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heat killed spneu serotype 3  (ATCC)


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    Structured Review

    ATCC heat killed spneu serotype 3
    Heat Killed Spneu Serotype 3, supplied by ATCC, used in various techniques. Bioz Stars score: 96/100, based on 580 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/heat+killed+streptococcus+pneumoniae+atcc/Streptococcus+Pneumoniae/pm36535641-43-16-21
    Average 96 stars, based on 580 article reviews
    heat killed spneu serotype 3 - by Bioz Stars, 2026-10
    96/100 stars

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    Staining:

    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 Cat49619 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 Cat49619 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

    Virus:

    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 Cat49619 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 Cat49619 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 Cat49619 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 Cat49619 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

    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 Cat49619 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 Cat49619 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

    Protease Inhibitor:

    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 Cat49619 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 Cat49619 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



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    FIGURE 1. AMs and respiratory epithelial cells express CD36, and S. <t>pneumoniae</t> induces pulmonary CD36 expression. (A and B) FACS staining for CD36 on MH-S (A) and MLE-12 (B) cells. Black fill depicts CD36-stained cells, and open fill represents isotype control Ab. (C) CD36 IHC was conducted from uninfected lungs of WT and CD362/2 mice. The negative control represents Ag-retrieved lungs without incubation with Ab. Original magnification 3 100. (D) WT mice (n = 6 per time point) were intranasally inoculated with 105 CFU S. pneumoniae, and after indicated time points CD36 lung transcript levels were evaluated. (E–J) WT AMs (E, G, H) or respiratory epithelial cells (F, I, J) were treated with heat-killed S. pneumoniae for indicated time points, and CD36 RT-PCR (E, F) and CD36 FACS (G–J) were conducted. (K, L) WT mice (n = 4 per time point) were intranasally inoculated with 105 CFU S. pneumoniae, and CD36 expression was evaluated on AMs from BAL after indicated time points. Depicted is the percentage of CD45+/F4/80+/CD11c+/ CD11b2 cells (AMs) positive for CD36. Representative FACS plots are shown. Data presented are mean 6 SEM, and data are representative of duplicate experiments. *p , 0.05 versus time point 0.
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    Image Search Results


    FIGURE 1. AMs and respiratory epithelial cells express CD36, and S. pneumoniae induces pulmonary CD36 expression. (A and B) FACS staining for CD36 on MH-S (A) and MLE-12 (B) cells. Black fill depicts CD36-stained cells, and open fill represents isotype control Ab. (C) CD36 IHC was conducted from uninfected lungs of WT and CD362/2 mice. The negative control represents Ag-retrieved lungs without incubation with Ab. Original magnification 3 100. (D) WT mice (n = 6 per time point) were intranasally inoculated with 105 CFU S. pneumoniae, and after indicated time points CD36 lung transcript levels were evaluated. (E–J) WT AMs (E, G, H) or respiratory epithelial cells (F, I, J) were treated with heat-killed S. pneumoniae for indicated time points, and CD36 RT-PCR (E, F) and CD36 FACS (G–J) were conducted. (K, L) WT mice (n = 4 per time point) were intranasally inoculated with 105 CFU S. pneumoniae, and CD36 expression was evaluated on AMs from BAL after indicated time points. Depicted is the percentage of CD45+/F4/80+/CD11c+/ CD11b2 cells (AMs) positive for CD36. Representative FACS plots are shown. Data presented are mean 6 SEM, and data are representative of duplicate experiments. *p , 0.05 versus time point 0.

