bimake Cat#B26301 Protein A/G Magnetic Beads for IP Bimake Cat#B23201 Phosphatase Inhibitor Cocktail Bimake Cat#B15001 Protease Inhibitor Cocktail Bimake Cat#B14001 Critical commercial assays Amplex Red Cholesterol Assay Kit Invitrogen Cat#A12216 Cell Counting Kit-8 Dojindo Laboratories CatCK04 QuickMutation Site-directed Gene Mutagenesis Kit Beyotime Biotechnology Cat#D0206 Experimental models: Cell lines Human: HCCLM3 cells Liver Cancer Institute, Fudan University N/A Human: MHCC97-H cells Liver Cancer Institute, Fudan University N/A Human: PLC/PRF/5 cells Cell Resources Center, Chinese Academy of Sciences Cat#TCHu119; RRID:CVCL_0485 Human: Hep3B cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-5045; RRID:CVCL_0326 Human: HepG2 cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-510; RRID:CVCL_0027 Human: HuH-7 cells Cell Resources Center, Chinese Academy of Sciences Cat# SCSP-526; RRID:CVCL_0336 Human: HEK293T cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-502; RRID:CVCL_0063 Experimental models: Organisms/strains Mouse: BALBc nu/nu Shanghai Laboratory Animal Center, Chinese Academy of Science N/A Oligonucleotides qRT-PCR primers for MET/EGFR/GOLM1/ ATG5/ATG7, see Table S3 This paper N/A shRNA target sequences for GOLM1/ATG5/ ATG7/SLC38A9, see Table S4 This paper N/A PCR primers for GOLM1/MET/EGFR cDNA clone, see Table S5 This paper N/A Mutation primers for GOLM1, see Table S6 This paper N/A Recombinant DNA pCDH-CMV-MCS-EF1-Puro This paper N/A pLKO.1-TRC This paper N/A pMD2.G This paper N/A pSPAX2 This paper N/A pCDNA3.1-GFP-LC3 This paper N/A pcDNA3.1-mRFP-GFP-LC3 This paper N/A pcDNA3-c-5XMyc This paper N/A p3xFlag-CMV-14 This paper N/A Software and algorithms ImageJ (v1.53) NIH Image https://imagej.nih.gov/ij/index.html GraphPad Prism (v8.4.3) GraphPad Software http://www.graphpad-prism.cn ..

    Planar Chromatography:

    Article Title: Cholesterol suppresses GOLM1-dependent selective autophagy of RTKs in hepatocellular carcinoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Flag Magnetic Beads Bimake Cat#B26101 Anti-Myc Magnetic Beads Bimake Cat#B26301 Protein A/G Magnetic Beads for IP Bimake Cat#B23201 Phosphatase Inhibitor Cocktail Bimake Cat#B15001 Protease Inhibitor Cocktail Bimake Cat#B14001 Critical commercial assays Amplex Red Cholesterol Assay Kit Invitrogen Cat#A12216 Cell Counting Kit-8 Dojindo Laboratories CatCK04 QuickMutation Site-directed Gene Mutagenesis Kit Beyotime Biotechnology Cat#D0206 Experimental models: Cell lines Human: HCCLM3 cells Liver Cancer Institute, Fudan University N/A Human: MHCC97-H cells Liver Cancer Institute, Fudan University N/A Human: PLC/PRF/5 cells Cell Resources Center, Chinese Academy of Sciences Cat#TCHu119; RRID:CVCL_0485 Human: Hep3B cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-5045; RRID:CVCL_0326 Human: HepG2 cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-510; RRID:CVCL_0027 Human: HuH-7 cells Cell Resources Center, Chinese Academy of Sciences Cat# SCSP-526; RRID:CVCL_0336 Human: HEK293T cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-502; RRID:CVCL_0063 Experimental models: Organisms/strains Mouse: BALBc nu/nu Shanghai Laboratory Animal Center, Chinese Academy of Science N/A Oligonucleotides qRT-PCR primers for MET/EGFR/GOLM1/ ATG5/ATG7, see Table S3 This paper N/A shRNA target sequences for GOLM1/ATG5/ ATG7/SLC38A9, see Table S4 This paper N/A PCR primers for GOLM1/MET/EGFR cDNA clone, see Table S5 This paper N/A Mutation primers for GOLM1, see Table S6 This paper N/A Recombinant DNA pCDH-CMV-MCS-EF1-Puro This paper N/A pLKO.1-TRC This paper N/A pMD2.G This paper N/A pSPAX2 This paper N/A pCDNA3.1-GFP-LC3 This paper N/A pcDNA3.1-mRFP-GFP-LC3 This paper N/A pcDNA3-c-5XMyc This paper N/A p3xFlag-CMV-14 This paper N/A Software and algorithms ImageJ (v1.53) NIH Image https://imagej.nih.gov/ij/index.html GraphPad Prism (v8.4.3) GraphPad Software http://www.graphpad-prism.cn ..

