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u119a glycogen  (Thermo Fisher)


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    Thermo Fisher u119a glycogen
    U119a Glycogen, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/u119a+glycogen/GLYCOGEN/pm30293776-137-112-116
    Average 99 stars, based on 1 article reviews
    u119a glycogen - by Bioz Stars, 2026-10
    99/100 stars

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    RNA HS Assay:

    Article Title: The Itaconate Pathway Is a Central Regulatory Node Linking Innate Immune Tolerance and Trained Immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies a-IFN-alpha/beta R1 antibody R&D Systems AF3039; RRID:AB_664107 IgG isotype control R&D Systems AB-108-C; RRID:AB_354267 Rabbit polyclonal anti-H3K27ac Diagenode pAb-196-050; RRID:AB_2637079 Rabbit polyclonal anti-H3K4me1 Diagenode pAb-037-050; RRID:AB_2561054 Rabbit polyclonal anti-H3K4me3 Diagenode pAb-003-050; RRID:AB_2616052 Chemicals, Peptides, and Recombinant Proteins Gentamycin Thermo Fisher Scientific 15750060 Lipopolysaccharide from E. coli serotype 055:B5 Sigma-Aldrich L2880 Pam3Cys EMC Microcollections L2000 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 CD14+ beads MACS Miltenyi 130-050-201 TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 b1,3-(D)glucan (b-glucan) Saeed et al., 2014 N/A Mono methyl-fumarate Sigma-Aldrich 651419-1G Dimethylitaconate Sigma-Aldrich 592498-25G 4-octyl itaconate Mills et al., 2018 IRG1 siRNA (mouse) Santa Cruz sc-146287 control siRNA (mouse) Santa Cruz sc-37007 siRNA Transfection Medium Santa Cruz sc-36868 siRNA Dilution Buffer Santa Cruz sc-29527 siRNA Transfection Reagent Santa Cruz sc-29528 Seahorse XF Base Medium Agilent Technologies 102353-100 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 Luminol Sigma-Aldrich A8511-5G Zymosan (from S. cerevisiae) Sigma-Aldrich Z4250-1G Critical Commercial Assays Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Lactate Fluorometric Assay Kit Biovision K607 iScript cDNA Synthesis Kit Bio-Rad 1708891 Succinate Colometric Assay kit Sigma-Aldrich MAK184 Glutamate Assay Kit Sigma-Aldrich MAK004 CytoTox 96 Non-Radioactive Cytotoxicity Assay Promega G1780 Rneasy Mini Kit QIAGEN 74106 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 (Continued on next page) Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Ribozero Gold Kit Illumina MRZG12324 Qubit RNA HS assay kit Ribozero Life Technologies Q32852 DNase I QIAGEN 79254 Sodium Acetate (3M) Life Technologies AM9740 iQ SYBR Green Supermix Bio-Rad 1708880 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 100 x SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/mL) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E. coli Ligase New England Biolabs M0205L Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Ribozero Gold Kit Illumina MRZG12324 Deposited Data Raw data files for ChIP sequencing Novakovic et al., 2016 GSE85245 Raw data files for RNA sequencing Novakovic et al., 2016 GSE85243 Raw data files for b-glucan and LPS SuperSeries data Novakovic et al., 2016 GSE85246 Experimental Models: Cell Lines Mouse: RAW264.7 cells ATCC TIB-71 Experimental Models: Organisms/Strains Human: 200FG cohort (Human Functional Genomics project) Li et al., 2016 http://www.humanfunctionalgenomics.org Human: LLDeep cohort Tigchelaar et al., 2015 Human: primary monocytes from healthy volunteers Sanquin Blood Bank Oligonucleotides Primer HPRT fw 5’-CCTGGCGTCGTGATTAGTGAT-3’ Sigma-Aldrich Designed by BLAST Primer HPRT rv 5’-AGACGTTCAGTCCTGTCCATAA-3’ Sigma-Aldrich Designed by BLAST Primer IRG1 fw 5’-GTTCCTGGGAACCACTACG-3’ Lachmandas et al., 2016 Primer IRG1 rv 5’-GATGTCTGGCTGACCCCAAA-3’ Lachmandas et al., 2016 Primer IFNB1 fw 5’-ATGACCAACAAGTGTCTCCTCC-3’ Sigma-Aldrich Designed by BLAST Primer IFNB1 rv 5’-GGAATCCAAGCAAGTTGTAGCTC-3’ Sigma-Aldrich Designed by BLAST Software and Algorithms NanoDrop software N/A N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/; http://research-pub.gene.com/gmap Bamtools Barnett et al., 2011 https://github.com/pezmaster31/bamtools Samtools Li and Durbin, 2009 http://samtools.sourceforge.net (Continued on next page) e2 Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 ..

    Article Title: BCG Vaccination Protects against Experimental Viral Infection in Humans through the Induction of Cytokines Associated with Trained Immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Chemicals, Peptides, and Recombinant Proteins Bacille Calmette-Guérin Vaccin (BCG) Statens Serum Institute, Copenhagen 2016-04 Yellow fever vaccine Sanofi Pasteur Stamaril Lipopolysaccharide Sigma-Aldrich From E. coli serotype 055:B5, L2880 Mycobacterium tuberculosis Gift H27Rv Candida albicans Gift UC820 Staphylococcus aureus Clinical isolate Recombinant human Interleukin-1 b R&D Systems 201-LB-005 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 CD14+ beads MACS Miltenyi 130-050-201 iScript reverse transcriptase Bio-Rad 1708840 TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina Human IL-1b ELISA R&D Systems DY201 Human TNFa ELISA R&D Systems DY210 Human IL-17 ELISA R&D Systems D1700 Human IL-22 ELISA R&D Systems D2200 Human IL-6 ELISA Sanquin M1916 Human IL-8 ELISA Sanquin M1918 Human IFNg ELISA Sanquin M1933 Milliplex human TH17 panel Merck HTH17MAG-14K Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 (Continued on next page) Cell Host & Microbe 23, 89–100.e1–e5, January 10, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/mL) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E. coli Ligase New England Biolabs M0205L Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Deposited Data BCG in vivo trained monocytes ChIP-seq and RNA-seq data This paper GEO: GSE104149 Experimental Models: Organisms/Strains Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Oligonucleotides Primers for qPCR Table S1 Biolegio. .. Primers designed by BLAST Software Image Lab Bio-Rad CXP analysis software v2.2 Beckman Coulter GraphPad Prism Graphpad Software https://www.graphpad.com MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber, 2010 http://bioconductor.org/packages/release/ bioc/html/DESeq.html Bwa Li and Durbin, 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011; Li et al., 2009 https://github.com/kundajelab/ phantompeakqualtools, http://samtools. sourceforge.net/, https://github.com/ pezmaster31/bamtools MACS2 Zhang et al., 2008 http://github.com/taoliu/MACS/ HOMER Heinz et al., 2010 http://homer.salk.edu/homer/motif/ DAVID Huang et al., 2009 https://david.ncifcrf.gov/

    SYBR Green Assay:

    Article Title: The Itaconate Pathway Is a Central Regulatory Node Linking Innate Immune Tolerance and Trained Immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies a-IFN-alpha/beta R1 antibody R&D Systems AF3039; RRID:AB_664107 IgG isotype control R&D Systems AB-108-C; RRID:AB_354267 Rabbit polyclonal anti-H3K27ac Diagenode pAb-196-050; RRID:AB_2637079 Rabbit polyclonal anti-H3K4me1 Diagenode pAb-037-050; RRID:AB_2561054 Rabbit polyclonal anti-H3K4me3 Diagenode pAb-003-050; RRID:AB_2616052 Chemicals, Peptides, and Recombinant Proteins Gentamycin Thermo Fisher Scientific 15750060 Lipopolysaccharide from E. coli serotype 055:B5 Sigma-Aldrich L2880 Pam3Cys EMC Microcollections L2000 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 CD14+ beads MACS Miltenyi 130-050-201 TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 b1,3-(D)glucan (b-glucan) Saeed et al., 2014 N/A Mono methyl-fumarate Sigma-Aldrich 651419-1G Dimethylitaconate Sigma-Aldrich 592498-25G 4-octyl itaconate Mills et al., 2018 IRG1 siRNA (mouse) Santa Cruz sc-146287 control siRNA (mouse) Santa Cruz sc-37007 siRNA Transfection Medium Santa Cruz sc-36868 siRNA Dilution Buffer Santa Cruz sc-29527 siRNA Transfection Reagent Santa Cruz sc-29528 Seahorse XF Base Medium Agilent Technologies 102353-100 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 Luminol Sigma-Aldrich A8511-5G Zymosan (from S. cerevisiae) Sigma-Aldrich Z4250-1G Critical Commercial Assays Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Lactate Fluorometric Assay Kit Biovision K607 iScript cDNA Synthesis Kit Bio-Rad 1708891 Succinate Colometric Assay kit Sigma-Aldrich MAK184 Glutamate Assay Kit Sigma-Aldrich MAK004 CytoTox 96 Non-Radioactive Cytotoxicity Assay Promega G1780 Rneasy Mini Kit QIAGEN 74106 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 (Continued on next page) Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Ribozero Gold Kit Illumina MRZG12324 Qubit RNA HS assay kit Ribozero Life Technologies Q32852 DNase I QIAGEN 79254 Sodium Acetate (3M) Life Technologies AM9740 iQ SYBR Green Supermix Bio-Rad 1708880 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 100 x SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/mL) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E. coli Ligase New England Biolabs M0205L Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Ribozero Gold Kit Illumina MRZG12324 Deposited Data Raw data files for ChIP sequencing Novakovic et al., 2016 GSE85245 Raw data files for RNA sequencing Novakovic et al., 2016 GSE85243 Raw data files for b-glucan and LPS SuperSeries data Novakovic et al., 2016 GSE85246 Experimental Models: Cell Lines Mouse: RAW264.7 cells ATCC TIB-71 Experimental Models: Organisms/Strains Human: 200FG cohort (Human Functional Genomics project) Li et al., 2016 http://www.humanfunctionalgenomics.org Human: LLDeep cohort Tigchelaar et al., 2015 Human: primary monocytes from healthy volunteers Sanquin Blood Bank Oligonucleotides Primer HPRT fw 5’-CCTGGCGTCGTGATTAGTGAT-3’ Sigma-Aldrich Designed by BLAST Primer HPRT rv 5’-AGACGTTCAGTCCTGTCCATAA-3’ Sigma-Aldrich Designed by BLAST Primer IRG1 fw 5’-GTTCCTGGGAACCACTACG-3’ Lachmandas et al., 2016 Primer IRG1 rv 5’-GATGTCTGGCTGACCCCAAA-3’ Lachmandas et al., 2016 Primer IFNB1 fw 5’-ATGACCAACAAGTGTCTCCTCC-3’ Sigma-Aldrich Designed by BLAST Primer IFNB1 rv 5’-GGAATCCAAGCAAGTTGTAGCTC-3’ Sigma-Aldrich Designed by BLAST Software and Algorithms NanoDrop software N/A N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/; http://research-pub.gene.com/gmap Bamtools Barnett et al., 2011 https://github.com/pezmaster31/bamtools Samtools Li and Durbin, 2009 http://samtools.sourceforge.net (Continued on next page) e2 Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 ..

    Article Title: Metabolic Induction of Trained Immunity through the Mevalonate Pathway.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies human IGF1-R antibody R&D systems MAB391-100 IgG1 control antibody R&D systems MAB002 FITC-anti-CD16 Becton Dickinson Clone Leu11a, 555406 PE-anti-CD14 Becton Dickinson 555398 PC7-anti-CD45 Beckman Coulter IM3548 APC-anti-IGF1R Life Technologies 17-8849-42 Rabbit anti phospho-p70 S6K antibody Cell Signaling Monoclonal (Thr389, 108D2), 9234S Rabbit anti phosho-4EBP1 antibody Cell Signaling Polyclonal, T37/46, 2855S Rabbit anti phospho-mTOR antibody Cell Signaling Monoclonal Ser2448, 5536S Rabbit anti p70-S6K antibody Cell Signaling 9202L Rabbit anti 4EBP1 antibody Cell Signaling Polyclonal, 9452S Rabbit anti mTOR antibody Cell Signaling 2972S Rabbit anti Phospho-Akt antibody Cell Signaling Monoclonal (S473), 4060S Rabbit anti Akt antibody Cell Signaling Polyclonal, 9272S Rabbit anti Actin antibody Sigma-Aldrich A2066 Polyclonal Swine-anti-rabbit HRP antibody Dako P021702 Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Rabbit polyclonal anti-H3K4me1 Diagenode pab-037-050 Experimental Models: Organisms/Strains Mouse: wild type C57BL/6 N/A Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Chemicals, Peptides and Recombinant Proteins Bacille-Calmette Guérin Vaccin Statens Serum Institute, Copenhagen Denmark 2016-04 IGF1 R&D systems 291-G1-01M Lipopolysaccharide Sigma-Aldrich From E.coli serotype 055:B5, L2880 Pam3Cys EMC Microcollections L2000 Poly I:C Invivogen tlrl-pic-5 Macrophage-activating lipopeptide-2 Sigma-Aldrich E1036 Phytohemagglutinin Sigma-Aldrich 11249738001 Fluvastatin sodium hydrate Sigma-Aldrich SML0038 (R)-Mevalonic acid lithium salt Sigma-Aldrich 50838 Zaragozic acid SantaCruz Biotechnology CAS 142561-96-4, sc-391058 6-fluoromevalonate Sigma-Aldrich F2929 2-deoxy-D-glucose Sigma-Aldrich D6134 Rapamycin Sigma-Aldrich R-5000 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Picropodophyllin Santa Cruz 477-47-4, SC-204008 LXR-inhibitor Axon Medchem GSK2033 (Continued on next page) Cell 172, 135–146.e1–e6, January 11, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER PPARd-inhibitor Tocris GSK3787 Dimethyl sulfoxide (DMSO) Instruchemie WAK-DMSO-10 Mouse granulocyte-macrophage colonystimulating factor (GM-CSF) PeproTech 315-03 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Density gradient cell separation medium Histopaque 1083 Sigma-Aldrich 10831 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 SuperSignal West Femto Substrate Thermo Fisher Scientific 34096 4-15% gel Bio-Rad 456-1086 Nitrocellulose membrane Bio-Rad 1620145 CD14+ beads MACS Miltenyi 130-050-201 ELK, skimmed milk Campina NA TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina N/A Human IL-1b ELISA R&D systems DY201 Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Mouse TNFa ELISA Meso Scale Discovery RAB0477 Mouse IL-6 ELISA Meso Scale Discovery RAB0309 Lactate Fluorometric Assay Kit Biovision K607 Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/ml) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E.Coli Ligase New England Biolabs M0205L (Continued on next page) e2 Cell 172, 135–146.e1–e6, January 11, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Software and Algorithms Image Lab Biorad N/A CXP analysis software v2.2 Beckman Coulter N/A NanoDrop software N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bowtie 1 Langmead et al., 2009 http://bowtie-bio.sourceforge.net/index.shtml MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber 2010 http://bioconductor.org/packages/ release/bioc/html/DESeq.html Escher King et al., 2015 Bwa Li and Durbin 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011, Li et al., 2009 https://code.google.com/archive/p/ phantompeakqualtools/ http://samtools.sourceforge.net/ https://github.com/pezmaster31/bamtools MACS2 Zhang et al., 2008 https://github.com/taoliu/MACS/ Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/ GSNAP Wu and Nacu, 2010 http://research-pub.gene.com/gmap/ Caret https://cran.r-project.org/web/packages/caret/ index.html HOMER Heinz et al., 2010 http://homer.ucsd.edu/homer/motif/ DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ Deposited Data Mevalonate trained macrophage ChIP-seq and RNA-seq data This paper GEO: GSE104227 HIDS patients ChIP-seq and RNA-seq data This paper GEO: GSE104282 Oligonucleotides Primers for qPCR Table S4 N/A Primers for ChIP-qPCR Table S5 N/A

