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magnachip kit  (Merck KGaA)

 
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    Structured Review

    Merck KGaA magnachip kit
    Magnachip Kit, supplied by Merck KGaA, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/magnachip+kit/magnachip+kit/pmc12141851-87-5-7
    Average 90 stars, based on 1 article reviews
    magnachip kit - by Bioz Stars, 2026-10
    90/100 stars

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    Related Articles

    Immunoprecipitation:

    Article Title: Trained innate immunity in response to nuclear antigens in systemic lupus erythematosus.
    Article Snippet: Cells were sonicated at a concentration of 15 × 106 cells/ml using a Bioruptor pico sonicator (Diagenode; 10 cycles, 30 s on, 30 s off, at 4 ◦C). .. Immunoprecipitation was performed using the MagnaChIP kit (Merck Millipore) according to the manufacturer’s instruction using 1 μg H3K4me3 antibody (Diagenode) per 500,000 cells. .. ChIP-seq libraries were prepared using the Kapa Hyper Prep Kit (KAPA Biosystems) according to the manufacturer’s protocol, with the following modifications.

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons.
    Article Snippet: Cells were sonicated at a concentration of 15 million cells/ml using a Bioruptor pico sonicator (Diagenode; 10 cycles, 30 s on, 30 s off, at 4 C). .. Immunoprecipitation was performed using the MagnaChIP kit (Merck Millipore) according to manufacturer’s instruction. .. In short, 500,000 cells were incubated overnight with 1 mg H3K4me3 or H3K27Ac antibody (Diagenode) and protein A magnetic beads at 4 C. Beads and chromatin/antibody mixture were washed four times for 5 minutes at 4 C. After washing chromatin was eluted and proteins were degraded using proteinase K. DNA was purified using spin columns and eluted in millliQ.

    Article Title: C1q reprograms innate immune memory
    Article Snippet: Cells were sonicated at a concentration of 15 million cells/ml using a Bioruptor pico sonicator (Diagenode, Liege, Belgium; 10–20 cycles, 30s on, 30s off), at 4°C. .. Immunoprecipitation was performed using the MagnaChIP kit (Merck Millipore, Darmstad, Germany) according to the manufacturer’s instructions. .. In short, 500,000 cells were incubated overnight with 1 mg H3K4me3 (Diagenode, Liege, Belgium) and protein A magnetic beads at 4°C.

    Article Title: Hydroxychloroquine inhibits trained immunity – implications for COVID-19
    Article Snippet: Cells were sonicated at a concentration of 15 million cells/ml using a Bioruptor pico sonicator (Diagenode; 10 cycles, 30s on, 30s off, at 4 °C). .. Immunoprecipitation was performed using the MagnaChIP kit (Merck Millipore) according to manufacturer’s instruction. .. In short, 500,000 cells were incubated overnight with 1 μg H3K4me3 or H3K27Ac antibody (Diagenode) and protein A magnetic beads at 4 °C.

    Recombinant:

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ ..

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ Article ll OPEN ACCESS ..

    Magnetic Cell Separation:

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ ..

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ Article ll OPEN ACCESS ..

    Isolation:

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ ..

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ Article ll OPEN ACCESS ..

    Enzyme-linked Immunosorbent Assay:

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ ..