    Quantitative RT-PCR:

    Article Title: Cholesterol suppresses GOLM1-dependent selective autophagy of RTKs in hepatocellular carcinoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Flag Magnetic Beads Bimake Cat#B26101 Anti-Myc Magnetic Beads Bimake Cat#B26301 Protein A/G Magnetic Beads for IP Bimake Cat#B23201 Phosphatase Inhibitor Cocktail Bimake Cat#B15001 Protease Inhibitor Cocktail Bimake Cat#B14001 Critical commercial assays Amplex Red Cholesterol Assay Kit Invitrogen Cat#A12216 Cell Counting Kit-8 Dojindo Laboratories CatCK04 QuickMutation Site-directed Gene Mutagenesis Kit Beyotime Biotechnology Cat#D0206 Experimental models: Cell lines Human: HCCLM3 cells Liver Cancer Institute, Fudan University N/A Human: MHCC97-H cells Liver Cancer Institute, Fudan University N/A Human: PLC/PRF/5 cells Cell Resources Center, Chinese Academy of Sciences Cat#TCHu119; RRID:CVCL_0485 Human: Hep3B cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-5045; RRID:CVCL_0326 Human: HepG2 cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-510; RRID:CVCL_0027 Human: HuH-7 cells Cell Resources Center, Chinese Academy of Sciences Cat# SCSP-526; RRID:CVCL_0336 Human: HEK293T cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-502; RRID:CVCL_0063 Experimental models: Organisms/strains Mouse: BALBc nu/nu Shanghai Laboratory Animal Center, Chinese Academy of Science N/A Oligonucleotides qRT-PCR primers for MET/EGFR/GOLM1/ ATG5/ATG7, see Table S3 This paper N/A shRNA target sequences for GOLM1/ATG5/ ATG7/SLC38A9, see Table S4 This paper N/A PCR primers for GOLM1/MET/EGFR cDNA clone, see Table S5 This paper N/A Mutation primers for GOLM1, see Table S6 This paper N/A Recombinant DNA pCDH-CMV-MCS-EF1-Puro This paper N/A pLKO.1-TRC This paper N/A pMD2.G This paper N/A pSPAX2 This paper N/A pCDNA3.1-GFP-LC3 This paper N/A pcDNA3.1-mRFP-GFP-LC3 This paper N/A pcDNA3-c-5XMyc This paper N/A p3xFlag-CMV-14 This paper N/A Software and algorithms ImageJ (v1.53) NIH Image https://imagej.nih.gov/ij/index.html GraphPad Prism (v8.4.3) GraphPad Software http://www.graphpad-prism.cn ..

    shRNA:

    Article Title: Cholesterol suppresses GOLM1-dependent selective autophagy of RTKs in hepatocellular carcinoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Flag Magnetic Beads Bimake Cat#B26101 Anti-Myc Magnetic Beads Bimake Cat#B26301 Protein A/G Magnetic Beads for IP Bimake Cat#B23201 Phosphatase Inhibitor Cocktail Bimake Cat#B15001 Protease Inhibitor Cocktail Bimake Cat#B14001 Critical commercial assays Amplex Red Cholesterol Assay Kit Invitrogen Cat#A12216 Cell Counting Kit-8 Dojindo Laboratories CatCK04 QuickMutation Site-directed Gene Mutagenesis Kit Beyotime Biotechnology Cat#D0206 Experimental models: Cell lines Human: HCCLM3 cells Liver Cancer Institute, Fudan University N/A Human: MHCC97-H cells Liver Cancer Institute, Fudan University N/A Human: PLC/PRF/5 cells Cell Resources Center, Chinese Academy of Sciences Cat#TCHu119; RRID:CVCL_0485 Human: Hep3B cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-5045; RRID:CVCL_0326 Human: HepG2 cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-510; RRID:CVCL_0027 Human: HuH-7 cells Cell Resources Center, Chinese Academy of Sciences Cat# SCSP-526; RRID:CVCL_0336 Human: HEK293T cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-502; RRID:CVCL_0063 Experimental models: Organisms/strains Mouse: BALBc nu/nu Shanghai Laboratory Animal Center, Chinese Academy of Science N/A Oligonucleotides qRT-PCR primers for MET/EGFR/GOLM1/ ATG5/ATG7, see Table S3 This paper N/A shRNA target sequences for GOLM1/ATG5/ ATG7/SLC38A9, see Table S4 This paper N/A PCR primers for GOLM1/MET/EGFR cDNA clone, see Table S5 This paper N/A Mutation primers for GOLM1, see Table S6 This paper N/A Recombinant DNA pCDH-CMV-MCS-EF1-Puro This paper N/A pLKO.1-TRC This paper N/A pMD2.G This paper N/A pSPAX2 This paper N/A pCDNA3.1-GFP-LC3 This paper N/A pcDNA3.1-mRFP-GFP-LC3 This paper N/A pcDNA3-c-5XMyc This paper N/A p3xFlag-CMV-14 This paper N/A Software and algorithms ImageJ (v1.53) NIH Image https://imagej.nih.gov/ij/index.html GraphPad Prism (v8.4.3) GraphPad Software http://www.graphpad-prism.cn ..

    Polymerase Chain Reaction:

    Article Title: Cholesterol suppresses GOLM1-dependent selective autophagy of RTKs in hepatocellular carcinoma.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Anti-Flag Magnetic Beads Bimake Cat#B26101 Anti-Myc Magnetic Beads Bimake Cat#B26301 Protein A/G Magnetic Beads for IP Bimake Cat#B23201 Phosphatase Inhibitor Cocktail Bimake Cat#B15001 Protease Inhibitor Cocktail Bimake Cat#B14001 Critical commercial assays Amplex Red Cholesterol Assay Kit Invitrogen Cat#A12216 Cell Counting Kit-8 Dojindo Laboratories CatCK04 QuickMutation Site-directed Gene Mutagenesis Kit Beyotime Biotechnology Cat#D0206 Experimental models: Cell lines Human: HCCLM3 cells Liver Cancer Institute, Fudan University N/A Human: MHCC97-H cells Liver Cancer Institute, Fudan University N/A Human: PLC/PRF/5 cells Cell Resources Center, Chinese Academy of Sciences Cat#TCHu119; RRID:CVCL_0485 Human: Hep3B cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-5045; RRID:CVCL_0326 Human: HepG2 cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-510; RRID:CVCL_0027 Human: HuH-7 cells Cell Resources Center, Chinese Academy of Sciences Cat# SCSP-526; RRID:CVCL_0336 Human: HEK293T cells Cell Resources Center, Chinese Academy of Sciences Cat#SCSP-502; RRID:CVCL_0063 Experimental models: Organisms/strains Mouse: BALBc nu/nu Shanghai Laboratory Animal Center, Chinese Academy of Science N/A Oligonucleotides qRT-PCR primers for MET/EGFR/GOLM1/ ATG5/ATG7, see Table S3 This paper N/A shRNA target sequences for GOLM1/ATG5/ ATG7/SLC38A9, see Table S4 This paper N/A PCR primers for GOLM1/MET/EGFR cDNA clone, see Table S5 This paper N/A Mutation primers for GOLM1, see Table S6 This paper N/A Recombinant DNA pCDH-CMV-MCS-EF1-Puro This paper N/A pLKO.1-TRC This paper N/A pMD2.G This paper N/A pSPAX2 This paper N/A pCDNA3.1-GFP-LC3 This paper N/A pcDNA3.1-mRFP-GFP-LC3 This paper N/A pcDNA3-c-5XMyc This paper N/A p3xFlag-CMV-14 This paper N/A Software and algorithms ImageJ (v1.53) NIH Image https://imagej.nih.gov/ij/index.html GraphPad Prism (v8.4.3) GraphPad Software http://www.graphpad-prism.cn ..