    Polymerase Chain Reaction:

    Article Title: The Itaconate Pathway Is a Central Regulatory Node Linking Innate Immune Tolerance and Trained Immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies a-IFN-alpha/beta R1 antibody R&D Systems AF3039; RRID:AB_664107 IgG isotype control R&D Systems AB-108-C; RRID:AB_354267 Rabbit polyclonal anti-H3K27ac Diagenode pAb-196-050; RRID:AB_2637079 Rabbit polyclonal anti-H3K4me1 Diagenode pAb-037-050; RRID:AB_2561054 Rabbit polyclonal anti-H3K4me3 Diagenode pAb-003-050; RRID:AB_2616052 Chemicals, Peptides, and Recombinant Proteins Gentamycin Thermo Fisher Scientific 15750060 Lipopolysaccharide from E. coli serotype 055:B5 Sigma-Aldrich L2880 Pam3Cys EMC Microcollections L2000 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 CD14+ beads MACS Miltenyi 130-050-201 TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 b1,3-(D)glucan (b-glucan) Saeed et al., 2014 N/A Mono methyl-fumarate Sigma-Aldrich 651419-1G Dimethylitaconate Sigma-Aldrich 592498-25G 4-octyl itaconate Mills et al., 2018 IRG1 siRNA (mouse) Santa Cruz sc-146287 control siRNA (mouse) Santa Cruz sc-37007 siRNA Transfection Medium Santa Cruz sc-36868 siRNA Dilution Buffer Santa Cruz sc-29527 siRNA Transfection Reagent Santa Cruz sc-29528 Seahorse XF Base Medium Agilent Technologies 102353-100 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 Luminol Sigma-Aldrich A8511-5G Zymosan (from S. cerevisiae) Sigma-Aldrich Z4250-1G Critical Commercial Assays Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Lactate Fluorometric Assay Kit Biovision K607 iScript cDNA Synthesis Kit Bio-Rad 1708891 Succinate Colometric Assay kit Sigma-Aldrich MAK184 Glutamate Assay Kit Sigma-Aldrich MAK004 CytoTox 96 Non-Radioactive Cytotoxicity Assay Promega G1780 Rneasy Mini Kit QIAGEN 74106 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 (Continued on next page) Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Ribozero Gold Kit Illumina MRZG12324 Qubit RNA HS assay kit Ribozero Life Technologies Q32852 DNase I QIAGEN 79254 Sodium Acetate (3M) Life Technologies AM9740 iQ SYBR Green Supermix Bio-Rad 1708880 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 100 x SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/mL) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E. coli Ligase New England Biolabs M0205L Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Ribozero Gold Kit Illumina MRZG12324 Deposited Data Raw data files for ChIP sequencing Novakovic et al., 2016 GSE85245 Raw data files for RNA sequencing Novakovic et al., 2016 GSE85243 Raw data files for b-glucan and LPS SuperSeries data Novakovic et al., 2016 GSE85246 Experimental Models: Cell Lines Mouse: RAW264.7 cells ATCC TIB-71 Experimental Models: Organisms/Strains Human: 200FG cohort (Human Functional Genomics project) Li et al., 2016 http://www.humanfunctionalgenomics.org Human: LLDeep cohort Tigchelaar et al., 2015 Human: primary monocytes from healthy volunteers Sanquin Blood Bank Oligonucleotides Primer HPRT fw 5’-CCTGGCGTCGTGATTAGTGAT-3’ Sigma-Aldrich Designed by BLAST Primer HPRT rv 5’-AGACGTTCAGTCCTGTCCATAA-3’ Sigma-Aldrich Designed by BLAST Primer IRG1 fw 5’-GTTCCTGGGAACCACTACG-3’ Lachmandas et al., 2016 Primer IRG1 rv 5’-GATGTCTGGCTGACCCCAAA-3’ Lachmandas et al., 2016 Primer IFNB1 fw 5’-ATGACCAACAAGTGTCTCCTCC-3’ Sigma-Aldrich Designed by BLAST Primer IFNB1 rv 5’-GGAATCCAAGCAAGTTGTAGCTC-3’ Sigma-Aldrich Designed by BLAST Software and Algorithms NanoDrop software N/A N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/; http://research-pub.gene.com/gmap Bamtools Barnett et al., 2011 https://github.com/pezmaster31/bamtools Samtools Li and Durbin, 2009 http://samtools.sourceforge.net (Continued on next page) e2 Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 ..

    Article Title: Metabolic Induction of Trained Immunity through the Mevalonate Pathway.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies human IGF1-R antibody R&D systems MAB391-100 IgG1 control antibody R&D systems MAB002 FITC-anti-CD16 Becton Dickinson Clone Leu11a, 555406 PE-anti-CD14 Becton Dickinson 555398 PC7-anti-CD45 Beckman Coulter IM3548 APC-anti-IGF1R Life Technologies 17-8849-42 Rabbit anti phospho-p70 S6K antibody Cell Signaling Monoclonal (Thr389, 108D2), 9234S Rabbit anti phosho-4EBP1 antibody Cell Signaling Polyclonal, T37/46, 2855S Rabbit anti phospho-mTOR antibody Cell Signaling Monoclonal Ser2448, 5536S Rabbit anti p70-S6K antibody Cell Signaling 9202L Rabbit anti 4EBP1 antibody Cell Signaling Polyclonal, 9452S Rabbit anti mTOR antibody Cell Signaling 2972S Rabbit anti Phospho-Akt antibody Cell Signaling Monoclonal (S473), 4060S Rabbit anti Akt antibody Cell Signaling Polyclonal, 9272S Rabbit anti Actin antibody Sigma-Aldrich A2066 Polyclonal Swine-anti-rabbit HRP antibody Dako P021702 Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Rabbit polyclonal anti-H3K4me1 Diagenode pab-037-050 Experimental Models: Organisms/Strains Mouse: wild type C57BL/6 N/A Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Chemicals, Peptides and Recombinant Proteins Bacille-Calmette Guérin Vaccin Statens Serum Institute, Copenhagen Denmark 2016-04 IGF1 R&D systems 291-G1-01M Lipopolysaccharide Sigma-Aldrich From E.coli serotype 055:B5, L2880 Pam3Cys EMC Microcollections L2000 Poly I:C Invivogen tlrl-pic-5 Macrophage-activating lipopeptide-2 Sigma-Aldrich E1036 Phytohemagglutinin Sigma-Aldrich 11249738001 Fluvastatin sodium hydrate Sigma-Aldrich SML0038 (R)-Mevalonic acid lithium salt Sigma-Aldrich 50838 Zaragozic acid SantaCruz Biotechnology CAS 142561-96-4, sc-391058 6-fluoromevalonate Sigma-Aldrich F2929 2-deoxy-D-glucose Sigma-Aldrich D6134 Rapamycin Sigma-Aldrich R-5000 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Picropodophyllin Santa Cruz 477-47-4, SC-204008 LXR-inhibitor Axon Medchem GSK2033 (Continued on next page) Cell 172, 135–146.e1–e6, January 11, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER PPARd-inhibitor Tocris GSK3787 Dimethyl sulfoxide (DMSO) Instruchemie WAK-DMSO-10 Mouse granulocyte-macrophage colonystimulating factor (GM-CSF) PeproTech 315-03 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Density gradient cell separation medium Histopaque 1083 Sigma-Aldrich 10831 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 SuperSignal West Femto Substrate Thermo Fisher Scientific 34096 4-15% gel Bio-Rad 456-1086 Nitrocellulose membrane Bio-Rad 1620145 CD14+ beads MACS Miltenyi 130-050-201 ELK, skimmed milk Campina NA TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina N/A Human IL-1b ELISA R&D systems DY201 Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Mouse TNFa ELISA Meso Scale Discovery RAB0477 Mouse IL-6 ELISA Meso Scale Discovery RAB0309 Lactate Fluorometric Assay Kit Biovision K607 Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/ml) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E.Coli Ligase New England Biolabs M0205L (Continued on next page) e2 Cell 172, 135–146.e1–e6, January 11, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Software and Algorithms Image Lab Biorad N/A CXP analysis software v2.2 Beckman Coulter N/A NanoDrop software N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bowtie 1 Langmead et al., 2009 http://bowtie-bio.sourceforge.net/index.shtml MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber 2010 http://bioconductor.org/packages/ release/bioc/html/DESeq.html Escher King et al., 2015 Bwa Li and Durbin 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011, Li et al., 2009 https://code.google.com/archive/p/ phantompeakqualtools/ http://samtools.sourceforge.net/ https://github.com/pezmaster31/bamtools MACS2 Zhang et al., 2008 https://github.com/taoliu/MACS/ Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/ GSNAP Wu and Nacu, 2010 http://research-pub.gene.com/gmap/ Caret https://cran.r-project.org/web/packages/caret/ index.html HOMER Heinz et al., 2010 http://homer.ucsd.edu/homer/motif/ DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ Deposited Data Mevalonate trained macrophage ChIP-seq and RNA-seq data This paper GEO: GSE104227 HIDS patients ChIP-seq and RNA-seq data This paper GEO: GSE104282 Oligonucleotides Primers for qPCR Table S4 N/A Primers for ChIP-qPCR Table S5 N/A

    Staining:

    Article Title: The Itaconate Pathway Is a Central Regulatory Node Linking Innate Immune Tolerance and Trained Immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies a-IFN-alpha/beta R1 antibody R&D Systems AF3039; RRID:AB_664107 IgG isotype control R&D Systems AB-108-C; RRID:AB_354267 Rabbit polyclonal anti-H3K27ac Diagenode pAb-196-050; RRID:AB_2637079 Rabbit polyclonal anti-H3K4me1 Diagenode pAb-037-050; RRID:AB_2561054 Rabbit polyclonal anti-H3K4me3 Diagenode pAb-003-050; RRID:AB_2616052 Chemicals, Peptides, and Recombinant Proteins Gentamycin Thermo Fisher Scientific 15750060 Lipopolysaccharide from E. coli serotype 055:B5 Sigma-Aldrich L2880 Pam3Cys EMC Microcollections L2000 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 CD14+ beads MACS Miltenyi 130-050-201 TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 b1,3-(D)glucan (b-glucan) Saeed et al., 2014 N/A Mono methyl-fumarate Sigma-Aldrich 651419-1G Dimethylitaconate Sigma-Aldrich 592498-25G 4-octyl itaconate Mills et al., 2018 IRG1 siRNA (mouse) Santa Cruz sc-146287 control siRNA (mouse) Santa Cruz sc-37007 siRNA Transfection Medium Santa Cruz sc-36868 siRNA Dilution Buffer Santa Cruz sc-29527 siRNA Transfection Reagent Santa Cruz sc-29528 Seahorse XF Base Medium Agilent Technologies 102353-100 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 Luminol Sigma-Aldrich A8511-5G Zymosan (from S. cerevisiae) Sigma-Aldrich Z4250-1G Critical Commercial Assays Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Lactate Fluorometric Assay Kit Biovision K607 iScript cDNA Synthesis Kit Bio-Rad 1708891 Succinate Colometric Assay kit Sigma-Aldrich MAK184 Glutamate Assay Kit Sigma-Aldrich MAK004 CytoTox 96 Non-Radioactive Cytotoxicity Assay Promega G1780 Rneasy Mini Kit QIAGEN 74106 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 (Continued on next page) Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Ribozero Gold Kit Illumina MRZG12324 Qubit RNA HS assay kit Ribozero Life Technologies Q32852 DNase I QIAGEN 79254 Sodium Acetate (3M) Life Technologies AM9740 iQ SYBR Green Supermix Bio-Rad 1708880 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 100 x SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/mL) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E. coli Ligase New England Biolabs M0205L Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Ribozero Gold Kit Illumina MRZG12324 Deposited Data Raw data files for ChIP sequencing Novakovic et al., 2016 GSE85245 Raw data files for RNA sequencing Novakovic et al., 2016 GSE85243 Raw data files for b-glucan and LPS SuperSeries data Novakovic et al., 2016 GSE85246 Experimental Models: Cell Lines Mouse: RAW264.7 cells ATCC TIB-71 Experimental Models: Organisms/Strains Human: 200FG cohort (Human Functional Genomics project) Li et al., 2016 http://www.humanfunctionalgenomics.org Human: LLDeep cohort Tigchelaar et al., 2015 Human: primary monocytes from healthy volunteers Sanquin Blood Bank Oligonucleotides Primer HPRT fw 5’-CCTGGCGTCGTGATTAGTGAT-3’ Sigma-Aldrich Designed by BLAST Primer HPRT rv 5’-AGACGTTCAGTCCTGTCCATAA-3’ Sigma-Aldrich Designed by BLAST Primer IRG1 fw 5’-GTTCCTGGGAACCACTACG-3’ Lachmandas et al., 2016 Primer IRG1 rv 5’-GATGTCTGGCTGACCCCAAA-3’ Lachmandas et al., 2016 Primer IFNB1 fw 5’-ATGACCAACAAGTGTCTCCTCC-3’ Sigma-Aldrich Designed by BLAST Primer IFNB1 rv 5’-GGAATCCAAGCAAGTTGTAGCTC-3’ Sigma-Aldrich Designed by BLAST Software and Algorithms NanoDrop software N/A N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/; http://research-pub.gene.com/gmap Bamtools Barnett et al., 2011 https://github.com/pezmaster31/bamtools Samtools Li and Durbin, 2009 http://samtools.sourceforge.net (Continued on next page) e2 Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 ..