    Journal: Journal of immunology (Baltimore, Md. : 1950)

    Article Title: The scavenger receptor CD36 downmodulates the early inflammatory response while enhancing bacterial phagocytosis during pneumococcal pneumonia.

    doi: 10.4049/jimmunol.1202270

    Figure Lengend Snippet: FIGURE 1. AMs and respiratory epithelial cells express CD36, and S. pneumoniae induces pulmonary CD36 expression. (A and B) FACS staining for CD36 on MH-S (A) and MLE-12 (B) cells. Black fill depicts CD36-stained cells, and open fill represents isotype control Ab. (C) CD36 IHC was conducted from uninfected lungs of WT and CD362/2 mice. The negative control represents Ag-retrieved lungs without incubation with Ab. Original magnification 3 100. (D) WT mice (n = 6 per time point) were intranasally inoculated with 105 CFU S. pneumoniae, and after indicated time points CD36 lung transcript levels were evaluated. (E–J) WT AMs (E, G, H) or respiratory epithelial cells (F, I, J) were treated with heat-killed S. pneumoniae for indicated time points, and CD36 RT-PCR (E, F) and CD36 FACS (G–J) were conducted. (K, L) WT mice (n = 4 per time point) were intranasally inoculated with 105 CFU S. pneumoniae, and CD36 expression was evaluated on AMs from BAL after indicated time points. Depicted is the percentage of CD45+/F4/80+/CD11c+/ CD11b2 cells (AMs) positive for CD36. Representative FACS plots are shown. Data presented are mean 6 SEM, and data are representative of duplicate experiments. *p , 0.05 versus time point 0.

    Article Snippet: AMs from WT and CD362/2 mice were plated at 0.5 3 106 per well in 12- well microtiter plates, allowed to adhere, and following washing steps, FITClabeled heat-killed S. pneumoniae (ATCC 6303) were added in the presence of RPMI 1640 for 1 h [multiplicity of infection (MOI) 100] at 37 ̊C or 4 ̊C (as a negative control), respectively.

    Techniques: Expressing, Staining, Control, Negative Control, Incubation, Reverse Transcription Polymerase Chain Reaction

    FIGURE 2. CD36 suppresses S. pneumoniae–medi- ated inflammation in vitro in AMs and respiratory ep- ithelial cells. (A, B) WT primary respiratory epithelial cells (A) or AMs (B) seeded at 106/ml were treated with 2 3 107 CFU/ml S. pneumoniae for 6 h with and without pretreatment with a CD36 blocking or isotype control Ab, and levels of the indicated cytokines were evaluated in the supernatant, using ELISA. (C) WT or CD362/2 AMs were treated with 2 3 107 CFU/ml heat-killed S. pneumoniae for 6 h, and levels of TNF-a and MIP-2 were evaluated in the supernatant. (D) WT or CD362/2 AMs were treated with 2 3 107 CFU/ml heat-killed S. pneumoniae or 10 mg/ml S. aureus LTA for 6 h, and levels of TNF-a were evaluated in the supernatant. All data presented are mean 6 SEM and representative of duplicate experiments. *p , 0.05 versus isotype at the identical concentration (A, B) or WT.

    Journal: Journal of immunology (Baltimore, Md. : 1950)

    Article Title: The scavenger receptor CD36 downmodulates the early inflammatory response while enhancing bacterial phagocytosis during pneumococcal pneumonia.

    doi: 10.4049/jimmunol.1202270

    Figure Lengend Snippet: FIGURE 2. CD36 suppresses S. pneumoniae–medi- ated inflammation in vitro in AMs and respiratory ep- ithelial cells. (A, B) WT primary respiratory epithelial cells (A) or AMs (B) seeded at 106/ml were treated with 2 3 107 CFU/ml S. pneumoniae for 6 h with and without pretreatment with a CD36 blocking or isotype control Ab, and levels of the indicated cytokines were evaluated in the supernatant, using ELISA. (C) WT or CD362/2 AMs were treated with 2 3 107 CFU/ml heat-killed S. pneumoniae for 6 h, and levels of TNF-a and MIP-2 were evaluated in the supernatant. (D) WT or CD362/2 AMs were treated with 2 3 107 CFU/ml heat-killed S. pneumoniae or 10 mg/ml S. aureus LTA for 6 h, and levels of TNF-a were evaluated in the supernatant. All data presented are mean 6 SEM and representative of duplicate experiments. *p , 0.05 versus isotype at the identical concentration (A, B) or WT.