    other:

    Article Title: Spleen-targeted neoantigen mRNA vaccine induces ISG15 + CD8 + T cell-mediated tertiary lymphoid structure formation in hepatocellular carcinoma.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER CD4 (TSA-mIF, rabbit mAb) AiFang Biological Cat#AFRM0003; RRID: N/A CD19 (TSA-mIF, rabbit mAb) AiFang Biological Cat#AFRM0354; RRID: N/A CD20 (TSA-mIF, rabbit mAb) Abcam Cat#ab64088; RRID:AB_1139386 CD23 (TSA-mIF, rabbit mAb) Abcam Cat#ab315289; RRID: N/A CD21 (TSA-mIF, rabbit mAb) Abcam Cat#ab227662; RRID: N/A CD34 (TSA-mIF, rabbit mAb) AiFang Biological Cat#AFRM0080; RRID: N/A Bcl6 (TSA-mIF, rabbit pAb) Invitrogen Cat#PA5-27390; RRID:AB_2544866 CD138 (TSA-mIF, rabbit pAb) Proteintech Cat#10593-1-AP; RRID:AB_2182736 CD27 (TSA-mIF, rabbit mAb) Abcam Cat#ab214043; RRID: N/A CD86 (TSA-mIF, rabbit mAb) AiFang Biological Cat#AFRM0167; RRID: N/A Chemicals, peptides, and recombinant proteins DOTMA Sinopeg Cat#06040009700 DOPE Sinopeg Cat#06030000500 SM-102 Sinopeg Cat#06040008800 DSPC Sinopeg Cat#06030001100 cholesterol Sinopeg Cat#06040015200 DMG-PEG2000 AVT Cat#O02005 HindIII restriction enzyme Thermo-Fisher Cat#FD0505 Luciferin substrate PerkinElmer Cat#122799 Heparin sodium Achem-block Cat#ABC-B132998 SCH79797 (F2R antagonist, F2RA) MCE Cat#HY-14994 Recombinant GZMA MCE Cat#HY-P76377 OKT3 T&L biotechnology Cat#GMP-TL101-0500 Trypan Blue Solution Gibco Cat#15250-061 Critical commercial assays Mouse IFN-γ ELISpot Kit Mabtech Cat#3321-4AST-2 H&E Stain Kit Solarbio Cat#G1120 One Step TUNEL Apoptosis Assay Kit Beyotime Cat#C1086 Mouse IL-12 ELISA kit Boster Bio Cat#EK0422 Mouse IFN-γ ELISA kit Boster Bio Cat# EK0375 Mouse IgG ELISA kit Boster Bio Cat#EK0101 Mouse IL-1β ELISA kit Boster Bio Cat#EK0394 Mouse IL-6 ELISA kit Boster Bio Cat#EK0411 Mouse TNF-α ELISA kit Boster Bio Cat#EK0527 Mouse IFN-β ELISA kit FANKEW Cat#F2124-A Mouse C3a ELISA kit Cusabio Biotech Cat#CSB-E08666r Mouse C5a ELISA kit Cusabio Biotech Cat#CSB-E14363r Fixation/Permeabilization Solution Kit BD Bioscience Cat#554715 HyperScribe TM All in One mRNA Synthesis Kit Plus 1 APExBIO Cat#K1064 HyperScribe TM T7 High Yield Cy5 RNA Labeling Kit APExBIO Cat#K1063 VAHTS RNA Clean Beads Vazyme Cat#N412-01 Cell Counting Kit-8 Dojindo Laboratories Cat#CK04-01 sCelLive Tissue Digestion Solution Singleron Cat#1020012 FocuSCOPE Single Cell Multiomics mRNA × Mouse Liver Mutation Detection Kit Singleron Cat#4212122 GEXSCOPE Single Cell RNA Library Kit Singleron Cat#4180022 DynaSpatial FFPE Spatial Gene Expression Reagents Kit (for Mouse Transcriptome) Dynamic Biosystems Cat#13010060 (Continued on next page) Cell Reports Medicine 7, 102754, May 19, 2026 e2 OPEN ACCESS



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