    Article Title: Metabolic Induction of Trained Immunity through the Mevalonate Pathway.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies human IGF1-R antibody R&D systems MAB391-100 IgG1 control antibody R&D systems MAB002 FITC-anti-CD16 Becton Dickinson Clone Leu11a, 555406 PE-anti-CD14 Becton Dickinson 555398 PC7-anti-CD45 Beckman Coulter IM3548 APC-anti-IGF1R Life Technologies 17-8849-42 Rabbit anti phospho-p70 S6K antibody Cell Signaling Monoclonal (Thr389, 108D2), 9234S Rabbit anti phosho-4EBP1 antibody Cell Signaling Polyclonal, T37/46, 2855S Rabbit anti phospho-mTOR antibody Cell Signaling Monoclonal Ser2448, 5536S Rabbit anti p70-S6K antibody Cell Signaling 9202L Rabbit anti 4EBP1 antibody Cell Signaling Polyclonal, 9452S Rabbit anti mTOR antibody Cell Signaling 2972S Rabbit anti Phospho-Akt antibody Cell Signaling Monoclonal (S473), 4060S Rabbit anti Akt antibody Cell Signaling Polyclonal, 9272S Rabbit anti Actin antibody Sigma-Aldrich A2066 Polyclonal Swine-anti-rabbit HRP antibody Dako P021702 Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Rabbit polyclonal anti-H3K4me1 Diagenode pab-037-050 Experimental Models: Organisms/Strains Mouse: wild type C57BL/6 N/A Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Chemicals, Peptides and Recombinant Proteins Bacille-Calmette Guérin Vaccin Statens Serum Institute, Copenhagen Denmark 2016-04 IGF1 R&D systems 291-G1-01M Lipopolysaccharide Sigma-Aldrich From E.coli serotype 055:B5, L2880 Pam3Cys EMC Microcollections L2000 Poly I:C Invivogen tlrl-pic-5 Macrophage-activating lipopeptide-2 Sigma-Aldrich E1036 Phytohemagglutinin Sigma-Aldrich 11249738001 Fluvastatin sodium hydrate Sigma-Aldrich SML0038 (R)-Mevalonic acid lithium salt Sigma-Aldrich 50838 Zaragozic acid SantaCruz Biotechnology CAS 142561-96-4, sc-391058 6-fluoromevalonate Sigma-Aldrich F2929 2-deoxy-D-glucose Sigma-Aldrich D6134 Rapamycin Sigma-Aldrich R-5000 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Picropodophyllin Santa Cruz 477-47-4, SC-204008 LXR-inhibitor Axon Medchem GSK2033 (Continued on next page) Cell 172, 135–146.e1–e6, January 11, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER PPARd-inhibitor Tocris GSK3787 Dimethyl sulfoxide (DMSO) Instruchemie WAK-DMSO-10 Mouse granulocyte-macrophage colonystimulating factor (GM-CSF) PeproTech 315-03 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Density gradient cell separation medium Histopaque 1083 Sigma-Aldrich 10831 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 SuperSignal West Femto Substrate Thermo Fisher Scientific 34096 4-15% gel Bio-Rad 456-1086 Nitrocellulose membrane Bio-Rad 1620145 CD14+ beads MACS Miltenyi 130-050-201 ELK, skimmed milk Campina NA TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina N/A Human IL-1b ELISA R&D systems DY201 Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Mouse TNFa ELISA Meso Scale Discovery RAB0477 Mouse IL-6 ELISA Meso Scale Discovery RAB0309 Lactate Fluorometric Assay Kit Biovision K607 Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/ml) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E.Coli Ligase New England Biolabs M0205L (Continued on next page) e2 Cell 172, 135–146.e1–e6, January 11, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Software and Algorithms Image Lab Biorad N/A CXP analysis software v2.2 Beckman Coulter N/A NanoDrop software N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bowtie 1 Langmead et al., 2009 http://bowtie-bio.sourceforge.net/index.shtml MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber 2010 http://bioconductor.org/packages/ release/bioc/html/DESeq.html Escher King et al., 2015 Bwa Li and Durbin 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011, Li et al., 2009 https://code.google.com/archive/p/ phantompeakqualtools/ http://samtools.sourceforge.net/ https://github.com/pezmaster31/bamtools MACS2 Zhang et al., 2008 https://github.com/taoliu/MACS/ Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/ GSNAP Wu and Nacu, 2010 http://research-pub.gene.com/gmap/ Caret https://cran.r-project.org/web/packages/caret/ index.html HOMER Heinz et al., 2010 http://homer.ucsd.edu/homer/motif/ DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ Deposited Data Mevalonate trained macrophage ChIP-seq and RNA-seq data This paper GEO: GSE104227 HIDS patients ChIP-seq and RNA-seq data This paper GEO: GSE104282 Oligonucleotides Primers for qPCR Table S4 N/A Primers for ChIP-qPCR Table S5 N/A

    Random Hexamer:

    Article Title: The Itaconate Pathway Is a Central Regulatory Node Linking Innate Immune Tolerance and Trained Immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies a-IFN-alpha/beta R1 antibody R&D Systems AF3039; RRID:AB_664107 IgG isotype control R&D Systems AB-108-C; RRID:AB_354267 Rabbit polyclonal anti-H3K27ac Diagenode pAb-196-050; RRID:AB_2637079 Rabbit polyclonal anti-H3K4me1 Diagenode pAb-037-050; RRID:AB_2561054 Rabbit polyclonal anti-H3K4me3 Diagenode pAb-003-050; RRID:AB_2616052 Chemicals, Peptides, and Recombinant Proteins Gentamycin Thermo Fisher Scientific 15750060 Lipopolysaccharide from E. coli serotype 055:B5 Sigma-Aldrich L2880 Pam3Cys EMC Microcollections L2000 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 CD14+ beads MACS Miltenyi 130-050-201 TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 b1,3-(D)glucan (b-glucan) Saeed et al., 2014 N/A Mono methyl-fumarate Sigma-Aldrich 651419-1G Dimethylitaconate Sigma-Aldrich 592498-25G 4-octyl itaconate Mills et al., 2018 IRG1 siRNA (mouse) Santa Cruz sc-146287 control siRNA (mouse) Santa Cruz sc-37007 siRNA Transfection Medium Santa Cruz sc-36868 siRNA Dilution Buffer Santa Cruz sc-29527 siRNA Transfection Reagent Santa Cruz sc-29528 Seahorse XF Base Medium Agilent Technologies 102353-100 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 Luminol Sigma-Aldrich A8511-5G Zymosan (from S. cerevisiae) Sigma-Aldrich Z4250-1G Critical Commercial Assays Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Lactate Fluorometric Assay Kit Biovision K607 iScript cDNA Synthesis Kit Bio-Rad 1708891 Succinate Colometric Assay kit Sigma-Aldrich MAK184 Glutamate Assay Kit Sigma-Aldrich MAK004 CytoTox 96 Non-Radioactive Cytotoxicity Assay Promega G1780 Rneasy Mini Kit QIAGEN 74106 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 (Continued on next page) Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Ribozero Gold Kit Illumina MRZG12324 Qubit RNA HS assay kit Ribozero Life Technologies Q32852 DNase I QIAGEN 79254 Sodium Acetate (3M) Life Technologies AM9740 iQ SYBR Green Supermix Bio-Rad 1708880 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 100 x SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/mL) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E. coli Ligase New England Biolabs M0205L Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Ribozero Gold Kit Illumina MRZG12324 Deposited Data Raw data files for ChIP sequencing Novakovic et al., 2016 GSE85245 Raw data files for RNA sequencing Novakovic et al., 2016 GSE85243 Raw data files for b-glucan and LPS SuperSeries data Novakovic et al., 2016 GSE85246 Experimental Models: Cell Lines Mouse: RAW264.7 cells ATCC TIB-71 Experimental Models: Organisms/Strains Human: 200FG cohort (Human Functional Genomics project) Li et al., 2016 http://www.humanfunctionalgenomics.org Human: LLDeep cohort Tigchelaar et al., 2015 Human: primary monocytes from healthy volunteers Sanquin Blood Bank Oligonucleotides Primer HPRT fw 5’-CCTGGCGTCGTGATTAGTGAT-3’ Sigma-Aldrich Designed by BLAST Primer HPRT rv 5’-AGACGTTCAGTCCTGTCCATAA-3’ Sigma-Aldrich Designed by BLAST Primer IRG1 fw 5’-GTTCCTGGGAACCACTACG-3’ Lachmandas et al., 2016 Primer IRG1 rv 5’-GATGTCTGGCTGACCCCAAA-3’ Lachmandas et al., 2016 Primer IFNB1 fw 5’-ATGACCAACAAGTGTCTCCTCC-3’ Sigma-Aldrich Designed by BLAST Primer IFNB1 rv 5’-GGAATCCAAGCAAGTTGTAGCTC-3’ Sigma-Aldrich Designed by BLAST Software and Algorithms NanoDrop software N/A N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/; http://research-pub.gene.com/gmap Bamtools Barnett et al., 2011 https://github.com/pezmaster31/bamtools Samtools Li and Durbin, 2009 http://samtools.sourceforge.net (Continued on next page) e2 Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 ..

    Article Title: BCG Vaccination Protects against Experimental Viral Infection in Humans through the Induction of Cytokines Associated with Trained Immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Chemicals, Peptides, and Recombinant Proteins Bacille Calmette-Guérin Vaccin (BCG) Statens Serum Institute, Copenhagen 2016-04 Yellow fever vaccine Sanofi Pasteur Stamaril Lipopolysaccharide Sigma-Aldrich From E. coli serotype 055:B5, L2880 Mycobacterium tuberculosis Gift H27Rv Candida albicans Gift UC820 Staphylococcus aureus Clinical isolate Recombinant human Interleukin-1 b R&D Systems 201-LB-005 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 CD14+ beads MACS Miltenyi 130-050-201 iScript reverse transcriptase Bio-Rad 1708840 TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina Human IL-1b ELISA R&D Systems DY201 Human TNFa ELISA R&D Systems DY210 Human IL-17 ELISA R&D Systems D1700 Human IL-22 ELISA R&D Systems D2200 Human IL-6 ELISA Sanquin M1916 Human IL-8 ELISA Sanquin M1918 Human IFNg ELISA Sanquin M1933 Milliplex human TH17 panel Merck HTH17MAG-14K Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 (Continued on next page) Cell Host & Microbe 23, 89–100.e1–e5, January 10, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/mL) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E. coli Ligase New England Biolabs M0205L Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Deposited Data BCG in vivo trained monocytes ChIP-seq and RNA-seq data This paper GEO: GSE104149 Experimental Models: Organisms/Strains Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Oligonucleotides Primers for qPCR Table S1 Biolegio. .. Primers designed by BLAST Software Image Lab Bio-Rad CXP analysis software v2.2 Beckman Coulter GraphPad Prism Graphpad Software https://www.graphpad.com MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber, 2010 http://bioconductor.org/packages/release/ bioc/html/DESeq.html Bwa Li and Durbin, 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011; Li et al., 2009 https://github.com/kundajelab/ phantompeakqualtools, http://samtools. sourceforge.net/, https://github.com/ pezmaster31/bamtools MACS2 Zhang et al., 2008 http://github.com/taoliu/MACS/ HOMER Heinz et al., 2010 http://homer.salk.edu/homer/motif/ DAVID Huang et al., 2009 https://david.ncifcrf.gov/

    Article Title: Metabolic Induction of Trained Immunity through the Mevalonate Pathway.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies human IGF1-R antibody R&D systems MAB391-100 IgG1 control antibody R&D systems MAB002 FITC-anti-CD16 Becton Dickinson Clone Leu11a, 555406 PE-anti-CD14 Becton Dickinson 555398 PC7-anti-CD45 Beckman Coulter IM3548 APC-anti-IGF1R Life Technologies 17-8849-42 Rabbit anti phospho-p70 S6K antibody Cell Signaling Monoclonal (Thr389, 108D2), 9234S Rabbit anti phosho-4EBP1 antibody Cell Signaling Polyclonal, T37/46, 2855S Rabbit anti phospho-mTOR antibody Cell Signaling Monoclonal Ser2448, 5536S Rabbit anti p70-S6K antibody Cell Signaling 9202L Rabbit anti 4EBP1 antibody Cell Signaling Polyclonal, 9452S Rabbit anti mTOR antibody Cell Signaling 2972S Rabbit anti Phospho-Akt antibody Cell Signaling Monoclonal (S473), 4060S Rabbit anti Akt antibody Cell Signaling Polyclonal, 9272S Rabbit anti Actin antibody Sigma-Aldrich A2066 Polyclonal Swine-anti-rabbit HRP antibody Dako P021702 Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Rabbit polyclonal anti-H3K4me1 Diagenode pab-037-050 Experimental Models: Organisms/Strains Mouse: wild type C57BL/6 N/A Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Chemicals, Peptides and Recombinant Proteins Bacille-Calmette Guérin Vaccin Statens Serum Institute, Copenhagen Denmark 2016-04 IGF1 R&D systems 291-G1-01M Lipopolysaccharide Sigma-Aldrich From E.coli serotype 055:B5, L2880 Pam3Cys EMC Microcollections L2000 Poly I:C Invivogen tlrl-pic-5 Macrophage-activating lipopeptide-2 Sigma-Aldrich E1036 Phytohemagglutinin Sigma-Aldrich 11249738001 Fluvastatin sodium hydrate Sigma-Aldrich SML0038 (R)-Mevalonic acid lithium salt Sigma-Aldrich 50838 Zaragozic acid SantaCruz Biotechnology CAS 142561-96-4, sc-391058 6-fluoromevalonate Sigma-Aldrich F2929 2-deoxy-D-glucose Sigma-Aldrich D6134 Rapamycin Sigma-Aldrich R-5000 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Picropodophyllin Santa Cruz 477-47-4, SC-204008 LXR-inhibitor Axon Medchem GSK2033 (Continued on next page) Cell 172, 135–146.e1–e6, January 11, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER PPARd-inhibitor Tocris GSK3787 Dimethyl sulfoxide (DMSO) Instruchemie WAK-DMSO-10 Mouse granulocyte-macrophage colonystimulating factor (GM-CSF) PeproTech 315-03 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Density gradient cell separation medium Histopaque 1083 Sigma-Aldrich 10831 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 SuperSignal West Femto Substrate Thermo Fisher Scientific 34096 4-15% gel Bio-Rad 456-1086 Nitrocellulose membrane Bio-Rad 1620145 CD14+ beads MACS Miltenyi 130-050-201 ELK, skimmed milk Campina NA TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina N/A Human IL-1b ELISA R&D systems DY201 Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Mouse TNFa ELISA Meso Scale Discovery RAB0477 Mouse IL-6 ELISA Meso Scale Discovery RAB0309 Lactate Fluorometric Assay Kit Biovision K607 Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/ml) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E.Coli Ligase New England Biolabs M0205L (Continued on next page) e2 Cell 172, 135–146.e1–e6, January 11, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Software and Algorithms Image Lab Biorad N/A CXP analysis software v2.2 Beckman Coulter N/A NanoDrop software N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bowtie 1 Langmead et al., 2009 http://bowtie-bio.sourceforge.net/index.shtml MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber 2010 http://bioconductor.org/packages/ release/bioc/html/DESeq.html Escher King et al., 2015 Bwa Li and Durbin 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011, Li et al., 2009 https://code.google.com/archive/p/ phantompeakqualtools/ http://samtools.sourceforge.net/ https://github.com/pezmaster31/bamtools MACS2 Zhang et al., 2008 https://github.com/taoliu/MACS/ Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/ GSNAP Wu and Nacu, 2010 http://research-pub.gene.com/gmap/ Caret https://cran.r-project.org/web/packages/caret/ index.html HOMER Heinz et al., 2010 http://homer.ucsd.edu/homer/motif/ DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ Deposited Data Mevalonate trained macrophage ChIP-seq and RNA-seq data This paper GEO: GSE104227 HIDS patients ChIP-seq and RNA-seq data This paper GEO: GSE104282 Oligonucleotides Primers for qPCR Table S4 N/A Primers for ChIP-qPCR Table S5 N/A

