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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