    Article Title: Acid ceramidase regulates innate immune memory.
    Article Snippet: PHENYLHYDRAZONE (FCCP) Sigma Aldrich Cat#C2920 2-DEOXY-D-GLUCOSE Sigma Aldrich Cat#D6134 LIPOPOLYSACCHARIDE (E. COLI, O55:B5), USED IN THE 300BCG STUDY Sigma-Aldrich Cat#L2880 Critical commercial assays MACS PAN MONOCYTE ISOLATION KIT Miltenyi Biotech Cat#130-096-537 HUMAN IL-6 ELISA R&D systems Cat#DY206 (Continued on next page) 18 Cell Reports 42, 113458, December 26, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER HUMAN TNFA ELISA R&D systems Cat#DY210 HUMAN IFNG ELISA R&D systems Cat#DY285B HUMAN IL-1SS ELISA R&D systems Cat#DY201 MBCA KIT Thermo Fisher Scientific Cat#23235 CYQUANT LDH CYTOTOXICITY ASSAY Thermo Fisher Scientific Cat#C20301 WESTERNBRIGHT QUANTUM KIT Advansta Cat#K-12042-D10 SLIDEFLASKS Thermo Fisher Scientific Cat#170920 RNEASY MINI KIT Qiagen Cat#74106 MAGNACHIP KIT Merck-Millipore Cat#17-408 KAPA RNA HYPERPREP KIT (WITH RIBOERASE) KAPA Biosystems Cat#08098140702 HIGH SENSITIVITY DNA BIOANALYZER KIT Agilent Technologies Cat#5067-4626 DSDNA HIGH SENSITIVITY ASSAY Denovix N/A KAPA HYPER PREP KIT KAPA Biosystems Cat#7962363001 Deposited data IN VITRO TRAINED MONOCYTE CHIP-SEQ AND RNA-SEQ DATA This paper GEO: GSE188641 .. 300BCG COHORT (HUMAN FUNCTIONAL GENOMICS PROJECT) N/A https://www.humanfunctionalgenomics.org13 Software and algorithms GRAPHPAD PRISM Graphpad software N/A LIPOTYPEZOOM Lipotype GmbH N/A R R Core Team71 https://www.r-project.org/ HISAT Kim et al.72 http://www.ccb.jhu.edu/software/ hisat/index.shtml SAMTOOLS Li et al.73 http://samtools.sourceforge.net DESEQ2 Love at al.74 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html GGPLOT2 Wickham75 https://ggplot2.tidyverse.org/ COMPLEX HEATMAPS Gu et al.76 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html FGSEA R PACKAGE Subramanian et al.77 https://bioconductor.org/packages/ release/bioc/html/fgsea.html BURROS WHEELER ALIGNER Li et al.78 http://maq.sourceforge.net/ MODEL-BASED ANALYSIS OF CHIP-SEQ Zhang et al.79 http://liulab.dfci.harvard.edu/MACS/ BEDTOOLS Quinlan et al.80 http://code.google.com/p/bedtools GREAT McLean81 http://great.stanford.edu/public/html/ MARTIX-EQTL Shabalin82 https://CRAN.R-project.org/ package=matrixEQTL

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ Article ll OPEN ACCESS ..

    Lactate Assay:

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ ..

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ Article ll OPEN ACCESS ..

    Sensitive Assay:

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ ..

    Article Title: Acid ceramidase regulates innate immune memory.
    Article Snippet: PHENYLHYDRAZONE (FCCP) Sigma Aldrich Cat#C2920 2-DEOXY-D-GLUCOSE Sigma Aldrich Cat#D6134 LIPOPOLYSACCHARIDE (E. COLI, O55:B5), USED IN THE 300BCG STUDY Sigma-Aldrich Cat#L2880 Critical commercial assays MACS PAN MONOCYTE ISOLATION KIT Miltenyi Biotech Cat#130-096-537 HUMAN IL-6 ELISA R&D systems Cat#DY206 (Continued on next page) 18 Cell Reports 42, 113458, December 26, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER HUMAN TNFA ELISA R&D systems Cat#DY210 HUMAN IFNG ELISA R&D systems Cat#DY285B HUMAN IL-1SS ELISA R&D systems Cat#DY201 MBCA KIT Thermo Fisher Scientific Cat#23235 CYQUANT LDH CYTOTOXICITY ASSAY Thermo Fisher Scientific Cat#C20301 WESTERNBRIGHT QUANTUM KIT Advansta Cat#K-12042-D10 SLIDEFLASKS Thermo Fisher Scientific Cat#170920 RNEASY MINI KIT Qiagen Cat#74106 MAGNACHIP KIT Merck-Millipore Cat#17-408 KAPA RNA HYPERPREP KIT (WITH RIBOERASE) KAPA Biosystems Cat#08098140702 HIGH SENSITIVITY DNA BIOANALYZER KIT Agilent Technologies Cat#5067-4626 DSDNA HIGH SENSITIVITY ASSAY Denovix N/A KAPA HYPER PREP KIT KAPA Biosystems Cat#7962363001 Deposited data IN VITRO TRAINED MONOCYTE CHIP-SEQ AND RNA-SEQ DATA This paper GEO: GSE188641 .. 300BCG COHORT (HUMAN FUNCTIONAL GENOMICS PROJECT) N/A https://www.humanfunctionalgenomics.org13 Software and algorithms GRAPHPAD PRISM Graphpad software N/A LIPOTYPEZOOM Lipotype GmbH N/A R R Core Team71 https://www.r-project.org/ HISAT Kim et al.72 http://www.ccb.jhu.edu/software/ hisat/index.shtml SAMTOOLS Li et al.73 http://samtools.sourceforge.net DESEQ2 Love at al.74 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html GGPLOT2 Wickham75 https://ggplot2.tidyverse.org/ COMPLEX HEATMAPS Gu et al.76 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html FGSEA R PACKAGE Subramanian et al.77 https://bioconductor.org/packages/ release/bioc/html/fgsea.html BURROS WHEELER ALIGNER Li et al.78 http://maq.sourceforge.net/ MODEL-BASED ANALYSIS OF CHIP-SEQ Zhang et al.79 http://liulab.dfci.harvard.edu/MACS/ BEDTOOLS Quinlan et al.80 http://code.google.com/p/bedtools GREAT McLean81 http://great.stanford.edu/public/html/ MARTIX-EQTL Shabalin82 https://CRAN.R-project.org/ package=matrixEQTL