    Chromatin Immunoprecipitation:

    Article Title: The Itaconate Pathway Is a Central Regulatory Node Linking Innate Immune Tolerance and Trained Immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies a-IFN-alpha/beta R1 antibody R&D Systems AF3039; RRID:AB_664107 IgG isotype control R&D Systems AB-108-C; RRID:AB_354267 Rabbit polyclonal anti-H3K27ac Diagenode pAb-196-050; RRID:AB_2637079 Rabbit polyclonal anti-H3K4me1 Diagenode pAb-037-050; RRID:AB_2561054 Rabbit polyclonal anti-H3K4me3 Diagenode pAb-003-050; RRID:AB_2616052 Chemicals, Peptides, and Recombinant Proteins Gentamycin Thermo Fisher Scientific 15750060 Lipopolysaccharide from E. coli serotype 055:B5 Sigma-Aldrich L2880 Pam3Cys EMC Microcollections L2000 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 CD14+ beads MACS Miltenyi 130-050-201 TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 b1,3-(D)glucan (b-glucan) Saeed et al., 2014 N/A Mono methyl-fumarate Sigma-Aldrich 651419-1G Dimethylitaconate Sigma-Aldrich 592498-25G 4-octyl itaconate Mills et al., 2018 IRG1 siRNA (mouse) Santa Cruz sc-146287 control siRNA (mouse) Santa Cruz sc-37007 siRNA Transfection Medium Santa Cruz sc-36868 siRNA Dilution Buffer Santa Cruz sc-29527 siRNA Transfection Reagent Santa Cruz sc-29528 Seahorse XF Base Medium Agilent Technologies 102353-100 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 Luminol Sigma-Aldrich A8511-5G Zymosan (from S. cerevisiae) Sigma-Aldrich Z4250-1G Critical Commercial Assays Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Lactate Fluorometric Assay Kit Biovision K607 iScript cDNA Synthesis Kit Bio-Rad 1708891 Succinate Colometric Assay kit Sigma-Aldrich MAK184 Glutamate Assay Kit Sigma-Aldrich MAK004 CytoTox 96 Non-Radioactive Cytotoxicity Assay Promega G1780 Rneasy Mini Kit QIAGEN 74106 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 (Continued on next page) Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Ribozero Gold Kit Illumina MRZG12324 Qubit RNA HS assay kit Ribozero Life Technologies Q32852 DNase I QIAGEN 79254 Sodium Acetate (3M) Life Technologies AM9740 iQ SYBR Green Supermix Bio-Rad 1708880 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 100 x SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/mL) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E. coli Ligase New England Biolabs M0205L Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Ribozero Gold Kit Illumina MRZG12324 Deposited Data Raw data files for ChIP sequencing Novakovic et al., 2016 GSE85245 Raw data files for RNA sequencing Novakovic et al., 2016 GSE85243 Raw data files for b-glucan and LPS SuperSeries data Novakovic et al., 2016 GSE85246 Experimental Models: Cell Lines Mouse: RAW264.7 cells ATCC TIB-71 Experimental Models: Organisms/Strains Human: 200FG cohort (Human Functional Genomics project) Li et al., 2016 http://www.humanfunctionalgenomics.org Human: LLDeep cohort Tigchelaar et al., 2015 Human: primary monocytes from healthy volunteers Sanquin Blood Bank Oligonucleotides Primer HPRT fw 5’-CCTGGCGTCGTGATTAGTGAT-3’ Sigma-Aldrich Designed by BLAST Primer HPRT rv 5’-AGACGTTCAGTCCTGTCCATAA-3’ Sigma-Aldrich Designed by BLAST Primer IRG1 fw 5’-GTTCCTGGGAACCACTACG-3’ Lachmandas et al., 2016 Primer IRG1 rv 5’-GATGTCTGGCTGACCCCAAA-3’ Lachmandas et al., 2016 Primer IFNB1 fw 5’-ATGACCAACAAGTGTCTCCTCC-3’ Sigma-Aldrich Designed by BLAST Primer IFNB1 rv 5’-GGAATCCAAGCAAGTTGTAGCTC-3’ Sigma-Aldrich Designed by BLAST Software and Algorithms NanoDrop software N/A N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/; http://research-pub.gene.com/gmap Bamtools Barnett et al., 2011 https://github.com/pezmaster31/bamtools Samtools Li and Durbin, 2009 http://samtools.sourceforge.net (Continued on next page) e2 Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 ..

    Article Title: BCG Vaccination Protects against Experimental Viral Infection in Humans through the Induction of Cytokines Associated with Trained Immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Chemicals, Peptides, and Recombinant Proteins Bacille Calmette-Guérin Vaccin (BCG) Statens Serum Institute, Copenhagen 2016-04 Yellow fever vaccine Sanofi Pasteur Stamaril Lipopolysaccharide Sigma-Aldrich From E. coli serotype 055:B5, L2880 Mycobacterium tuberculosis Gift H27Rv Candida albicans Gift UC820 Staphylococcus aureus Clinical isolate Recombinant human Interleukin-1 b R&D Systems 201-LB-005 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 CD14+ beads MACS Miltenyi 130-050-201 iScript reverse transcriptase Bio-Rad 1708840 TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina Human IL-1b ELISA R&D Systems DY201 Human TNFa ELISA R&D Systems DY210 Human IL-17 ELISA R&D Systems D1700 Human IL-22 ELISA R&D Systems D2200 Human IL-6 ELISA Sanquin M1916 Human IL-8 ELISA Sanquin M1918 Human IFNg ELISA Sanquin M1933 Milliplex human TH17 panel Merck HTH17MAG-14K Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 (Continued on next page) Cell Host & Microbe 23, 89–100.e1–e5, January 10, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/mL) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E. coli Ligase New England Biolabs M0205L Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Deposited Data BCG in vivo trained monocytes ChIP-seq and RNA-seq data This paper GEO: GSE104149 Experimental Models: Organisms/Strains Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Oligonucleotides Primers for qPCR Table S1 Biolegio. .. Primers designed by BLAST Software Image Lab Bio-Rad CXP analysis software v2.2 Beckman Coulter GraphPad Prism Graphpad Software https://www.graphpad.com MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber, 2010 http://bioconductor.org/packages/release/ bioc/html/DESeq.html Bwa Li and Durbin, 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011; Li et al., 2009 https://github.com/kundajelab/ phantompeakqualtools, http://samtools. sourceforge.net/, https://github.com/ pezmaster31/bamtools MACS2 Zhang et al., 2008 http://github.com/taoliu/MACS/ HOMER Heinz et al., 2010 http://homer.salk.edu/homer/motif/ DAVID Huang et al., 2009 https://david.ncifcrf.gov/

    Sequencing:

    Article Title: The Itaconate Pathway Is a Central Regulatory Node Linking Innate Immune Tolerance and Trained Immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies a-IFN-alpha/beta R1 antibody R&D Systems AF3039; RRID:AB_664107 IgG isotype control R&D Systems AB-108-C; RRID:AB_354267 Rabbit polyclonal anti-H3K27ac Diagenode pAb-196-050; RRID:AB_2637079 Rabbit polyclonal anti-H3K4me1 Diagenode pAb-037-050; RRID:AB_2561054 Rabbit polyclonal anti-H3K4me3 Diagenode pAb-003-050; RRID:AB_2616052 Chemicals, Peptides, and Recombinant Proteins Gentamycin Thermo Fisher Scientific 15750060 Lipopolysaccharide from E. coli serotype 055:B5 Sigma-Aldrich L2880 Pam3Cys EMC Microcollections L2000 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 CD14+ beads MACS Miltenyi 130-050-201 TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 b1,3-(D)glucan (b-glucan) Saeed et al., 2014 N/A Mono methyl-fumarate Sigma-Aldrich 651419-1G Dimethylitaconate Sigma-Aldrich 592498-25G 4-octyl itaconate Mills et al., 2018 IRG1 siRNA (mouse) Santa Cruz sc-146287 control siRNA (mouse) Santa Cruz sc-37007 siRNA Transfection Medium Santa Cruz sc-36868 siRNA Dilution Buffer Santa Cruz sc-29527 siRNA Transfection Reagent Santa Cruz sc-29528 Seahorse XF Base Medium Agilent Technologies 102353-100 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 Luminol Sigma-Aldrich A8511-5G Zymosan (from S. cerevisiae) Sigma-Aldrich Z4250-1G Critical Commercial Assays Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Lactate Fluorometric Assay Kit Biovision K607 iScript cDNA Synthesis Kit Bio-Rad 1708891 Succinate Colometric Assay kit Sigma-Aldrich MAK184 Glutamate Assay Kit Sigma-Aldrich MAK004 CytoTox 96 Non-Radioactive Cytotoxicity Assay Promega G1780 Rneasy Mini Kit QIAGEN 74106 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 (Continued on next page) Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Ribozero Gold Kit Illumina MRZG12324 Qubit RNA HS assay kit Ribozero Life Technologies Q32852 DNase I QIAGEN 79254 Sodium Acetate (3M) Life Technologies AM9740 iQ SYBR Green Supermix Bio-Rad 1708880 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 100 x SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/mL) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E. coli Ligase New England Biolabs M0205L Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Ribozero Gold Kit Illumina MRZG12324 Deposited Data Raw data files for ChIP sequencing Novakovic et al., 2016 GSE85245 Raw data files for RNA sequencing Novakovic et al., 2016 GSE85243 Raw data files for b-glucan and LPS SuperSeries data Novakovic et al., 2016 GSE85246 Experimental Models: Cell Lines Mouse: RAW264.7 cells ATCC TIB-71 Experimental Models: Organisms/Strains Human: 200FG cohort (Human Functional Genomics project) Li et al., 2016 http://www.humanfunctionalgenomics.org Human: LLDeep cohort Tigchelaar et al., 2015 Human: primary monocytes from healthy volunteers Sanquin Blood Bank Oligonucleotides Primer HPRT fw 5’-CCTGGCGTCGTGATTAGTGAT-3’ Sigma-Aldrich Designed by BLAST Primer HPRT rv 5’-AGACGTTCAGTCCTGTCCATAA-3’ Sigma-Aldrich Designed by BLAST Primer IRG1 fw 5’-GTTCCTGGGAACCACTACG-3’ Lachmandas et al., 2016 Primer IRG1 rv 5’-GATGTCTGGCTGACCCCAAA-3’ Lachmandas et al., 2016 Primer IFNB1 fw 5’-ATGACCAACAAGTGTCTCCTCC-3’ Sigma-Aldrich Designed by BLAST Primer IFNB1 rv 5’-GGAATCCAAGCAAGTTGTAGCTC-3’ Sigma-Aldrich Designed by BLAST Software and Algorithms NanoDrop software N/A N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/; http://research-pub.gene.com/gmap Bamtools Barnett et al., 2011 https://github.com/pezmaster31/bamtools Samtools Li and Durbin, 2009 http://samtools.sourceforge.net (Continued on next page) e2 Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 ..

    RNA Sequencing:

    Article Title: The Itaconate Pathway Is a Central Regulatory Node Linking Innate Immune Tolerance and Trained Immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies a-IFN-alpha/beta R1 antibody R&D Systems AF3039; RRID:AB_664107 IgG isotype control R&D Systems AB-108-C; RRID:AB_354267 Rabbit polyclonal anti-H3K27ac Diagenode pAb-196-050; RRID:AB_2637079 Rabbit polyclonal anti-H3K4me1 Diagenode pAb-037-050; RRID:AB_2561054 Rabbit polyclonal anti-H3K4me3 Diagenode pAb-003-050; RRID:AB_2616052 Chemicals, Peptides, and Recombinant Proteins Gentamycin Thermo Fisher Scientific 15750060 Lipopolysaccharide from E. coli serotype 055:B5 Sigma-Aldrich L2880 Pam3Cys EMC Microcollections L2000 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 CD14+ beads MACS Miltenyi 130-050-201 TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 b1,3-(D)glucan (b-glucan) Saeed et al., 2014 N/A Mono methyl-fumarate Sigma-Aldrich 651419-1G Dimethylitaconate Sigma-Aldrich 592498-25G 4-octyl itaconate Mills et al., 2018 IRG1 siRNA (mouse) Santa Cruz sc-146287 control siRNA (mouse) Santa Cruz sc-37007 siRNA Transfection Medium Santa Cruz sc-36868 siRNA Dilution Buffer Santa Cruz sc-29527 siRNA Transfection Reagent Santa Cruz sc-29528 Seahorse XF Base Medium Agilent Technologies 102353-100 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 Luminol Sigma-Aldrich A8511-5G Zymosan (from S. cerevisiae) Sigma-Aldrich Z4250-1G Critical Commercial Assays Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Lactate Fluorometric Assay Kit Biovision K607 iScript cDNA Synthesis Kit Bio-Rad 1708891 Succinate Colometric Assay kit Sigma-Aldrich MAK184 Glutamate Assay Kit Sigma-Aldrich MAK004 CytoTox 96 Non-Radioactive Cytotoxicity Assay Promega G1780 Rneasy Mini Kit QIAGEN 74106 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 (Continued on next page) Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Ribozero Gold Kit Illumina MRZG12324 Qubit RNA HS assay kit Ribozero Life Technologies Q32852 DNase I QIAGEN 79254 Sodium Acetate (3M) Life Technologies AM9740 iQ SYBR Green Supermix Bio-Rad 1708880 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 100 x SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/mL) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E. coli Ligase New England Biolabs M0205L Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Ribozero Gold Kit Illumina MRZG12324 Deposited Data Raw data files for ChIP sequencing Novakovic et al., 2016 GSE85245 Raw data files for RNA sequencing Novakovic et al., 2016 GSE85243 Raw data files for b-glucan and LPS SuperSeries data Novakovic et al., 2016 GSE85246 Experimental Models: Cell Lines Mouse: RAW264.7 cells ATCC TIB-71 Experimental Models: Organisms/Strains Human: 200FG cohort (Human Functional Genomics project) Li et al., 2016 http://www.humanfunctionalgenomics.org Human: LLDeep cohort Tigchelaar et al., 2015 Human: primary monocytes from healthy volunteers Sanquin Blood Bank Oligonucleotides Primer HPRT fw 5’-CCTGGCGTCGTGATTAGTGAT-3’ Sigma-Aldrich Designed by BLAST Primer HPRT rv 5’-AGACGTTCAGTCCTGTCCATAA-3’ Sigma-Aldrich Designed by BLAST Primer IRG1 fw 5’-GTTCCTGGGAACCACTACG-3’ Lachmandas et al., 2016 Primer IRG1 rv 5’-GATGTCTGGCTGACCCCAAA-3’ Lachmandas et al., 2016 Primer IFNB1 fw 5’-ATGACCAACAAGTGTCTCCTCC-3’ Sigma-Aldrich Designed by BLAST Primer IFNB1 rv 5’-GGAATCCAAGCAAGTTGTAGCTC-3’ Sigma-Aldrich Designed by BLAST Software and Algorithms NanoDrop software N/A N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/; http://research-pub.gene.com/gmap Bamtools Barnett et al., 2011 https://github.com/pezmaster31/bamtools Samtools Li and Durbin, 2009 http://samtools.sourceforge.net (Continued on next page) e2 Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 ..