    Article Snippet: AMs from WT and CD362/2 mice were plated at 0.5 3 106 per well in 12- well microtiter plates, allowed to adhere, and following washing steps, FITClabeled heat-killed S. pneumoniae (ATCC 6303) were added in the presence of RPMI 1640 for 1 h [multiplicity of infection (MOI) 100] at 37 ̊C or 4 ̊C (as a negative control), respectively.

    Techniques: In Vitro, Blocking Assay, Control, Enzyme-linked Immunosorbent Assay, Concentration Assay

    FIGURE 3. S. pneumoniae binds to CD36 via its PC, which suppresses inflammation. (A) WT BMDMs seeded at 1.6 3 106/ml were incubated with S. pneumoniae or E. coli (MOI 100) that were pretreated with either isotype (KLH) or EO6 Ab for 2 h at 4˚C, and bacterial binding was assessed using FACS. (B) WT or CD362/2 BMDMs seeded at 1.6 3 106/ml were incubated with FITC-labeled S. pneumoniae that had been pretreated with EO6 Ab (MOI 100) for 2 h at 4˚C, and bacterial binding was assessed using FACS. (C) WTAMs seeded at 106/ml were pretreated with either isotype or an EO6 Ab and incubated with 2 3 107 CFU/ml heat-killed S. pneumoniae or E. coli for 6 h, and levels of MIP-2 were evaluated in the su- pernatant. (D) WT or CD362/2 AMs seeded at 106/ml were pretreated with either PC-BSA or BSA and incu- bated with 2 3 107 CFU/ml heat-killed S. pneumoniae for 6 h, and levels of TNF-a were evaluated in the super- natant. (E) WT and CD362/2 BMDMs were incubated with heat-killed S. pneumoniae, 10 mg/ml S. pneumoniae LTA (R6 strain), or 1 mg/ml LPS for 6 h, and levels of MIP-2 were evaluated in the supernatant. All data pre- sented are mean 6 SEM and representative of duplicate experiments (A, B, E). *p , 0.05 versus isotype (A, C) or S. pneumoniae (B).

    Journal: Journal of immunology (Baltimore, Md. : 1950)

    Article Title: The scavenger receptor CD36 downmodulates the early inflammatory response while enhancing bacterial phagocytosis during pneumococcal pneumonia.

    doi: 10.4049/jimmunol.1202270

    Figure Lengend Snippet: FIGURE 3. S. pneumoniae binds to CD36 via its PC, which suppresses inflammation. (A) WT BMDMs seeded at 1.6 3 106/ml were incubated with S. pneumoniae or E. coli (MOI 100) that were pretreated with either isotype (KLH) or EO6 Ab for 2 h at 4˚C, and bacterial binding was assessed using FACS. (B) WT or CD362/2 BMDMs seeded at 1.6 3 106/ml were incubated with FITC-labeled S. pneumoniae that had been pretreated with EO6 Ab (MOI 100) for 2 h at 4˚C, and bacterial binding was assessed using FACS. (C) WTAMs seeded at 106/ml were pretreated with either isotype or an EO6 Ab and incubated with 2 3 107 CFU/ml heat-killed S. pneumoniae or E. coli for 6 h, and levels of MIP-2 were evaluated in the su- pernatant. (D) WT or CD362/2 AMs seeded at 106/ml were pretreated with either PC-BSA or BSA and incu- bated with 2 3 107 CFU/ml heat-killed S. pneumoniae for 6 h, and levels of TNF-a were evaluated in the super- natant. (E) WT and CD362/2 BMDMs were incubated with heat-killed S. pneumoniae, 10 mg/ml S. pneumoniae LTA (R6 strain), or 1 mg/ml LPS for 6 h, and levels of MIP-2 were evaluated in the supernatant. All data pre- sented are mean 6 SEM and representative of duplicate experiments (A, B, E). *p , 0.05 versus isotype (A, C) or S. pneumoniae (B).