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ Article ll OPEN ACCESS ..

    In Vitro:

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ ..

    Article Title: Acid ceramidase regulates innate immune memory.
    Article Snippet: PHENYLHYDRAZONE (FCCP) Sigma Aldrich Cat#C2920 2-DEOXY-D-GLUCOSE Sigma Aldrich Cat#D6134 LIPOPOLYSACCHARIDE (E. COLI, O55:B5), USED IN THE 300BCG STUDY Sigma-Aldrich Cat#L2880 Critical commercial assays MACS PAN MONOCYTE ISOLATION KIT Miltenyi Biotech Cat#130-096-537 HUMAN IL-6 ELISA R&D systems Cat#DY206 (Continued on next page) 18 Cell Reports 42, 113458, December 26, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER HUMAN TNFA ELISA R&D systems Cat#DY210 HUMAN IFNG ELISA R&D systems Cat#DY285B HUMAN IL-1SS ELISA R&D systems Cat#DY201 MBCA KIT Thermo Fisher Scientific Cat#23235 CYQUANT LDH CYTOTOXICITY ASSAY Thermo Fisher Scientific Cat#C20301 WESTERNBRIGHT QUANTUM KIT Advansta Cat#K-12042-D10 SLIDEFLASKS Thermo Fisher Scientific Cat#170920 RNEASY MINI KIT Qiagen Cat#74106 MAGNACHIP KIT Merck-Millipore Cat#17-408 KAPA RNA HYPERPREP KIT (WITH RIBOERASE) KAPA Biosystems Cat#08098140702 HIGH SENSITIVITY DNA BIOANALYZER KIT Agilent Technologies Cat#5067-4626 DSDNA HIGH SENSITIVITY ASSAY Denovix N/A KAPA HYPER PREP KIT KAPA Biosystems Cat#7962363001 Deposited data IN VITRO TRAINED MONOCYTE CHIP-SEQ AND RNA-SEQ DATA This paper GEO: GSE188641 .. 300BCG COHORT (HUMAN FUNCTIONAL GENOMICS PROJECT) N/A https://www.humanfunctionalgenomics.org13 Software and algorithms GRAPHPAD PRISM Graphpad software N/A LIPOTYPEZOOM Lipotype GmbH N/A R R Core Team71 https://www.r-project.org/ HISAT Kim et al.72 http://www.ccb.jhu.edu/software/ hisat/index.shtml SAMTOOLS Li et al.73 http://samtools.sourceforge.net DESEQ2 Love at al.74 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html GGPLOT2 Wickham75 https://ggplot2.tidyverse.org/ COMPLEX HEATMAPS Gu et al.76 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html FGSEA R PACKAGE Subramanian et al.77 https://bioconductor.org/packages/ release/bioc/html/fgsea.html BURROS WHEELER ALIGNER Li et al.78 http://maq.sourceforge.net/ MODEL-BASED ANALYSIS OF CHIP-SEQ Zhang et al.79 http://liulab.dfci.harvard.edu/MACS/ BEDTOOLS Quinlan et al.80 http://code.google.com/p/bedtools GREAT McLean81 http://great.stanford.edu/public/html/ MARTIX-EQTL Shabalin82 https://CRAN.R-project.org/ package=matrixEQTL

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ Article ll OPEN ACCESS ..