    Article Title: BCG Vaccination Protects against Experimental Viral Infection in Humans through the Induction of Cytokines Associated with Trained Immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Chemicals, Peptides, and Recombinant Proteins Bacille Calmette-Guérin Vaccin (BCG) Statens Serum Institute, Copenhagen 2016-04 Yellow fever vaccine Sanofi Pasteur Stamaril Lipopolysaccharide Sigma-Aldrich From E. coli serotype 055:B5, L2880 Mycobacterium tuberculosis Gift H27Rv Candida albicans Gift UC820 Staphylococcus aureus Clinical isolate Recombinant human Interleukin-1 b R&D Systems 201-LB-005 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 CD14+ beads MACS Miltenyi 130-050-201 iScript reverse transcriptase Bio-Rad 1708840 TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina Human IL-1b ELISA R&D Systems DY201 Human TNFa ELISA R&D Systems DY210 Human IL-17 ELISA R&D Systems D1700 Human IL-22 ELISA R&D Systems D2200 Human IL-6 ELISA Sanquin M1916 Human IL-8 ELISA Sanquin M1918 Human IFNg ELISA Sanquin M1933 Milliplex human TH17 panel Merck HTH17MAG-14K Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 (Continued on next page) Cell Host & Microbe 23, 89–100.e1–e5, January 10, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/mL) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E. coli Ligase New England Biolabs M0205L Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Deposited Data BCG in vivo trained monocytes ChIP-seq and RNA-seq data This paper GEO: GSE104149 Experimental Models: Organisms/Strains Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Oligonucleotides Primers for qPCR Table S1 Biolegio. .. Primers designed by BLAST Software Image Lab Bio-Rad CXP analysis software v2.2 Beckman Coulter GraphPad Prism Graphpad Software https://www.graphpad.com MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber, 2010 http://bioconductor.org/packages/release/ bioc/html/DESeq.html Bwa Li and Durbin, 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011; Li et al., 2009 https://github.com/kundajelab/ phantompeakqualtools, http://samtools. sourceforge.net/, https://github.com/ pezmaster31/bamtools MACS2 Zhang et al., 2008 http://github.com/taoliu/MACS/ HOMER Heinz et al., 2010 http://homer.salk.edu/homer/motif/ DAVID Huang et al., 2009 https://david.ncifcrf.gov/

    Functional Assay:

    Article Title: The Itaconate Pathway Is a Central Regulatory Node Linking Innate Immune Tolerance and Trained Immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies a-IFN-alpha/beta R1 antibody R&D Systems AF3039; RRID:AB_664107 IgG isotype control R&D Systems AB-108-C; RRID:AB_354267 Rabbit polyclonal anti-H3K27ac Diagenode pAb-196-050; RRID:AB_2637079 Rabbit polyclonal anti-H3K4me1 Diagenode pAb-037-050; RRID:AB_2561054 Rabbit polyclonal anti-H3K4me3 Diagenode pAb-003-050; RRID:AB_2616052 Chemicals, Peptides, and Recombinant Proteins Gentamycin Thermo Fisher Scientific 15750060 Lipopolysaccharide from E. coli serotype 055:B5 Sigma-Aldrich L2880 Pam3Cys EMC Microcollections L2000 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 CD14+ beads MACS Miltenyi 130-050-201 TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 b1,3-(D)glucan (b-glucan) Saeed et al., 2014 N/A Mono methyl-fumarate Sigma-Aldrich 651419-1G Dimethylitaconate Sigma-Aldrich 592498-25G 4-octyl itaconate Mills et al., 2018 IRG1 siRNA (mouse) Santa Cruz sc-146287 control siRNA (mouse) Santa Cruz sc-37007 siRNA Transfection Medium Santa Cruz sc-36868 siRNA Dilution Buffer Santa Cruz sc-29527 siRNA Transfection Reagent Santa Cruz sc-29528 Seahorse XF Base Medium Agilent Technologies 102353-100 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 Luminol Sigma-Aldrich A8511-5G Zymosan (from S. cerevisiae) Sigma-Aldrich Z4250-1G Critical Commercial Assays Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Lactate Fluorometric Assay Kit Biovision K607 iScript cDNA Synthesis Kit Bio-Rad 1708891 Succinate Colometric Assay kit Sigma-Aldrich MAK184 Glutamate Assay Kit Sigma-Aldrich MAK004 CytoTox 96 Non-Radioactive Cytotoxicity Assay Promega G1780 Rneasy Mini Kit QIAGEN 74106 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 (Continued on next page) Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Ribozero Gold Kit Illumina MRZG12324 Qubit RNA HS assay kit Ribozero Life Technologies Q32852 DNase I QIAGEN 79254 Sodium Acetate (3M) Life Technologies AM9740 iQ SYBR Green Supermix Bio-Rad 1708880 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 100 x SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/mL) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E. coli Ligase New England Biolabs M0205L Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Ribozero Gold Kit Illumina MRZG12324 Deposited Data Raw data files for ChIP sequencing Novakovic et al., 2016 GSE85245 Raw data files for RNA sequencing Novakovic et al., 2016 GSE85243 Raw data files for b-glucan and LPS SuperSeries data Novakovic et al., 2016 GSE85246 Experimental Models: Cell Lines Mouse: RAW264.7 cells ATCC TIB-71 Experimental Models: Organisms/Strains Human: 200FG cohort (Human Functional Genomics project) Li et al., 2016 http://www.humanfunctionalgenomics.org Human: LLDeep cohort Tigchelaar et al., 2015 Human: primary monocytes from healthy volunteers Sanquin Blood Bank Oligonucleotides Primer HPRT fw 5’-CCTGGCGTCGTGATTAGTGAT-3’ Sigma-Aldrich Designed by BLAST Primer HPRT rv 5’-AGACGTTCAGTCCTGTCCATAA-3’ Sigma-Aldrich Designed by BLAST Primer IRG1 fw 5’-GTTCCTGGGAACCACTACG-3’ Lachmandas et al., 2016 Primer IRG1 rv 5’-GATGTCTGGCTGACCCCAAA-3’ Lachmandas et al., 2016 Primer IFNB1 fw 5’-ATGACCAACAAGTGTCTCCTCC-3’ Sigma-Aldrich Designed by BLAST Primer IFNB1 rv 5’-GGAATCCAAGCAAGTTGTAGCTC-3’ Sigma-Aldrich Designed by BLAST Software and Algorithms NanoDrop software N/A N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/; http://research-pub.gene.com/gmap Bamtools Barnett et al., 2011 https://github.com/pezmaster31/bamtools Samtools Li and Durbin, 2009 http://samtools.sourceforge.net (Continued on next page) e2 Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 ..

    Article Title: BCG Vaccination Protects against Experimental Viral Infection in Humans through the Induction of Cytokines Associated with Trained Immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Chemicals, Peptides, and Recombinant Proteins Bacille Calmette-Guérin Vaccin (BCG) Statens Serum Institute, Copenhagen 2016-04 Yellow fever vaccine Sanofi Pasteur Stamaril Lipopolysaccharide Sigma-Aldrich From E. coli serotype 055:B5, L2880 Mycobacterium tuberculosis Gift H27Rv Candida albicans Gift UC820 Staphylococcus aureus Clinical isolate Recombinant human Interleukin-1 b R&D Systems 201-LB-005 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 CD14+ beads MACS Miltenyi 130-050-201 iScript reverse transcriptase Bio-Rad 1708840 TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina Human IL-1b ELISA R&D Systems DY201 Human TNFa ELISA R&D Systems DY210 Human IL-17 ELISA R&D Systems D1700 Human IL-22 ELISA R&D Systems D2200 Human IL-6 ELISA Sanquin M1916 Human IL-8 ELISA Sanquin M1918 Human IFNg ELISA Sanquin M1933 Milliplex human TH17 panel Merck HTH17MAG-14K Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 (Continued on next page) Cell Host & Microbe 23, 89–100.e1–e5, January 10, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/mL) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E. coli Ligase New England Biolabs M0205L Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Deposited Data BCG in vivo trained monocytes ChIP-seq and RNA-seq data This paper GEO: GSE104149 Experimental Models: Organisms/Strains Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Oligonucleotides Primers for qPCR Table S1 Biolegio. .. Primers designed by BLAST Software Image Lab Bio-Rad CXP analysis software v2.2 Beckman Coulter GraphPad Prism Graphpad Software https://www.graphpad.com MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber, 2010 http://bioconductor.org/packages/release/ bioc/html/DESeq.html Bwa Li and Durbin, 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011; Li et al., 2009 https://github.com/kundajelab/ phantompeakqualtools, http://samtools. sourceforge.net/, https://github.com/ pezmaster31/bamtools MACS2 Zhang et al., 2008 http://github.com/taoliu/MACS/ HOMER Heinz et al., 2010 http://homer.salk.edu/homer/motif/ DAVID Huang et al., 2009 https://david.ncifcrf.gov/

    Software:

    Article Title: The Itaconate Pathway Is a Central Regulatory Node Linking Innate Immune Tolerance and Trained Immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies a-IFN-alpha/beta R1 antibody R&D Systems AF3039; RRID:AB_664107 IgG isotype control R&D Systems AB-108-C; RRID:AB_354267 Rabbit polyclonal anti-H3K27ac Diagenode pAb-196-050; RRID:AB_2637079 Rabbit polyclonal anti-H3K4me1 Diagenode pAb-037-050; RRID:AB_2561054 Rabbit polyclonal anti-H3K4me3 Diagenode pAb-003-050; RRID:AB_2616052 Chemicals, Peptides, and Recombinant Proteins Gentamycin Thermo Fisher Scientific 15750060 Lipopolysaccharide from E. coli serotype 055:B5 Sigma-Aldrich L2880 Pam3Cys EMC Microcollections L2000 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 CD14+ beads MACS Miltenyi 130-050-201 TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 b1,3-(D)glucan (b-glucan) Saeed et al., 2014 N/A Mono methyl-fumarate Sigma-Aldrich 651419-1G Dimethylitaconate Sigma-Aldrich 592498-25G 4-octyl itaconate Mills et al., 2018 IRG1 siRNA (mouse) Santa Cruz sc-146287 control siRNA (mouse) Santa Cruz sc-37007 siRNA Transfection Medium Santa Cruz sc-36868 siRNA Dilution Buffer Santa Cruz sc-29527 siRNA Transfection Reagent Santa Cruz sc-29528 Seahorse XF Base Medium Agilent Technologies 102353-100 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 Luminol Sigma-Aldrich A8511-5G Zymosan (from S. cerevisiae) Sigma-Aldrich Z4250-1G Critical Commercial Assays Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Lactate Fluorometric Assay Kit Biovision K607 iScript cDNA Synthesis Kit Bio-Rad 1708891 Succinate Colometric Assay kit Sigma-Aldrich MAK184 Glutamate Assay Kit Sigma-Aldrich MAK004 CytoTox 96 Non-Radioactive Cytotoxicity Assay Promega G1780 Rneasy Mini Kit QIAGEN 74106 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 (Continued on next page) Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Ribozero Gold Kit Illumina MRZG12324 Qubit RNA HS assay kit Ribozero Life Technologies Q32852 DNase I QIAGEN 79254 Sodium Acetate (3M) Life Technologies AM9740 iQ SYBR Green Supermix Bio-Rad 1708880 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 100 x SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/mL) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E. coli Ligase New England Biolabs M0205L Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Ribozero Gold Kit Illumina MRZG12324 Deposited Data Raw data files for ChIP sequencing Novakovic et al., 2016 GSE85245 Raw data files for RNA sequencing Novakovic et al., 2016 GSE85243 Raw data files for b-glucan and LPS SuperSeries data Novakovic et al., 2016 GSE85246 Experimental Models: Cell Lines Mouse: RAW264.7 cells ATCC TIB-71 Experimental Models: Organisms/Strains Human: 200FG cohort (Human Functional Genomics project) Li et al., 2016 http://www.humanfunctionalgenomics.org Human: LLDeep cohort Tigchelaar et al., 2015 Human: primary monocytes from healthy volunteers Sanquin Blood Bank Oligonucleotides Primer HPRT fw 5’-CCTGGCGTCGTGATTAGTGAT-3’ Sigma-Aldrich Designed by BLAST Primer HPRT rv 5’-AGACGTTCAGTCCTGTCCATAA-3’ Sigma-Aldrich Designed by BLAST Primer IRG1 fw 5’-GTTCCTGGGAACCACTACG-3’ Lachmandas et al., 2016 Primer IRG1 rv 5’-GATGTCTGGCTGACCCCAAA-3’ Lachmandas et al., 2016 Primer IFNB1 fw 5’-ATGACCAACAAGTGTCTCCTCC-3’ Sigma-Aldrich Designed by BLAST Primer IFNB1 rv 5’-GGAATCCAAGCAAGTTGTAGCTC-3’ Sigma-Aldrich Designed by BLAST Software and Algorithms NanoDrop software N/A N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/; http://research-pub.gene.com/gmap Bamtools Barnett et al., 2011 https://github.com/pezmaster31/bamtools Samtools Li and Durbin, 2009 http://samtools.sourceforge.net (Continued on next page) e2 Cell Metabolism 29, 1–10.e1–e5, January 8, 2019 ..

