REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-CD3	eBioscience	Cat# 16-0037-85; RRID: AB_468855
Anti-CD28	eBioscience	Cat# 16-0289-85; RRID: AB_468927
Anti-SARS-CoV-2 Spike Antibody	Abcam	Cat# ab273073
Anti- SARS-CoV-2 Nucleocapsid Antibody	Abcam	Cat# ab272852
Anti-Human IgG Conjugated with Peroxidase	Sigma Aldrich	Cat# A6029; RRID: AB_258272
Anti-Human IgA Conjugated with Peroxidase	Sigma Aldrich	Cat# A0295; RRID: AB_257876
Anti-Human IgM Conjugated with Peroxidase	Abcam	Cat# ab97205; RRID: AB_10695942
Chemicals, peptides, and recombinant proteins
RBC lysis buffer	Miltenyi Biotech	Cat# 130-094-183
RPMI 1640 Medium	Gibco	Cat# 11875-093
FBS	Gibco	Cat# 15140-122
Glutamax	Gibco	Cat# 35050061
TotalSeq™-C0251 anti-human Hashtag 1 Antibody	Biolegend	Cat# 394661
TotalSeq™-C0252 anti-human Hashtag 2 Antibody	Biolegend	Cat# 394663
TotalSeq™-C0253 anti-human Hashtag 3 Antibody	Biolegend	Cat# 394665
TotalSeq™-C0254 anti-human Hashtag 4 Antibody	Biolegend	Cat# 394667
TotalSeq™-C0255 anti-human Hashtag 5 Antibody	Biolegend	Cat# 394669
TotalSeq™-C0256 anti-human Hashtag 6 Antibody	Biolegend	Cat# 394671
TotalSeq™-C0257 anti-human Hashtag 7 Antibody	Biolegend	Cat# 394673
TotalSeq™-C0258 anti-human Hashtag 8 Antibody	Biolegend	Cat# 394675
TotalSeq™-C0259 anti-human Hashtag 9 Antibody	Biolegend	Cat# 394677
TotalSeq™-C0260 anti-human Hashtag 10 Antibody	Biolegend	Cat# 394679
TotalSeq™-C Custom Human panel	Biolegend	Cat# 99814
CD8 Microbeads	Miltenyi Biotech	Cat# 130-045-201
CD4 Microbeads	Miltenyi Biotech	Cat# 130-045-101
CD56 Microbeads	Miltenyi Biotech	Cat# 130-050-401
Pan Monocyte Isolation Kit	Miltenyi Biotech	Cat# 130-096-537
IL-2	Biolegend	Cat# 589104
Lipopolysaccharide	Sigma Aldrich	Cat# L2654
PMA	Sigma Aldrich	Cat# 8139
Lonomycin	Sigma Aldrich	Cat# 10634
CryoStor CS-10	Biolife Solutions	Cat# 210102
PBS, 1X	Fisher Scientific	Cat# 21-040-CV
SARS-CoV-2 RBD Protein	Invitrogen	Cat# RP-87678
SARS-CoV-2 Spike Protein	Invitrogen	Cat# RP-87680
SARS-CoV-2 Nucleocapsid Protein	Invitrogen	Cat# RP-87707
TMB Peroxidase Substrate Kit	Seracare	Cat# 5120-0047
IFN-α2	Miltenyi Biotech	Cat# 130-093-874
U1-snRNP	Diarect	Cat# A13000
Ribosomal Phosphoprotein P1	Diarect	Cat# A14200
Ro/SS-A	Diarect	Cat# A12700
La/SS-B	Diarect	Cat# A12800
Jo-1	Diarect	Cat# A12900
Critical commercial assays
Chromium Next GEM Single Cell 5’ Library and Gel Bead Kit v1.1	10x Genomics	Cat# 1000165
Chromium Next GEM Chip G Single Cell Kit	10x Genomics	Cat# 1000120
Single Cell Polyfunctional Strength Panel Human	Isoplexis	Cat# PANEL-1001
Single Cell Polyfunctional Strength ISOCODE Chip	Isoplexis	Cat# ISOCODE-1000
Single Cell Innate Myeloid Panel Human	Isoplexis	Cat# PANEL-3L02
Single Cell Innate and Myeloid ISOCODE Chip	Isoplexis	Cat# ISOCODE-3000
Cardiovascular II panel	Olink	Cat# 95500
Inflammation panel	Olink	Cat# 95302
Metabolism panel	Olink	Cat# 95340
Immune Response panel	Olink	Cat# 95320
Organ Damage panel	Olink	Cat# 95331
Deposited data
Processed scRNA-seq data	This paper	Array Express: E-MTAB-10129
Software and algorithms
Robustbase (Python package)	Maechler et al., 2021	https://github.com/cran/robustbase
CellRanger v3.1.0	10x Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
Scrublet v0.2.1 (Python package)	Wolock et al., 2019	https://github.com/AllonKleinLab/scrublet
Scanpy v1.6.0 (Python package)	Wolf et al., 2018	https://github.com/theislab/scanpy
UMAP v0.5.1 (Python package)	McInnes et al., 2020	https://github.com/lmcinnes/umap
Leiden v0.8.0 (Python package)	Traag et al., 2019	https://github.com/vtraag/leidenalg
bbKNN v1.3.12 (Python package)	Polański et al., 2020	https://github.com/Teichlab/bbknn
Scirpy v0.3 (Python package)	Sturm et al., 2020	https://github.com/icbi-lab/scirpy
BLASTp v2.12.0+	Altschul et al., 1997	https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins
Lifelines v0.26.0 (Python package)	Davidson-Pilon, 2021	https://github.com/CamDavidsonPilon/lifelines
scikit-learn v0.24.2 (Python package)	Pedregosa et al., 2011	https://github.com/scikit-learn/scikit-learn
IgBLAST	Ye et al., 2013	https://www.ncbi.nlm.nih.gov/igblast/
Immunarch v0.6.5 (R package)	ImmunoMind Team, 2019	https://immunarch.com/
IsoSpeak Software	Isoplexis	Product Code: ISOSPEAK-1000-1
Other
IsoLight System	Isoplexis	Product Code: ISOLIGHT-1000-1
EDTA-coated Vacutainer Tubes	BD	Cat# 366643
384-well plates	Thermo Fisher	Cat# 464718