    Chromatin Immunoprecipitation:

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ ..

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ Article ll OPEN ACCESS ..

    RNA Sequencing:

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ ..

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ Article ll OPEN ACCESS ..

    Software:

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons.
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ ..

    Article Title: Hydroxychloroquine Inhibits the Trained Innate Immune Response to Interferons
    Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Rabbit polyclonal anti H3K4me3 Diagenode Cat#pab-003-050; RRID: AB_2616052 Rabbit polyclonal anti-H3K27Ac Diagenode Cat#pab-196-050; RRID: AB_2637079 Anti-CD16 FITC eBioscience Cat#11-0168-42; RRID: AB_10805747 Anti-HLA-DR PE Coulter Cat#IM1639; RRID: AB_131284 Anti-CD14 PC7 eBioscience Cat#25-0149; RRID: AB_1582277 Anti-CD56 APC Coulter Cat#IM2474; RRID: AB_130791 Anti-CD3 APC-750 Coulter Cat#A94680; RRID: AB_2876783 Anti-CCR2 BV421 Beckton Dickinson Cat#564067; RRID: AB_2738573 Anti-CD11b BV785 Biolegend Cat#301346; RRID: AB_2563794 Live/Dead stain FVS620 Beckton Dickinson Cat#564996; RRID: AB_2869636 Anti-CD19 APC-R700 Beckton Dickinson Cat#564978; RRID: AB_2744308 Anti-CX3CR1 BV650 Biolegend Cat#341625; RRID: AB_2716244 Anti-CD45 BV510 Biolegend Cat#304035; RRID: AB_2561383 Bacterial or Virus strain Heat-killed SARS-CoV2 Isolated from patient N/A Biological Samples COVID-19 patient samples This paper N/A Human PBMCs from buffy coats Sanquin bloodbank Cat#B2825R00 Chemicals, Peptide and Recombinant Proteins Ficoll-Paque (Lymphoprep) StemCell Technologies, Inc. Cat#07861 Glutamax Thermo Fisher Scientific Cat#35050 Pyruvate Thermo Fisher Scientific Cat#11360 Penicillin/Streptomycin Thermo Fisher Scientific Cat#15140 RPMI Thermo Fisher Scientific Cat#22409 EDTA Sigma Cat#E5134 DNase I QIAGEN Cat#79254 Chloroquine diphosphate Sigma Cat#C6628 Hydroxychloroquine sulfate Sigma Cat#H0915 Rapamycin (Sirolimus) Selleckchem Cat#S1039 Heat-killed Candida albicans Invivogen Cat#tlrl-hkca Lipopolysaccharide (E.coli, O55:B5) Sigma Cat#L6529 Pam3CSK4 Invivogen Cat#tlrl-pms R848 Invivogen Cat#tlrl-R848 Heat-killed staphylococcus aureus ATCC Cat#25923 Heat-killed streptococcus pneumoniae ATCC Cat#49619 16% Formaldehyde Sigma Cat#28908 Protease Inhibitor Cocktail (tablets) Roche Cat#04693132001 Phenylmethylsulfonyl fluoride (PMSF) Roche Cat#11359061001 NextFlex DNA barcodes Bioo Scientific N/A NEXTflex adaptor stock Bioo Scientific N/A Recombinant human IFNg Invivogen Cat#rcyec-hinfg polyI:C Invivogen Cat#tlrl-pic Recombinant human IFNa Invivogen Cat#tlrl-hinfa8 (Continued on next page) Cell Reports Medicine 1, 100146, December 22, 2020 e1 .. REAGENT or RESOURCE SOURCE IDENTIFIER Recombinant human IFNb R&D systems Cat#8499-IF-010 Critical Commercial Assays MACS Pan Monocyte isolation kit Miltenyi Biotech Cat#130-096-537 Human IL-6 ELISA R&D systems Cat#DY206 Human TNFa ELISA R&D systems Cat#DY210 Human IFNg ELISA R&D systems Cat#DY285B Human IL-22 ELISA R&D systems Cat#DY782 Human IL-17 ELISA R&D systems Cat#DY317 Human Lactate assay Biovision Cat#K607 RNeasy Mini kit QIAGEN Cat#74106 MagnaChIP kit Merck-Millipore Cat#17-408 KAPA RNA HyperPrep Kit (with RiboErase) KAPA Biosystems Cat#08098140702 High Sensitivity DNA bioanalyzer kit Agilent Technologies Cat#5067-4626 dsDNA High Sensitivity Assay Denovix N/A Kapa Hyper Prep Kit KAPA Biosystems Cat#7962363001 Deposited Data In vitro trained monocyte ChIP-seq and RNA-seq data This paper GEO: GSE159678 COVID-19 patient RNA-seq data This paper GEO: GSE159678 Software and Algorithms GraphPad Prism Graphpad software N/A LipotypeZoom Lipotype GmbH N/A R R Core Team50 https://www.r-project.org/ Hisat Kim et al.51 http://www.ccb.jhu.edu/software/hisat/ index.shtml Samtools Li et al.52 http://samtools.sourceforge.net DESeq2 Love at al.53 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html ggplot2 Wickham54 https://ggplot2.tidyverse.org/ Complex Heatmaps Gu et al.55 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html fgsea R package Subramanian et al.56 https://bioconductor.org/packages/ release/bioc/html/fgsea.html Burros Wheeler Aligner Li and Durbin57 http://maq.sourceforge.net/ Model-based analysis of ChIP-Seq Zhang et al.58 https://github.com/macs3-project/MACS BEDtools Quinlan and Hall59 https://code.google.com/p/bedtools GREAT McLean et al.60 http://great.stanford.edu/public/html/ Article ll OPEN ACCESS ..