    Reverse Transcription:

    Article Title: BCG Vaccination Protects against Experimental Viral Infection in Humans through the Induction of Cytokines Associated with Trained Immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Chemicals, Peptides, and Recombinant Proteins Bacille Calmette-Guérin Vaccin (BCG) Statens Serum Institute, Copenhagen 2016-04 Yellow fever vaccine Sanofi Pasteur Stamaril Lipopolysaccharide Sigma-Aldrich From E. coli serotype 055:B5, L2880 Mycobacterium tuberculosis Gift H27Rv Candida albicans Gift UC820 Staphylococcus aureus Clinical isolate Recombinant human Interleukin-1 b R&D Systems 201-LB-005 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 CD14+ beads MACS Miltenyi 130-050-201 iScript reverse transcriptase Bio-Rad 1708840 TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina Human IL-1b ELISA R&D Systems DY201 Human TNFa ELISA R&D Systems DY210 Human IL-17 ELISA R&D Systems D1700 Human IL-22 ELISA R&D Systems D2200 Human IL-6 ELISA Sanquin M1916 Human IL-8 ELISA Sanquin M1918 Human IFNg ELISA Sanquin M1933 Milliplex human TH17 panel Merck HTH17MAG-14K Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 (Continued on next page) Cell Host & Microbe 23, 89–100.e1–e5, January 10, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/mL) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E. coli Ligase New England Biolabs M0205L Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Deposited Data BCG in vivo trained monocytes ChIP-seq and RNA-seq data This paper GEO: GSE104149 Experimental Models: Organisms/Strains Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Oligonucleotides Primers for qPCR Table S1 Biolegio. .. Primers designed by BLAST Software Image Lab Bio-Rad CXP analysis software v2.2 Beckman Coulter GraphPad Prism Graphpad Software https://www.graphpad.com MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber, 2010 http://bioconductor.org/packages/release/ bioc/html/DESeq.html Bwa Li and Durbin, 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011; Li et al., 2009 https://github.com/kundajelab/ phantompeakqualtools, http://samtools. sourceforge.net/, https://github.com/ pezmaster31/bamtools MACS2 Zhang et al., 2008 http://github.com/taoliu/MACS/ HOMER Heinz et al., 2010 http://homer.salk.edu/homer/motif/ DAVID Huang et al., 2009 https://david.ncifcrf.gov/

    Article Title: Metabolic Induction of Trained Immunity through the Mevalonate Pathway.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies human IGF1-R antibody R&D systems MAB391-100 IgG1 control antibody R&D systems MAB002 FITC-anti-CD16 Becton Dickinson Clone Leu11a, 555406 PE-anti-CD14 Becton Dickinson 555398 PC7-anti-CD45 Beckman Coulter IM3548 APC-anti-IGF1R Life Technologies 17-8849-42 Rabbit anti phospho-p70 S6K antibody Cell Signaling Monoclonal (Thr389, 108D2), 9234S Rabbit anti phosho-4EBP1 antibody Cell Signaling Polyclonal, T37/46, 2855S Rabbit anti phospho-mTOR antibody Cell Signaling Monoclonal Ser2448, 5536S Rabbit anti p70-S6K antibody Cell Signaling 9202L Rabbit anti 4EBP1 antibody Cell Signaling Polyclonal, 9452S Rabbit anti mTOR antibody Cell Signaling 2972S Rabbit anti Phospho-Akt antibody Cell Signaling Monoclonal (S473), 4060S Rabbit anti Akt antibody Cell Signaling Polyclonal, 9272S Rabbit anti Actin antibody Sigma-Aldrich A2066 Polyclonal Swine-anti-rabbit HRP antibody Dako P021702 Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Rabbit polyclonal anti-H3K4me1 Diagenode pab-037-050 Experimental Models: Organisms/Strains Mouse: wild type C57BL/6 N/A Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Chemicals, Peptides and Recombinant Proteins Bacille-Calmette Guérin Vaccin Statens Serum Institute, Copenhagen Denmark 2016-04 IGF1 R&D systems 291-G1-01M Lipopolysaccharide Sigma-Aldrich From E.coli serotype 055:B5, L2880 Pam3Cys EMC Microcollections L2000 Poly I:C Invivogen tlrl-pic-5 Macrophage-activating lipopeptide-2 Sigma-Aldrich E1036 Phytohemagglutinin Sigma-Aldrich 11249738001 Fluvastatin sodium hydrate Sigma-Aldrich SML0038 (R)-Mevalonic acid lithium salt Sigma-Aldrich 50838 Zaragozic acid SantaCruz Biotechnology CAS 142561-96-4, sc-391058 6-fluoromevalonate Sigma-Aldrich F2929 2-deoxy-D-glucose Sigma-Aldrich D6134 Rapamycin Sigma-Aldrich R-5000 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Picropodophyllin Santa Cruz 477-47-4, SC-204008 LXR-inhibitor Axon Medchem GSK2033 (Continued on next page) Cell 172, 135–146.e1–e6, January 11, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER PPARd-inhibitor Tocris GSK3787 Dimethyl sulfoxide (DMSO) Instruchemie WAK-DMSO-10 Mouse granulocyte-macrophage colonystimulating factor (GM-CSF) PeproTech 315-03 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Density gradient cell separation medium Histopaque 1083 Sigma-Aldrich 10831 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 SuperSignal West Femto Substrate Thermo Fisher Scientific 34096 4-15% gel Bio-Rad 456-1086 Nitrocellulose membrane Bio-Rad 1620145 CD14+ beads MACS Miltenyi 130-050-201 ELK, skimmed milk Campina NA TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina N/A Human IL-1b ELISA R&D systems DY201 Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Mouse TNFa ELISA Meso Scale Discovery RAB0477 Mouse IL-6 ELISA Meso Scale Discovery RAB0309 Lactate Fluorometric Assay Kit Biovision K607 Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/ml) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E.Coli Ligase New England Biolabs M0205L (Continued on next page) e2 Cell 172, 135–146.e1–e6, January 11, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Software and Algorithms Image Lab Biorad N/A CXP analysis software v2.2 Beckman Coulter N/A NanoDrop software N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bowtie 1 Langmead et al., 2009 http://bowtie-bio.sourceforge.net/index.shtml MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber 2010 http://bioconductor.org/packages/ release/bioc/html/DESeq.html Escher King et al., 2015 Bwa Li and Durbin 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011, Li et al., 2009 https://code.google.com/archive/p/ phantompeakqualtools/ http://samtools.sourceforge.net/ https://github.com/pezmaster31/bamtools MACS2 Zhang et al., 2008 https://github.com/taoliu/MACS/ Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/ GSNAP Wu and Nacu, 2010 http://research-pub.gene.com/gmap/ Caret https://cran.r-project.org/web/packages/caret/ index.html HOMER Heinz et al., 2010 http://homer.ucsd.edu/homer/motif/ DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ Deposited Data Mevalonate trained macrophage ChIP-seq and RNA-seq data This paper GEO: GSE104227 HIDS patients ChIP-seq and RNA-seq data This paper GEO: GSE104282 Oligonucleotides Primers for qPCR Table S4 N/A Primers for ChIP-qPCR Table S5 N/A

    In Vivo:

    Article Title: BCG Vaccination Protects against Experimental Viral Infection in Humans through the Induction of Cytokines Associated with Trained Immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Chemicals, Peptides, and Recombinant Proteins Bacille Calmette-Guérin Vaccin (BCG) Statens Serum Institute, Copenhagen 2016-04 Yellow fever vaccine Sanofi Pasteur Stamaril Lipopolysaccharide Sigma-Aldrich From E. coli serotype 055:B5, L2880 Mycobacterium tuberculosis Gift H27Rv Candida albicans Gift UC820 Staphylococcus aureus Clinical isolate Recombinant human Interleukin-1 b R&D Systems 201-LB-005 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 CD14+ beads MACS Miltenyi 130-050-201 iScript reverse transcriptase Bio-Rad 1708840 TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina Human IL-1b ELISA R&D Systems DY201 Human TNFa ELISA R&D Systems DY210 Human IL-17 ELISA R&D Systems D1700 Human IL-22 ELISA R&D Systems D2200 Human IL-6 ELISA Sanquin M1916 Human IL-8 ELISA Sanquin M1918 Human IFNg ELISA Sanquin M1933 Milliplex human TH17 panel Merck HTH17MAG-14K Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 (Continued on next page) Cell Host & Microbe 23, 89–100.e1–e5, January 10, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/mL) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E. coli Ligase New England Biolabs M0205L Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Deposited Data BCG in vivo trained monocytes ChIP-seq and RNA-seq data This paper GEO: GSE104149 Experimental Models: Organisms/Strains Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Oligonucleotides Primers for qPCR Table S1 Biolegio. .. Primers designed by BLAST Software Image Lab Bio-Rad CXP analysis software v2.2 Beckman Coulter GraphPad Prism Graphpad Software https://www.graphpad.com MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber, 2010 http://bioconductor.org/packages/release/ bioc/html/DESeq.html Bwa Li and Durbin, 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011; Li et al., 2009 https://github.com/kundajelab/ phantompeakqualtools, http://samtools. sourceforge.net/, https://github.com/ pezmaster31/bamtools MACS2 Zhang et al., 2008 http://github.com/taoliu/MACS/ HOMER Heinz et al., 2010 http://homer.salk.edu/homer/motif/ DAVID Huang et al., 2009 https://david.ncifcrf.gov/

    Real-time Polymerase Chain Reaction:

    Article Title: BCG Vaccination Protects against Experimental Viral Infection in Humans through the Induction of Cytokines Associated with Trained Immunity.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Chemicals, Peptides, and Recombinant Proteins Bacille Calmette-Guérin Vaccin (BCG) Statens Serum Institute, Copenhagen 2016-04 Yellow fever vaccine Sanofi Pasteur Stamaril Lipopolysaccharide Sigma-Aldrich From E. coli serotype 055:B5, L2880 Mycobacterium tuberculosis Gift H27Rv Candida albicans Gift UC820 Staphylococcus aureus Clinical isolate Recombinant human Interleukin-1 b R&D Systems 201-LB-005 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 CD14+ beads MACS Miltenyi 130-050-201 iScript reverse transcriptase Bio-Rad 1708840 TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina Human IL-1b ELISA R&D Systems DY201 Human TNFa ELISA R&D Systems DY210 Human IL-17 ELISA R&D Systems D1700 Human IL-22 ELISA R&D Systems D2200 Human IL-6 ELISA Sanquin M1916 Human IL-8 ELISA Sanquin M1918 Human IFNg ELISA Sanquin M1933 Milliplex human TH17 panel Merck HTH17MAG-14K Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 (Continued on next page) Cell Host & Microbe 23, 89–100.e1–e5, January 10, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/mL) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E. coli Ligase New England Biolabs M0205L Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Deposited Data BCG in vivo trained monocytes ChIP-seq and RNA-seq data This paper GEO: GSE104149 Experimental Models: Organisms/Strains Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Oligonucleotides Primers for qPCR Table S1 Biolegio. .. Primers designed by BLAST Software Image Lab Bio-Rad CXP analysis software v2.2 Beckman Coulter GraphPad Prism Graphpad Software https://www.graphpad.com MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber, 2010 http://bioconductor.org/packages/release/ bioc/html/DESeq.html Bwa Li and Durbin, 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011; Li et al., 2009 https://github.com/kundajelab/ phantompeakqualtools, http://samtools. sourceforge.net/, https://github.com/ pezmaster31/bamtools MACS2 Zhang et al., 2008 http://github.com/taoliu/MACS/ HOMER Heinz et al., 2010 http://homer.salk.edu/homer/motif/ DAVID Huang et al., 2009 https://david.ncifcrf.gov/

    Membrane:

    Article Title: Metabolic Induction of Trained Immunity through the Mevalonate Pathway.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies human IGF1-R antibody R&D systems MAB391-100 IgG1 control antibody R&D systems MAB002 FITC-anti-CD16 Becton Dickinson Clone Leu11a, 555406 PE-anti-CD14 Becton Dickinson 555398 PC7-anti-CD45 Beckman Coulter IM3548 APC-anti-IGF1R Life Technologies 17-8849-42 Rabbit anti phospho-p70 S6K antibody Cell Signaling Monoclonal (Thr389, 108D2), 9234S Rabbit anti phosho-4EBP1 antibody Cell Signaling Polyclonal, T37/46, 2855S Rabbit anti phospho-mTOR antibody Cell Signaling Monoclonal Ser2448, 5536S Rabbit anti p70-S6K antibody Cell Signaling 9202L Rabbit anti 4EBP1 antibody Cell Signaling Polyclonal, 9452S Rabbit anti mTOR antibody Cell Signaling 2972S Rabbit anti Phospho-Akt antibody Cell Signaling Monoclonal (S473), 4060S Rabbit anti Akt antibody Cell Signaling Polyclonal, 9272S Rabbit anti Actin antibody Sigma-Aldrich A2066 Polyclonal Swine-anti-rabbit HRP antibody Dako P021702 Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Rabbit polyclonal anti-H3K4me1 Diagenode pab-037-050 Experimental Models: Organisms/Strains Mouse: wild type C57BL/6 N/A Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Chemicals, Peptides and Recombinant Proteins Bacille-Calmette Guérin Vaccin Statens Serum Institute, Copenhagen Denmark 2016-04 IGF1 R&D systems 291-G1-01M Lipopolysaccharide Sigma-Aldrich From E.coli serotype 055:B5, L2880 Pam3Cys EMC Microcollections L2000 Poly I:C Invivogen tlrl-pic-5 Macrophage-activating lipopeptide-2 Sigma-Aldrich E1036 Phytohemagglutinin Sigma-Aldrich 11249738001 Fluvastatin sodium hydrate Sigma-Aldrich SML0038 (R)-Mevalonic acid lithium salt Sigma-Aldrich 50838 Zaragozic acid SantaCruz Biotechnology CAS 142561-96-4, sc-391058 6-fluoromevalonate Sigma-Aldrich F2929 2-deoxy-D-glucose Sigma-Aldrich D6134 Rapamycin Sigma-Aldrich R-5000 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Picropodophyllin Santa Cruz 477-47-4, SC-204008 LXR-inhibitor Axon Medchem GSK2033 (Continued on next page) Cell 172, 135–146.e1–e6, January 11, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER PPARd-inhibitor Tocris GSK3787 Dimethyl sulfoxide (DMSO) Instruchemie WAK-DMSO-10 Mouse granulocyte-macrophage colonystimulating factor (GM-CSF) PeproTech 315-03 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Density gradient cell separation medium Histopaque 1083 Sigma-Aldrich 10831 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 SuperSignal West Femto Substrate Thermo Fisher Scientific 34096 4-15% gel Bio-Rad 456-1086 Nitrocellulose membrane Bio-Rad 1620145 CD14+ beads MACS Miltenyi 130-050-201 ELK, skimmed milk Campina NA TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina N/A Human IL-1b ELISA R&D systems DY201 Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Mouse TNFa ELISA Meso Scale Discovery RAB0477 Mouse IL-6 ELISA Meso Scale Discovery RAB0309 Lactate Fluorometric Assay Kit Biovision K607 Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/ml) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E.Coli Ligase New England Biolabs M0205L (Continued on next page) e2 Cell 172, 135–146.e1–e6, January 11, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Software and Algorithms Image Lab Biorad N/A CXP analysis software v2.2 Beckman Coulter N/A NanoDrop software N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bowtie 1 Langmead et al., 2009 http://bowtie-bio.sourceforge.net/index.shtml MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber 2010 http://bioconductor.org/packages/ release/bioc/html/DESeq.html Escher King et al., 2015 Bwa Li and Durbin 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011, Li et al., 2009 https://code.google.com/archive/p/ phantompeakqualtools/ http://samtools.sourceforge.net/ https://github.com/pezmaster31/bamtools MACS2 Zhang et al., 2008 https://github.com/taoliu/MACS/ Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/ GSNAP Wu and Nacu, 2010 http://research-pub.gene.com/gmap/ Caret https://cran.r-project.org/web/packages/caret/ index.html HOMER Heinz et al., 2010 http://homer.ucsd.edu/homer/motif/ DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ Deposited Data Mevalonate trained macrophage ChIP-seq and RNA-seq data This paper GEO: GSE104227 HIDS patients ChIP-seq and RNA-seq data This paper GEO: GSE104282 Oligonucleotides Primers for qPCR Table S4 N/A Primers for ChIP-qPCR Table S5 N/A

