REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rabbit polyclonal anti H3K4me3	Diagenode	Cat#pab-003-050; RRID: AB_2616052
Rabbit polyclonal anti-H3K27Ac	Diagenode	Cat#pab-196-050; RRID: AB_2637079
Anti-CD16 FITC	eBioscience	Cat#11-0168-42; RRID: AB_10805747
Anti-HLA-DR PE	Coulter	Cat#IM1639; RRID: AB_131284
Anti-CD14 PC7	eBioscience	Cat#25-0149; RRID: AB_1582277
Anti-CD56 APC	Coulter	Cat#IM2474; RRID: AB_130791
Anti-CD3 APC-750	Coulter	Cat#A94680; RRID: AB_2876783
Anti-CCR2 BV421	Beckton Dickinson	Cat#564067; RRID: AB_2738573
Anti-CD11b BV785	Biolegend	Cat#301346; RRID: AB_2563794
Live/Dead stain FVS620	Beckton Dickinson	Cat#564996; RRID: AB_2869636
Anti-CD19 APC-R700	Beckton Dickinson	Cat#564978; RRID: AB_2744308
Anti-CX3CR1 BV650	Biolegend	Cat#341625; RRID: AB_2716244
Anti-CD45 BV510	Biolegend	Cat#304035; RRID: AB_2561383
Bacterial or Virus strain
Heat-killed SARS-CoV2	Isolated from patient	N/A
Biological Samples
COVID-19 patient samples	This paper	N/A
Human PBMCs from buffy coats	Sanquin bloodbank	Cat#B2825R00
Chemicals, Peptide and Recombinant Proteins
Ficoll-Paque (Lymphoprep)	StemCell Technologies, Inc.	Cat#07861
Glutamax	Thermo Fisher Scientific	Cat#35050
Pyruvate	Thermo Fisher Scientific	Cat#11360
Penicillin/Streptomycin	Thermo Fisher Scientific	Cat#15140
RPMI	Thermo Fisher Scientific	Cat#22409
EDTA	Sigma	Cat#E5134
DNase I	QIAGEN	Cat#79254
Chloroquine diphosphate	Sigma	Cat#C6628
Hydroxychloroquine sulfate	Sigma	Cat#H0915
Rapamycin (Sirolimus)	Selleckchem	Cat#S1039
Heat-killed Candida albicans	Invivogen	Cat#tlrl-hkca
Lipopolysaccharide (E.coli, O55:B5)	Sigma	Cat#L6529
Pam3CSK4	Invivogen	Cat#tlrl-pms
R848	Invivogen	Cat#tlrl-R848
Heat-killed staphylococcus aureus	ATCC	Cat#25923
Heat-killed streptococcus pneumoniae	ATCC	Cat#49619
16% Formaldehyde	Sigma	Cat#28908
Protease Inhibitor Cocktail (tablets)	Roche	Cat#04693132001
Phenylmethylsulfonyl fluoride (PMSF)	Roche	Cat#11359061001
NextFlex DNA barcodes	Bioo Scientific	N/A
NEXTflex adaptor stock	Bioo Scientific	N/A
Recombinant human IFNγ	Invivogen	Cat#rcyec-hinfg
polyI:C	Invivogen	Cat#tlrl-pic
Recombinant human IFNα	Invivogen	Cat#tlrl-hinfa8
Recombinant human IFNβ	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 TNFα ELISA	R&D systems	Cat#DY210
Human IFNγ 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/