    CyQUANT Assay:

    Article Title: Acid ceramidase regulates innate immune memory.
    Article Snippet: PHENYLHYDRAZONE (FCCP) Sigma Aldrich Cat#C2920 2-DEOXY-D-GLUCOSE Sigma Aldrich Cat#D6134 LIPOPOLYSACCHARIDE (E. COLI, O55:B5), USED IN THE 300BCG STUDY Sigma-Aldrich Cat#L2880 Critical commercial assays MACS PAN MONOCYTE ISOLATION KIT Miltenyi Biotech Cat#130-096-537 HUMAN IL-6 ELISA R&D systems Cat#DY206 (Continued on next page) 18 Cell Reports 42, 113458, December 26, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER HUMAN TNFA ELISA R&D systems Cat#DY210 HUMAN IFNG ELISA R&D systems Cat#DY285B HUMAN IL-1SS ELISA R&D systems Cat#DY201 MBCA KIT Thermo Fisher Scientific Cat#23235 CYQUANT LDH CYTOTOXICITY ASSAY Thermo Fisher Scientific Cat#C20301 WESTERNBRIGHT QUANTUM KIT Advansta Cat#K-12042-D10 SLIDEFLASKS Thermo Fisher Scientific Cat#170920 RNEASY MINI KIT Qiagen Cat#74106 MAGNACHIP KIT Merck-Millipore Cat#17-408 KAPA RNA HYPERPREP KIT (WITH RIBOERASE) KAPA Biosystems Cat#08098140702 HIGH SENSITIVITY DNA BIOANALYZER KIT Agilent Technologies Cat#5067-4626 DSDNA HIGH SENSITIVITY ASSAY Denovix N/A KAPA HYPER PREP KIT KAPA Biosystems Cat#7962363001 Deposited data IN VITRO TRAINED MONOCYTE CHIP-SEQ AND RNA-SEQ DATA This paper GEO: GSE188641 .. 300BCG COHORT (HUMAN FUNCTIONAL GENOMICS PROJECT) N/A https://www.humanfunctionalgenomics.org13 Software and algorithms GRAPHPAD PRISM Graphpad software N/A LIPOTYPEZOOM Lipotype GmbH N/A R R Core Team71 https://www.r-project.org/ HISAT Kim et al.72 http://www.ccb.jhu.edu/software/ hisat/index.shtml SAMTOOLS Li et al.73 http://samtools.sourceforge.net DESEQ2 Love at al.74 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html GGPLOT2 Wickham75 https://ggplot2.tidyverse.org/ COMPLEX HEATMAPS Gu et al.76 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html FGSEA R PACKAGE Subramanian et al.77 https://bioconductor.org/packages/ release/bioc/html/fgsea.html BURROS WHEELER ALIGNER Li et al.78 http://maq.sourceforge.net/ MODEL-BASED ANALYSIS OF CHIP-SEQ Zhang et al.79 http://liulab.dfci.harvard.edu/MACS/ BEDTOOLS Quinlan et al.80 http://code.google.com/p/bedtools GREAT McLean81 http://great.stanford.edu/public/html/ MARTIX-EQTL Shabalin82 https://CRAN.R-project.org/ package=matrixEQTL