    Magnetic Cell Separation:

    Article Title: Metabolic Induction of Trained Immunity through the Mevalonate Pathway.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies human IGF1-R antibody R&D systems MAB391-100 IgG1 control antibody R&D systems MAB002 FITC-anti-CD16 Becton Dickinson Clone Leu11a, 555406 PE-anti-CD14 Becton Dickinson 555398 PC7-anti-CD45 Beckman Coulter IM3548 APC-anti-IGF1R Life Technologies 17-8849-42 Rabbit anti phospho-p70 S6K antibody Cell Signaling Monoclonal (Thr389, 108D2), 9234S Rabbit anti phosho-4EBP1 antibody Cell Signaling Polyclonal, T37/46, 2855S Rabbit anti phospho-mTOR antibody Cell Signaling Monoclonal Ser2448, 5536S Rabbit anti p70-S6K antibody Cell Signaling 9202L Rabbit anti 4EBP1 antibody Cell Signaling Polyclonal, 9452S Rabbit anti mTOR antibody Cell Signaling 2972S Rabbit anti Phospho-Akt antibody Cell Signaling Monoclonal (S473), 4060S Rabbit anti Akt antibody Cell Signaling Polyclonal, 9272S Rabbit anti Actin antibody Sigma-Aldrich A2066 Polyclonal Swine-anti-rabbit HRP antibody Dako P021702 Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Rabbit polyclonal anti-H3K4me1 Diagenode pab-037-050 Experimental Models: Organisms/Strains Mouse: wild type C57BL/6 N/A Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Chemicals, Peptides and Recombinant Proteins Bacille-Calmette Guérin Vaccin Statens Serum Institute, Copenhagen Denmark 2016-04 IGF1 R&D systems 291-G1-01M Lipopolysaccharide Sigma-Aldrich From E.coli serotype 055:B5, L2880 Pam3Cys EMC Microcollections L2000 Poly I:C Invivogen tlrl-pic-5 Macrophage-activating lipopeptide-2 Sigma-Aldrich E1036 Phytohemagglutinin Sigma-Aldrich 11249738001 Fluvastatin sodium hydrate Sigma-Aldrich SML0038 (R)-Mevalonic acid lithium salt Sigma-Aldrich 50838 Zaragozic acid SantaCruz Biotechnology CAS 142561-96-4, sc-391058 6-fluoromevalonate Sigma-Aldrich F2929 2-deoxy-D-glucose Sigma-Aldrich D6134 Rapamycin Sigma-Aldrich R-5000 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Picropodophyllin Santa Cruz 477-47-4, SC-204008 LXR-inhibitor Axon Medchem GSK2033 (Continued on next page) Cell 172, 135–146.e1–e6, January 11, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER PPARd-inhibitor Tocris GSK3787 Dimethyl sulfoxide (DMSO) Instruchemie WAK-DMSO-10 Mouse granulocyte-macrophage colonystimulating factor (GM-CSF) PeproTech 315-03 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Density gradient cell separation medium Histopaque 1083 Sigma-Aldrich 10831 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 SuperSignal West Femto Substrate Thermo Fisher Scientific 34096 4-15% gel Bio-Rad 456-1086 Nitrocellulose membrane Bio-Rad 1620145 CD14+ beads MACS Miltenyi 130-050-201 ELK, skimmed milk Campina NA TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina N/A Human IL-1b ELISA R&D systems DY201 Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Mouse TNFa ELISA Meso Scale Discovery RAB0477 Mouse IL-6 ELISA Meso Scale Discovery RAB0309 Lactate Fluorometric Assay Kit Biovision K607 Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/ml) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E.Coli Ligase New England Biolabs M0205L (Continued on next page) e2 Cell 172, 135–146.e1–e6, January 11, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Software and Algorithms Image Lab Biorad N/A CXP analysis software v2.2 Beckman Coulter N/A NanoDrop software N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bowtie 1 Langmead et al., 2009 http://bowtie-bio.sourceforge.net/index.shtml MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber 2010 http://bioconductor.org/packages/ release/bioc/html/DESeq.html Escher King et al., 2015 Bwa Li and Durbin 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011, Li et al., 2009 https://code.google.com/archive/p/ phantompeakqualtools/ http://samtools.sourceforge.net/ https://github.com/pezmaster31/bamtools MACS2 Zhang et al., 2008 https://github.com/taoliu/MACS/ Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/ GSNAP Wu and Nacu, 2010 http://research-pub.gene.com/gmap/ Caret https://cran.r-project.org/web/packages/caret/ index.html HOMER Heinz et al., 2010 http://homer.ucsd.edu/homer/motif/ DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ Deposited Data Mevalonate trained macrophage ChIP-seq and RNA-seq data This paper GEO: GSE104227 HIDS patients ChIP-seq and RNA-seq data This paper GEO: GSE104282 Oligonucleotides Primers for qPCR Table S4 N/A Primers for ChIP-qPCR Table S5 N/A

    Magnetic Beads:

    Article Title: Metabolic Induction of Trained Immunity through the Mevalonate Pathway.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies human IGF1-R antibody R&D systems MAB391-100 IgG1 control antibody R&D systems MAB002 FITC-anti-CD16 Becton Dickinson Clone Leu11a, 555406 PE-anti-CD14 Becton Dickinson 555398 PC7-anti-CD45 Beckman Coulter IM3548 APC-anti-IGF1R Life Technologies 17-8849-42 Rabbit anti phospho-p70 S6K antibody Cell Signaling Monoclonal (Thr389, 108D2), 9234S Rabbit anti phosho-4EBP1 antibody Cell Signaling Polyclonal, T37/46, 2855S Rabbit anti phospho-mTOR antibody Cell Signaling Monoclonal Ser2448, 5536S Rabbit anti p70-S6K antibody Cell Signaling 9202L Rabbit anti 4EBP1 antibody Cell Signaling Polyclonal, 9452S Rabbit anti mTOR antibody Cell Signaling 2972S Rabbit anti Phospho-Akt antibody Cell Signaling Monoclonal (S473), 4060S Rabbit anti Akt antibody Cell Signaling Polyclonal, 9272S Rabbit anti Actin antibody Sigma-Aldrich A2066 Polyclonal Swine-anti-rabbit HRP antibody Dako P021702 Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Rabbit polyclonal anti-H3K4me1 Diagenode pab-037-050 Experimental Models: Organisms/Strains Mouse: wild type C57BL/6 N/A Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Chemicals, Peptides and Recombinant Proteins Bacille-Calmette Guérin Vaccin Statens Serum Institute, Copenhagen Denmark 2016-04 IGF1 R&D systems 291-G1-01M Lipopolysaccharide Sigma-Aldrich From E.coli serotype 055:B5, L2880 Pam3Cys EMC Microcollections L2000 Poly I:C Invivogen tlrl-pic-5 Macrophage-activating lipopeptide-2 Sigma-Aldrich E1036 Phytohemagglutinin Sigma-Aldrich 11249738001 Fluvastatin sodium hydrate Sigma-Aldrich SML0038 (R)-Mevalonic acid lithium salt Sigma-Aldrich 50838 Zaragozic acid SantaCruz Biotechnology CAS 142561-96-4, sc-391058 6-fluoromevalonate Sigma-Aldrich F2929 2-deoxy-D-glucose Sigma-Aldrich D6134 Rapamycin Sigma-Aldrich R-5000 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Picropodophyllin Santa Cruz 477-47-4, SC-204008 LXR-inhibitor Axon Medchem GSK2033 (Continued on next page) Cell 172, 135–146.e1–e6, January 11, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER PPARd-inhibitor Tocris GSK3787 Dimethyl sulfoxide (DMSO) Instruchemie WAK-DMSO-10 Mouse granulocyte-macrophage colonystimulating factor (GM-CSF) PeproTech 315-03 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Density gradient cell separation medium Histopaque 1083 Sigma-Aldrich 10831 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 SuperSignal West Femto Substrate Thermo Fisher Scientific 34096 4-15% gel Bio-Rad 456-1086 Nitrocellulose membrane Bio-Rad 1620145 CD14+ beads MACS Miltenyi 130-050-201 ELK, skimmed milk Campina NA TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina N/A Human IL-1b ELISA R&D systems DY201 Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Mouse TNFa ELISA Meso Scale Discovery RAB0477 Mouse IL-6 ELISA Meso Scale Discovery RAB0309 Lactate Fluorometric Assay Kit Biovision K607 Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/ml) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E.Coli Ligase New England Biolabs M0205L (Continued on next page) e2 Cell 172, 135–146.e1–e6, January 11, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Software and Algorithms Image Lab Biorad N/A CXP analysis software v2.2 Beckman Coulter N/A NanoDrop software N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bowtie 1 Langmead et al., 2009 http://bowtie-bio.sourceforge.net/index.shtml MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber 2010 http://bioconductor.org/packages/ release/bioc/html/DESeq.html Escher King et al., 2015 Bwa Li and Durbin 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011, Li et al., 2009 https://code.google.com/archive/p/ phantompeakqualtools/ http://samtools.sourceforge.net/ https://github.com/pezmaster31/bamtools MACS2 Zhang et al., 2008 https://github.com/taoliu/MACS/ Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/ GSNAP Wu and Nacu, 2010 http://research-pub.gene.com/gmap/ Caret https://cran.r-project.org/web/packages/caret/ index.html HOMER Heinz et al., 2010 http://homer.ucsd.edu/homer/motif/ DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ Deposited Data Mevalonate trained macrophage ChIP-seq and RNA-seq data This paper GEO: GSE104227 HIDS patients ChIP-seq and RNA-seq data This paper GEO: GSE104282 Oligonucleotides Primers for qPCR Table S4 N/A Primers for ChIP-qPCR Table S5 N/A

    Enzyme-linked Immunosorbent Assay:

    Article Title: Metabolic Induction of Trained Immunity through the Mevalonate Pathway.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies human IGF1-R antibody R&D systems MAB391-100 IgG1 control antibody R&D systems MAB002 FITC-anti-CD16 Becton Dickinson Clone Leu11a, 555406 PE-anti-CD14 Becton Dickinson 555398 PC7-anti-CD45 Beckman Coulter IM3548 APC-anti-IGF1R Life Technologies 17-8849-42 Rabbit anti phospho-p70 S6K antibody Cell Signaling Monoclonal (Thr389, 108D2), 9234S Rabbit anti phosho-4EBP1 antibody Cell Signaling Polyclonal, T37/46, 2855S Rabbit anti phospho-mTOR antibody Cell Signaling Monoclonal Ser2448, 5536S Rabbit anti p70-S6K antibody Cell Signaling 9202L Rabbit anti 4EBP1 antibody Cell Signaling Polyclonal, 9452S Rabbit anti mTOR antibody Cell Signaling 2972S Rabbit anti Phospho-Akt antibody Cell Signaling Monoclonal (S473), 4060S Rabbit anti Akt antibody Cell Signaling Polyclonal, 9272S Rabbit anti Actin antibody Sigma-Aldrich A2066 Polyclonal Swine-anti-rabbit HRP antibody Dako P021702 Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Rabbit polyclonal anti-H3K4me1 Diagenode pab-037-050 Experimental Models: Organisms/Strains Mouse: wild type C57BL/6 N/A Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Chemicals, Peptides and Recombinant Proteins Bacille-Calmette Guérin Vaccin Statens Serum Institute, Copenhagen Denmark 2016-04 IGF1 R&D systems 291-G1-01M Lipopolysaccharide Sigma-Aldrich From E.coli serotype 055:B5, L2880 Pam3Cys EMC Microcollections L2000 Poly I:C Invivogen tlrl-pic-5 Macrophage-activating lipopeptide-2 Sigma-Aldrich E1036 Phytohemagglutinin Sigma-Aldrich 11249738001 Fluvastatin sodium hydrate Sigma-Aldrich SML0038 (R)-Mevalonic acid lithium salt Sigma-Aldrich 50838 Zaragozic acid SantaCruz Biotechnology CAS 142561-96-4, sc-391058 6-fluoromevalonate Sigma-Aldrich F2929 2-deoxy-D-glucose Sigma-Aldrich D6134 Rapamycin Sigma-Aldrich R-5000 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Picropodophyllin Santa Cruz 477-47-4, SC-204008 LXR-inhibitor Axon Medchem GSK2033 (Continued on next page) Cell 172, 135–146.e1–e6, January 11, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER PPARd-inhibitor Tocris GSK3787 Dimethyl sulfoxide (DMSO) Instruchemie WAK-DMSO-10 Mouse granulocyte-macrophage colonystimulating factor (GM-CSF) PeproTech 315-03 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Density gradient cell separation medium Histopaque 1083 Sigma-Aldrich 10831 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 SuperSignal West Femto Substrate Thermo Fisher Scientific 34096 4-15% gel Bio-Rad 456-1086 Nitrocellulose membrane Bio-Rad 1620145 CD14+ beads MACS Miltenyi 130-050-201 ELK, skimmed milk Campina NA TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina N/A Human IL-1b ELISA R&D systems DY201 Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Mouse TNFa ELISA Meso Scale Discovery RAB0477 Mouse IL-6 ELISA Meso Scale Discovery RAB0309 Lactate Fluorometric Assay Kit Biovision K607 Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/ml) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E.Coli Ligase New England Biolabs M0205L (Continued on next page) e2 Cell 172, 135–146.e1–e6, January 11, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Software and Algorithms Image Lab Biorad N/A CXP analysis software v2.2 Beckman Coulter N/A NanoDrop software N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bowtie 1 Langmead et al., 2009 http://bowtie-bio.sourceforge.net/index.shtml MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber 2010 http://bioconductor.org/packages/ release/bioc/html/DESeq.html Escher King et al., 2015 Bwa Li and Durbin 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011, Li et al., 2009 https://code.google.com/archive/p/ phantompeakqualtools/ http://samtools.sourceforge.net/ https://github.com/pezmaster31/bamtools MACS2 Zhang et al., 2008 https://github.com/taoliu/MACS/ Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/ GSNAP Wu and Nacu, 2010 http://research-pub.gene.com/gmap/ Caret https://cran.r-project.org/web/packages/caret/ index.html HOMER Heinz et al., 2010 http://homer.ucsd.edu/homer/motif/ DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ Deposited Data Mevalonate trained macrophage ChIP-seq and RNA-seq data This paper GEO: GSE104227 HIDS patients ChIP-seq and RNA-seq data This paper GEO: GSE104282 Oligonucleotides Primers for qPCR Table S4 N/A Primers for ChIP-qPCR Table S5 N/A

