REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
CD8a, BV711, clone RPA-T8	Biolegend	301044; RRID:AB_11218793
CD11c, PE/Dazzle 594, clone 3.9	Biolegend	301642; RRID:AB_2564083
CD16, BV570, clone 3G8	Biolegend	302036; RRID:AB_2632790
CD19, AF488, clone HIB19	Biolegend	302219; RRID:AB_389313
CD25, PerCP/Cy5.5, clone BC96	Biolegend	302626; RRID:AB_2125479
CD45RA, AF488, clone HI100	Biolegend	304114; RRID:AB_528816
CD123, BV711, clone 6H6	Biolegend	306030; RRID:AB_2566353
HLA-DR, PE/Cy5, clone L243	Biolegend	307608; RRID:AB_314686
HLA-DR, BV570, clone L243	Biolegend	307638; RRID:AB_2650882
CD24, PerCP/Cy5.5, clone ML5	Biolegend	311116; RRID:AB_10962689
IgM, BV421, clone MHM-88	Biolegend	314516; RRID:AB_2561443
CD3, BV510, clone OKT3	Biolegend	317332; RRID:AB_2561943
CD4, BV605, clone OKT4	Biolegend	317438; RRID:AB_11204077
CD279 (PD1), PE, clone EH12.2H7	Biolegend	329906; RRID:AB_940481
CD1c, AF647, clone L161	Biolegend	331510; RRID:AB_1186032
CD161, PE, clone HP-3G10	Biolegend	339904; RRID:AB_1501086
TCR Vα24-Jα18, BV421, clone 6B11	Biolegend	342916; RRID:AB_2564004
CD141, PE/Cy7, clone M80	Biolegend	344110; RRID:AB_256122
IgD, PE, clone IA6-2	Biolegend	348204; RRID:AB_10553900
CD127, BV650, clone A019D5	Biolegend	351326; RRID:AB_2562095
TCR Vα7.2, PE/Cy7, clone 3C10	Biolegend	351712; RRID:AB_2561993
CCR7, BV421, clone G043H7	Biolegend	353208; RRID:AB_10915137
CCR6, BV650, clone G034E3	Biolegend	353426; RRID:AB_2563869
CXCR3, PE/Dazzle 594, clone G025H7	Biolegend	353736; RRID:AB_2564287
CD38, PE/Cy7, clone HB-7	Biolegend	356608; RRID:AB_2561903
CCR4, PE/Dazzle 594, clone L291H4	Biolegend	359420; RRID:AB_2564094
CD57, PerCP/Cy5.5, clone HNK-1	Biolegend	359622; RRID:AB_2565930
CD56, Pacific Blue, clone 5.1H11	Biolegend	362520; RRID:AB_2564096
CD56, BV510, clone 5.1H11	Biolegend	362534; RRID:AB_2565633
CD14, Pacific Blue, clone 63D3	Biolegend	367122; RRID:AB_2687385
CD45, PerCP, clone 2D1	Biolegend	368506; RRID:AB_2566358
CD45, BV605, clone 2D1	Biolegend	368524; RRID:AB_2715826
Zombie NIR	Biolegend	423105
CD4, PE-AF610, clone S3.5	Thermofisher	MHCD0422; RRID:AB_10371763
Biological samples
Human blood samples	Patients and healthy donors	This paper
Human blood samples	Etablissement Francais du Sang	This paper
Human PBMC	PromoCell	434Z036
Chemicals, peptides, and recombinant proteins
Recombinant human IFN-β	PBL assay	11410
ADUS100	Sanofi compound	RA14447001A
JAK1/2-inhibitor (baricitinib)	Sanofi compound	RA14836171
Ficoll	Eurobio Scientific	Cat#CMSMSL01-01
Fetal Bovine Serum	Gibco, Thermo Fisher Scientific	Cat#10270106
DMSO	Sigma Aldrich	Cat#D2650
Fc Block	Miltenyi Biotec	130-059-901
TruStain FcX	Biolegend	4422302
PierceTM 16% Formaldehyde (w/v), Methanolfree	Thermo Fisher Scientific	Cat# 28906 (10∗1 mL)
Cell ID Intercalator	Standard BioTools	201325
pBSSVD2005	Addgene	21826
EQ Beads	Standard BioTools	Cat# 201078
Critical commercial assays
Maxpar Direct Immune Profiling Assay	Standard BioTools	Cat# 201325
Chromium Single Cell 3′ Library & Gel Bead Kit v2	10X Genomics	Not available anymore
Chromium Single Cell 3′ Library & Gel Bead Kit v3	10X Genomics	1000075
Chromium Single Cell 3′ Library & Gel Bead Kit v3.1	10X Genomics	1000268
Proximity extension assay Inflammation	Olink	Targeted 96 inflammation
Oligonucleotides
EIF2AK3 primers: Forward TCAGATATGAACAGCCTTCAGTGT Reverse AACCAAAATTTCACAAGTGGCT	Eurofins Genomics	N/A
Deposited data
Single-Cell RNA-sequencing data – SAVI dataset	This paper	GSE226598
Single-Cell RNA-sequencing data – IFN dataset	This paper	GSE226572
Software and algorithms
CellRanger V6	10x Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
R V3.6.1	R-project	https://www.r-project.org/
Seurat v4	Hao et al.51	https://satijalab.org/seurat/
FlowJo v10	BD	https://www.flowjo.com/solutions/flowjo
EnrichR	Chen et al.52	https://maayanlab.cloud/Enrichr/
Spotfire® v.10.3.2.7	TIBCO®	https://www.tibco.com/products/tibco-spotfire
CyTOF software version 8.0.14050	Standard BioTools	https://go.fluidigm.com/cytofsw/v8
MaxPar Pathsetter V.2.0.45.4	Standard BioTools	https://www.standardbio.com/products/software/maxpar-pathsetter
Ingenuity pathway analysis v57662101	Qiagen	https://www.qiagen.com/us/products/discovery-and-translational-research/next-generation-sequencing/informatics-and-data/interpretation-content-databases/ingenuity-pathway-analysis