    LDH Cytotoxicity Assay:

    Article Title: Acid ceramidase regulates innate immune memory.
    Article Snippet: PHENYLHYDRAZONE (FCCP) Sigma Aldrich Cat#C2920 2-DEOXY-D-GLUCOSE Sigma Aldrich Cat#D6134 LIPOPOLYSACCHARIDE (E. COLI, O55:B5), USED IN THE 300BCG STUDY Sigma-Aldrich Cat#L2880 Critical commercial assays MACS PAN MONOCYTE ISOLATION KIT Miltenyi Biotech Cat#130-096-537 HUMAN IL-6 ELISA R&D systems Cat#DY206 (Continued on next page) 18 Cell Reports 42, 113458, December 26, 2023 .. REAGENT or RESOURCE SOURCE IDENTIFIER HUMAN TNFA ELISA R&D systems Cat#DY210 HUMAN IFNG ELISA R&D systems Cat#DY285B HUMAN IL-1SS ELISA R&D systems Cat#DY201 MBCA KIT Thermo Fisher Scientific Cat#23235 CYQUANT LDH CYTOTOXICITY ASSAY Thermo Fisher Scientific Cat#C20301 WESTERNBRIGHT QUANTUM KIT Advansta Cat#K-12042-D10 SLIDEFLASKS Thermo Fisher Scientific Cat#170920 RNEASY MINI KIT Qiagen Cat#74106 MAGNACHIP KIT Merck-Millipore Cat#17-408 KAPA RNA HYPERPREP KIT (WITH RIBOERASE) KAPA Biosystems Cat#08098140702 HIGH SENSITIVITY DNA BIOANALYZER KIT Agilent Technologies Cat#5067-4626 DSDNA HIGH SENSITIVITY ASSAY Denovix N/A KAPA HYPER PREP KIT KAPA Biosystems Cat#7962363001 Deposited data IN VITRO TRAINED MONOCYTE CHIP-SEQ AND RNA-SEQ DATA This paper GEO: GSE188641 .. 300BCG COHORT (HUMAN FUNCTIONAL GENOMICS PROJECT) N/A https://www.humanfunctionalgenomics.org13 Software and algorithms GRAPHPAD PRISM Graphpad software N/A LIPOTYPEZOOM Lipotype GmbH N/A R R Core Team71 https://www.r-project.org/ HISAT Kim et al.72 http://www.ccb.jhu.edu/software/ hisat/index.shtml SAMTOOLS Li et al.73 http://samtools.sourceforge.net DESEQ2 Love at al.74 http://www.bioconductor.org/packages/ release/bioc/html/DESeq2.html GGPLOT2 Wickham75 https://ggplot2.tidyverse.org/ COMPLEX HEATMAPS Gu et al.76 http://www.bioconductor.org/packages/ devel/bioc/html/ComplexHeatmap.html FGSEA R PACKAGE Subramanian et al.77 https://bioconductor.org/packages/ release/bioc/html/fgsea.html BURROS WHEELER ALIGNER Li et al.78 http://maq.sourceforge.net/ MODEL-BASED ANALYSIS OF CHIP-SEQ Zhang et al.79 http://liulab.dfci.harvard.edu/MACS/ BEDTOOLS Quinlan et al.80 http://code.google.com/p/bedtools GREAT McLean81 http://great.stanford.edu/public/html/ MARTIX-EQTL Shabalin82 https://CRAN.R-project.org/ package=matrixEQTL



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