REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
abTCR PE-Dazzle594 (IP26)	BioLegend	Cat#306726; RRID:AB_2566599
CD11b PerCp-Cy5.5 (M1/70)	BD	Cat#561114; RRID:AB_2033995
CD11c BUV805 (B-ly6)	BD	Cat#742005; RRID:AB_2868409
CD123 BV650 (6H6)	BioLegend	Cat#306020; RRID:AB_2563827
CD127 BV711 (A019D5)	BioLegend	Cat#351328; RRID:AB_2562908
CD14 BUV661 (MϕP9)	BD	Cat#741684; RRID:AB_2868407
CD14 PerCPCy5.5 (M5E2)	BioLegend	Cat#301824; RRID:AB_893251
CD141 APC (1A4)	BD	Cat#564123; RRID:AB_2738608
CD141 BB515 (1A4)	BD	Cat#565084; RRID:AB_2739058
CD15 APC/Fire750 (SSEA-1)	BioLegend	Cat#323042; RRID:AB_2572103
CD15 BUV563 (W6D3)	BD	Cat#741417; RRID:AB_2868406
CD16 BV605 (3G8)	BD	Cat#563172; RRID:AB_2744297
CD19 BB790 (HIB19)	BD	Cat#624296
CD19 BUV395 (HIB19)	BD	Cat#740287; RRID:AB_2740026
CD197 PE-Cy7 (G043H7)	BioLegend	Cat#353226; RRID:AB_11126145
CD25 BV421 (M-A251)	BD	Cat#562442; RRID:AB_11154578
CD27 PE (O323)	BioLegend	Cat#302808; RRID:AB_314300
CD3 BUV395 (UCHT1)	BD	Cat#563546; RRID:AB_2744387
CD304 PE (AD5-17F6)	Miltenyi Biotec	Cat#130-114-043; RRID:AB_2751190
CD304 BV786 (U21-1283)	BD	Cat#743132; RRID:AB_2741299
CD34 PE-Cy5 (581)	BD	Cat#555823; RRID:AB_396152
CD38 APC (HB-7)	BioLegend	Cat#356606; RRID:AB_2561902
CD4 BV421 (SK3)	BioLegend	Cat#344632; RRID:AB_2566015
CD4 BV480 (SK3)	BD	Cat#566104; RRID:AB_2739506
CD45 BUV496 (HI30)	BD	Cat#750179; RRID:AB_2868405
CD45 BUV805 (HI30)	BD	Cat#612891; RRID:AB_2870179
CD45RA BUV615 (HI100)	BD	Cat#624297
CD56 APC-R700 (NCAM16.2)	BD	Cat#565139; RRID:AB_2744429
CD56 BV786 (NCAM16.2)	BD	Cat#564058; RRID:AB_2738569
CD8a BUV496 (RPA-T8)	BD	Cat#612942; RRID:AB_2870223
CD8a BUV737 (RPA-T8)	BD	Cat#749367; RRID:AB_2868408
HLA-DR AF488 (L243)	BioLegend	Cat#307620; RRID:AB_493175
HLADR APC-Cy7 (L243)	BioLegend	Cat#307618; RRID:AB_493586
IgD BV750 (IA6-2)	BD	Cat#747484; RRID:AB_2868411
Fixable Viability Stain 510	BD	Cat#564406; RRID:AB_2869572
TCRab PE-Cy7 (IP26)	BioLegend	Cat#306719; RRID:AB_10640829
TCRgd PE-CF594 (B1)	BD	Cat#562511; RRID:AB_2737631
Biological samples
Human PBMC	Benaroya Research Institute	Table S7
Human PBMC	Bloodworks Northwest	Table S8
Critical commercial assays
nCounter Evaluation Gene Expression Assay	Nanostring Technologies	Hs Immunology v2 CodeSet
Discovery Assay 2019	Olink Proteomics	Olink CARDIOMETABOLIC(v.3603)
Discovery Assay 2019	Olink Proteomics	Olink CARDIOVASCULAR II(v.5004)
Discovery Assay 2019	Olink Proteomics	Olink CARDIOVASCULAR III(v.6112)
Discovery Assay 2019	Olink Proteomics	Olink CELL REGULATION(v.3701)
Discovery Assay 2019	Olink Proteomics	Olink DEVELOPMENT(v.3512)
Discovery Assay 2019	Olink Proteomics	Olink IMMUNE RESPONSE(v.3203)
Discovery Assay 2019	Olink Proteomics	Olink INFLAMMATION(v.3021)
Discovery Assay 2019	Olink Proteomics	Olink METABOLISM(v.3402)
Discovery Assay 2019	Olink Proteomics	Olink NEURO EXPLORATORY(v.3901)
Discovery Assay 2019	Olink Proteomics	Olink NEUROLOGY(v.8011)
Discovery Assay 2019	Olink Proteomics	Olink ONCOLOGY II(v.7003)
Discovery Assay 2019	Olink Proteomics	Olink ONCOLOGY III(v.4001)
Discovery Assay 2019	Olink Proteomics	Olink ORGAN DAMAGE(v.3311)
Chromium Single Cell 3′ Library & Gel Bead Kit v3	10X Genomics	Cat#1000075
Chromium™ Chip B Single Cell Kit	10X Genomics	Cat#1000073
i7 Multiplex Kit	10X Genomics	Cat#120262
GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1	10X Genomics	Cat#1000121
Bead kit	10X Genomics	Cat#1000122
Chip B	10X Genomics	Cat#1000120
Deposited data
Single-cell RNA-sequencing	GEO	GSE156989
Single-cell RNA-sequencing	dbGaP	phs002280
Software and algorithms
NanoStringNorm	Waggott et al. (2012)	https://github.com/cran/NanoStringNorm
CellRanger v3.1.0	10x Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome
FastQC v0.11.3		https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Bioconductor v3.1.0		https://bioconductor.org/news/bioc_3_1_release/
Seurat v3	Stuart et al. (2019a)	https://satijalab.org/seurat/articles/install.html
MAST (Seurat v3)	Finak et al. (2015)	https://github.com/RGLab/MAST
glmmTMB version 1.0.1		https://github.com/glmmTMB/glmmTMB
lme4 v1.1-14		https://github.com/lme4/lme4
Ingenuity Pathway Analysis (release: Summer 2020)	Qiagen	https://digitalinsights.qiagen.com/products-overview/discovery-insights-portfolio/analysis-and-visualization/qiagen-ipa/
FlowJo v10	BD	https://www.flowjo.com/solutions/flowjo/downloads
Prism v9	GraphPad	https://www.graphpad.com/
Illustrator 2019	Adobe	https://www.adobe.com/products/illustrator.html