    Concentration Assay:

    Article Title: Metabolic Induction of Trained Immunity through the Mevalonate Pathway.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies human IGF1-R antibody R&D systems MAB391-100 IgG1 control antibody R&D systems MAB002 FITC-anti-CD16 Becton Dickinson Clone Leu11a, 555406 PE-anti-CD14 Becton Dickinson 555398 PC7-anti-CD45 Beckman Coulter IM3548 APC-anti-IGF1R Life Technologies 17-8849-42 Rabbit anti phospho-p70 S6K antibody Cell Signaling Monoclonal (Thr389, 108D2), 9234S Rabbit anti phosho-4EBP1 antibody Cell Signaling Polyclonal, T37/46, 2855S Rabbit anti phospho-mTOR antibody Cell Signaling Monoclonal Ser2448, 5536S Rabbit anti p70-S6K antibody Cell Signaling 9202L Rabbit anti 4EBP1 antibody Cell Signaling Polyclonal, 9452S Rabbit anti mTOR antibody Cell Signaling 2972S Rabbit anti Phospho-Akt antibody Cell Signaling Monoclonal (S473), 4060S Rabbit anti Akt antibody Cell Signaling Polyclonal, 9272S Rabbit anti Actin antibody Sigma-Aldrich A2066 Polyclonal Swine-anti-rabbit HRP antibody Dako P021702 Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Rabbit polyclonal anti-H3K4me1 Diagenode pab-037-050 Experimental Models: Organisms/Strains Mouse: wild type C57BL/6 N/A Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Chemicals, Peptides and Recombinant Proteins Bacille-Calmette Guérin Vaccin Statens Serum Institute, Copenhagen Denmark 2016-04 IGF1 R&D systems 291-G1-01M Lipopolysaccharide Sigma-Aldrich From E.coli serotype 055:B5, L2880 Pam3Cys EMC Microcollections L2000 Poly I:C Invivogen tlrl-pic-5 Macrophage-activating lipopeptide-2 Sigma-Aldrich E1036 Phytohemagglutinin Sigma-Aldrich 11249738001 Fluvastatin sodium hydrate Sigma-Aldrich SML0038 (R)-Mevalonic acid lithium salt Sigma-Aldrich 50838 Zaragozic acid SantaCruz Biotechnology CAS 142561-96-4, sc-391058 6-fluoromevalonate Sigma-Aldrich F2929 2-deoxy-D-glucose Sigma-Aldrich D6134 Rapamycin Sigma-Aldrich R-5000 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Picropodophyllin Santa Cruz 477-47-4, SC-204008 LXR-inhibitor Axon Medchem GSK2033 (Continued on next page) Cell 172, 135–146.e1–e6, January 11, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER PPARd-inhibitor Tocris GSK3787 Dimethyl sulfoxide (DMSO) Instruchemie WAK-DMSO-10 Mouse granulocyte-macrophage colonystimulating factor (GM-CSF) PeproTech 315-03 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Density gradient cell separation medium Histopaque 1083 Sigma-Aldrich 10831 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 SuperSignal West Femto Substrate Thermo Fisher Scientific 34096 4-15% gel Bio-Rad 456-1086 Nitrocellulose membrane Bio-Rad 1620145 CD14+ beads MACS Miltenyi 130-050-201 ELK, skimmed milk Campina NA TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina N/A Human IL-1b ELISA R&D systems DY201 Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Mouse TNFa ELISA Meso Scale Discovery RAB0477 Mouse IL-6 ELISA Meso Scale Discovery RAB0309 Lactate Fluorometric Assay Kit Biovision K607 Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/ml) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E.Coli Ligase New England Biolabs M0205L (Continued on next page) e2 Cell 172, 135–146.e1–e6, January 11, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Software and Algorithms Image Lab Biorad N/A CXP analysis software v2.2 Beckman Coulter N/A NanoDrop software N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bowtie 1 Langmead et al., 2009 http://bowtie-bio.sourceforge.net/index.shtml MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber 2010 http://bioconductor.org/packages/ release/bioc/html/DESeq.html Escher King et al., 2015 Bwa Li and Durbin 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011, Li et al., 2009 https://code.google.com/archive/p/ phantompeakqualtools/ http://samtools.sourceforge.net/ https://github.com/pezmaster31/bamtools MACS2 Zhang et al., 2008 https://github.com/taoliu/MACS/ Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/ GSNAP Wu and Nacu, 2010 http://research-pub.gene.com/gmap/ Caret https://cran.r-project.org/web/packages/caret/ index.html HOMER Heinz et al., 2010 http://homer.ucsd.edu/homer/motif/ DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ Deposited Data Mevalonate trained macrophage ChIP-seq and RNA-seq data This paper GEO: GSE104227 HIDS patients ChIP-seq and RNA-seq data This paper GEO: GSE104282 Oligonucleotides Primers for qPCR Table S4 N/A Primers for ChIP-qPCR Table S5 N/A

    cDNA Synthesis:

    Article Title: Metabolic Induction of Trained Immunity through the Mevalonate Pathway.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies human IGF1-R antibody R&D systems MAB391-100 IgG1 control antibody R&D systems MAB002 FITC-anti-CD16 Becton Dickinson Clone Leu11a, 555406 PE-anti-CD14 Becton Dickinson 555398 PC7-anti-CD45 Beckman Coulter IM3548 APC-anti-IGF1R Life Technologies 17-8849-42 Rabbit anti phospho-p70 S6K antibody Cell Signaling Monoclonal (Thr389, 108D2), 9234S Rabbit anti phosho-4EBP1 antibody Cell Signaling Polyclonal, T37/46, 2855S Rabbit anti phospho-mTOR antibody Cell Signaling Monoclonal Ser2448, 5536S Rabbit anti p70-S6K antibody Cell Signaling 9202L Rabbit anti 4EBP1 antibody Cell Signaling Polyclonal, 9452S Rabbit anti mTOR antibody Cell Signaling 2972S Rabbit anti Phospho-Akt antibody Cell Signaling Monoclonal (S473), 4060S Rabbit anti Akt antibody Cell Signaling Polyclonal, 9272S Rabbit anti Actin antibody Sigma-Aldrich A2066 Polyclonal Swine-anti-rabbit HRP antibody Dako P021702 Rabbit polyclonal anti-H3K4me3 Diagenode pab-003-050 Rabbit polyclonal anti-H3K27Ac Diagenode pab-196-050, C15410196 Rabbit polyclonal anti-H3K9me3 Diagenode pab-193-050, C15410193 Rabbit polyclonal anti-H3K4me1 Diagenode pab-037-050 Experimental Models: Organisms/Strains Mouse: wild type C57BL/6 N/A Human genome assembly hg19 NCBI Version 37 200FG cohort (Human Functional Genomics project) http://www.humanfunctionalgenomics.org Chemicals, Peptides and Recombinant Proteins Bacille-Calmette Guérin Vaccin Statens Serum Institute, Copenhagen Denmark 2016-04 IGF1 R&D systems 291-G1-01M Lipopolysaccharide Sigma-Aldrich From E.coli serotype 055:B5, L2880 Pam3Cys EMC Microcollections L2000 Poly I:C Invivogen tlrl-pic-5 Macrophage-activating lipopeptide-2 Sigma-Aldrich E1036 Phytohemagglutinin Sigma-Aldrich 11249738001 Fluvastatin sodium hydrate Sigma-Aldrich SML0038 (R)-Mevalonic acid lithium salt Sigma-Aldrich 50838 Zaragozic acid SantaCruz Biotechnology CAS 142561-96-4, sc-391058 6-fluoromevalonate Sigma-Aldrich F2929 2-deoxy-D-glucose Sigma-Aldrich D6134 Rapamycin Sigma-Aldrich R-5000 50-Deoxy-50-(methylthio) adenosine (MTA) Sigma-Aldrich D5011 Picropodophyllin Santa Cruz 477-47-4, SC-204008 LXR-inhibitor Axon Medchem GSK2033 (Continued on next page) Cell 172, 135–146.e1–e6, January 11, 2018 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER PPARd-inhibitor Tocris GSK3787 Dimethyl sulfoxide (DMSO) Instruchemie WAK-DMSO-10 Mouse granulocyte-macrophage colonystimulating factor (GM-CSF) PeproTech 315-03 Percoll Sigma-Aldrich P1644 Ficoll-Paque GE Healthcare 17-1440-03 Roswell Park Memorial Institute medium (RPMI) Invitrogen 22406031 Density gradient cell separation medium Histopaque 1083 Sigma-Aldrich 10831 Bovine Serum Albumin (BSA) Sigma-Aldrich A7030 SuperSignal West Femto Substrate Thermo Fisher Scientific 34096 4-15% gel Bio-Rad 456-1086 Nitrocellulose membrane Bio-Rad 1620145 CD14+ beads MACS Miltenyi 130-050-201 ELK, skimmed milk Campina NA TRIzol reagent Life Technologies 15596018 SYBR Green Applied Biosciences 4368708 16% Formaldehyde Fisher Scientific 28908, 11835835 Protein A/G Magnetic beads Diagenode C03010021-150 Critical Commercial Assays Illumina Infinium SNP array Illumina N/A Human IL-1b ELISA R&D systems DY201 Human TNFa ELISA R&D systems DY210 Human IL-6 ELISA R&D systems DY206 Mouse TNFa ELISA Meso Scale Discovery RAB0477 Mouse IL-6 ELISA Meso Scale Discovery RAB0309 Lactate Fluorometric Assay Kit Biovision K607 Bradford Concentration Assay Thermo Fisher Scientific 23246 iScript cDNA Synthesis Kit Bio-Rad 1708891 KAPA library preparation kit Kapa Biosystems KK8400 riboZero gold rRNA removal kit Illumina MRZG12324 Nextera DNA Library Prep Kit Illumina FC-121-1031 TruSeq SBS KIT v3 - HS (50 cycles) Illumina FC-401-3002 NextSeq 500/550 High Output v2 kit (75 cycles) Illumina FC-404-2005 NEBNext High-Fidelity 2 3 PCR Master Mix New England Biolabs M0541 iQ SYBR Green Supermix Bio-Rad 1708880 100 3 SYBR Green I Nucleic Acid Gel Stain Thermo Fisher Scientific S7563 SPRIselect reagent kit Beckman Coulter B23218 E-Gel SizeSelect Agarose Gels, 2% Thermo Fisher Scientific G661002 dNTP set 100 mM Life Technologies 10297-018 dUTP 100 mM Promega U119A Glycogen (20 mg/ml) Life Technologies 10814-010 Random Hexamer primers Sigma-Aldrich 11034731001 Second Strand Buffer Life Technologies 10812-014 Superscript III Reverse Transcriptase Life Technologies 18080-044 DNA polymerase I, E. coli New England Biolabs M0209S USER enzyme New England Biolabs M5505L E.Coli Ligase New England Biolabs M0205L (Continued on next page) e2 Cell 172, 135–146.e1–e6, January 11, 2018 .. REAGENT or RESOURCE SOURCE IDENTIFIER Rnasin Plus Rnase Inhibitor Promega N2615 Ribonuclease H Life Technologies AM2293 T4 DNA polymerase New England Biolabs M0203L Sodium Acetate (3M) Life Technologies AM9740 DNase I QIAGEN 79254 Qubit RNA HS assay kit Life Technologies Q32852 Ribozero Gold Kit Illumina MRZG12324 Rneasy Mini Kit QIAGEN 74106 Software and Algorithms Image Lab Biorad N/A CXP analysis software v2.2 Beckman Coulter N/A NanoDrop software N/A GraphPad Prism Graphpad Software https://www.graphpad.com Bowtie 1 Langmead et al., 2009 http://bowtie-bio.sourceforge.net/index.shtml MMSEQ Turro et al., 2011 https://github.com/eturro/mmseq DEseq Anders and Huber 2010 http://bioconductor.org/packages/ release/bioc/html/DESeq.html Escher King et al., 2015 Bwa Li and Durbin 2009 http://bio-bwa.sourceforge.net/ Samtools and Bamtools Barnett et al., 2011, Li et al., 2009 https://code.google.com/archive/p/ phantompeakqualtools/ http://samtools.sourceforge.net/ https://github.com/pezmaster31/bamtools MACS2 Zhang et al., 2008 https://github.com/taoliu/MACS/ Bedtools Quinlan and Hall, 2010 http://bedtools.readthedocs.io/en/latest/ GSNAP Wu and Nacu, 2010 http://research-pub.gene.com/gmap/ Caret https://cran.r-project.org/web/packages/caret/ index.html HOMER Heinz et al., 2010 http://homer.ucsd.edu/homer/motif/ DAVID Huang da et al., 2009 https://david.ncifcrf.gov/ Deposited Data Mevalonate trained macrophage ChIP-seq and RNA-seq data This paper GEO: GSE104227 HIDS patients ChIP-seq and RNA-seq data This paper GEO: GSE104282 Oligonucleotides Primers for qPCR Table S4 N/A Primers for ChIP-qPCR Table S5 N/A



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