    Article Snippet: AMs from WT and CD362/2 mice were plated at 0.5 3 106 per well in 12- well microtiter plates, allowed to adhere, and following washing steps, FITClabeled heat-killed S. pneumoniae (ATCC 6303) were added in the presence of RPMI 1640 for 1 h [multiplicity of infection (MOI) 100] at 37 ̊C or 4 ̊C (as a negative control), respectively.

    Techniques: Incubation, Binding Assay, Labeling

    FIGURE 4. CD36 suppresses early S. pneumoniae– mediated inflammation in vivo. (A–F) WT and CD362/2

    Journal: Journal of immunology (Baltimore, Md. : 1950)

    Article Title: The scavenger receptor CD36 downmodulates the early inflammatory response while enhancing bacterial phagocytosis during pneumococcal pneumonia.

    doi: 10.4049/jimmunol.1202270

    Figure Lengend Snippet: FIGURE 4. CD36 suppresses early S. pneumoniae– mediated inflammation in vivo. (A–F) WT and CD362/2

    Article Snippet: AMs from WT and CD362/2 mice were plated at 0.5 3 106 per well in 12- well microtiter plates, allowed to adhere, and following washing steps, FITClabeled heat-killed S. pneumoniae (ATCC 6303) were added in the presence of RPMI 1640 for 1 h [multiplicity of infection (MOI) 100] at 37 ̊C or 4 ̊C (as a negative control), respectively.

    Techniques: In Vivo

    FIGURE 5. CD36 contributes to S. pneumoniae clearance in vivo but has no effects on mortality. (A) WT and CD362/2 mice (n = 7) were intranasally in- oculated with 105 CFU S. pneumoniae, and at 44 h post infection pulmonary bacterial load was evaluated. (B) WT or CD362/2 AMs seeded at 1.6 3 106/ml were incubated with FITC-labeled S. pneumoniae (MOI 100), and phagocytosis was assessed using FACS. (C and D) WT and CD362/2 mice (n = 12–13) were in- tranasally inoculated with (C) 105 or (D) 5 3 103 CFU S. pneumoniae, and survival was monitored for 10 d. Data in (A) and (B) are mean 6 SEM. *p , 0.05 versus WT.

    Journal: Journal of immunology (Baltimore, Md. : 1950)

    Article Title: The scavenger receptor CD36 downmodulates the early inflammatory response while enhancing bacterial phagocytosis during pneumococcal pneumonia.

    doi: 10.4049/jimmunol.1202270

    Figure Lengend Snippet: FIGURE 5. CD36 contributes to S. pneumoniae clearance in vivo but has no effects on mortality. (A) WT and CD362/2 mice (n = 7) were intranasally in- oculated with 105 CFU S. pneumoniae, and at 44 h post infection pulmonary bacterial load was evaluated. (B) WT or CD362/2 AMs seeded at 1.6 3 106/ml were incubated with FITC-labeled S. pneumoniae (MOI 100), and phagocytosis was assessed using FACS. (C and D) WT and CD362/2 mice (n = 12–13) were in- tranasally inoculated with (C) 105 or (D) 5 3 103 CFU S. pneumoniae, and survival was monitored for 10 d. Data in (A) and (B) are mean 6 SEM. *p , 0.05 versus WT.

    Article Snippet: AMs from WT and CD362/2 mice were plated at 0.5 3 106 per well in 12- well microtiter plates, allowed to adhere, and following washing steps, FITClabeled heat-killed S. pneumoniae (ATCC 6303) were added in the presence of RPMI 1640 for 1 h [multiplicity of infection (MOI) 100] at 37 ̊C or 4 ̊C (as a negative control), respectively.

    Techniques: In Vivo, Infection, Incubation, Labeling