REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-Human HLA-DR BUV395	BD	G46-6; Cat #564040; RRID:AB_2738558
Anti-Human CD16 BUV496	BD	3G8; Cat #612944; RRID:AB_2870224
Anti-Human CD163 BUV563	BD OptiBuild	GHI/61; Cat #741402; RRID:AB_2870894
Anti-Human CD33 BUV615	BD OptiBuild	WM53; Cat #751275; RRID:AB_2875289
Anti-Human PD-1 BUV661	BD OptiBuild	EH12.1; Cat #750260: RRID:AB_2874457
Anti-Human CD56 BUV737	BD	NCAM16.2; Cat #612766; RRID:AB_2813880
Anti-Human CD64 BUV805	BD OptiBuild	10.1; Cat #742023; RRID:AB_2871319
Anti-Human CCR7 BV421	BioLegend	G043H7; #353208; RRID:AB_11203894
Anti-Human CD86 SB436	eBioscience	IT2.2; Cat #62-0869-42; RRID:AB_2637395
Anti-Human CD28 eFluor 450	eBioscience	CD28.2; Cat #48-0289-42; RRID:AB_11151697
Anti-Human CD8 BV480	BD	RPA-T8; Cat #566121; RRID:AB_2739523
Anti-Human CD20 Pacific Orange	Invitrogen	HI47; Cat #MHCD2030; RRID:AB_10375578
Anti-Human CD3 BV510	BioLegend	UCHT1; Cat #300448; RRID:AB_2563468
Anti-Human CD45RA BV570	BioLegend	HI100; Cat #304132; RRID:AB_2563813
Anti-Human CD25 BV605	BioLegend	BC96; Cat #302632; RRID:AB_11218989
Anti-Human CD27 BV650	BioLegend	O323; Cat #302828; RRID:AB_2562096
Anti-Human CD69 BV711	BioLegend	FN50; Cat #310944; RRID:AB_2566466
Anti-Human CXCR5 BV750	BD OptiBuild	RF8B2; Cat #747111; RRID:AB_2871862
Anti-Human CD335 BV785	BioLegend	9E2: Cat #331946; RRID:AB_2810509
Anti-Human CD103 BB515	BD	Ber-ACT8; Cat #564578; RRID:AB_2738852
Anti-Human CD66b FITC	BioLegend	G10F5; Cat #305104; RRID:AB_314496
Anti-Human CD14 Spark Blue 550	BioLegend	63D3; Cat #367148; RRID:AB_2832724
Anti-Human CD45 PerCP	BioLegend	HI30; Cat #304026; RRID:AB_893337
Anti-Human CD57 PerCP-Cy5.5	BioLegend	HNK-1; Cat #359622; RRID:AB_2565930
Anti-Human TCR gamma/delta PerCP-eFluor 710	eBioscience	B1.1; Cat #46-9959-42; RRID:AB_2573926
Anti-Human CD138 PE	BioLegend	MI15; Cat #356504; RRID:AB_2561878
Anti-Human CD4 YG584	Cytek	SK3; Cat #R7-20041; RRID:AB_2885083
Anti-Human CD123 PE-CF594	BioLegend	6H6; Cat #306034; RRID:AB_2566450
Anti-Human CD95 PE-Cy5	BioLegend	DX2; Cat #305610; RRID:AB_314548
Anti-Human CD11c PE-Cy7	BioLegend	3.9; Cat #301608; RRID:AB_389351
Anti-Human CD19 Spark NIR 685	BioLegend	HIB19; Cat #302270; RRID:AB_2832581
Anti-Human CD127 APC-R700	BD	HIL-7R-M21; Cat #565185; RRID:AB_2739099
Anti-Human KLRG1 APC/Fire 750	BioLegend	SA231A2; Cat #367718; RRID:AB_2687392
Anti-Human FoxP3 Alexa Fluor 647	BioLegend	259D; Cat #320214; RRID:AB_492984
Anti-human CD19	Leica	BT51E; Cat #CD19-163-L-CE
Anti-human CD8	Leica	4B11; Cat #CD8-4B11-L-CE
Anti-human CD163	Leica	10D6; Cat #CD163-L-CE
Anti-human CD4	Abcam	EPR6855; Cat #ab133616; RRID:AB_2750883
Anti-human GzmB	Leica	11F1; Cat #GRAN-B-L-CE
Anti-human MMP9	Santa Cruz Biotechnology	2C3; Cat #sc-21733; RRID:AB_627959
Anti-human CD66b Biotin	BioLegend	G10F5; Cat #305120; RRID:AB_2566608
Anti-human CD235b Biotin	BioLegend	HIR2; Cat #306618; RRID:AB_2565773
Chemicals, peptides, and recombinant proteins
LIVE/DEAD Fixable Blue Dead Cell Stain	Thermo Fisher Scientific	Cat #L23105
DAPI	BioLegend	Cat #422801
True-Stain Monocyte Blocker	BioLegend	Cat #426102
TrueStain FcX	BioLegend	Cat #422302
RPMI 1640	Corning	Cat #10-040-CM
Ficoll-Paque PLUS	GE	Cat #17-1440-03
RosetteSep Granulocyte Depletion Cocktail	STEMCELL Technologies	Cat #15624
Benzonase	Millipore Sigma	Cat #E1014-5KU
DPBS	Corning	Cat #20-030-CV
EDTA	Corning	Cat #46-034-CI
Foxp3 / Transcription Factor Staining Buffer Set	eBioscience	Cat #00-5523-00
10% Zinc Formalin	Anatech	Cat # 170
Vectashield Hard Set mounting media	Vector Labs	Cat #H1600
Opal 7-Color IHC Kits	Akoya Biosciences	Cat #NEL811001KT
Critical commercial assays
Chromium Next GEM Single Cell 3′ Reagent kit v3.1	10x Genomics	https://support.10xgenomics.com/single-cell-gene-expression/library-prep
Deposited data
scRNA-seq Data	This article	https://www.covid19cellatlas.org/index.patient.html
Tables S5, S6, and S8	This article	http://dx.doi.org/10.17632/fm7v43jrbk.4
Software and algorithms
Python version 3.7	Python (2020)	https://www.python.org/downloads/release/python-370/
Anaconda version 4	Anaconda (2020)	https://www.anaconda.com/products/individual
Rstudio version 1.2.1335	RStudio (2019)	https://www.rstudio.com
R version 3.5	R Foundation for Statistical Computing (2017)	https://www.R-project.org
inform Version 2.3	Perkin Elmer, Akoya Biosceinces	https://www.akoyabio.com/phenoptics/software/inform-tissue-finder/
FlowJo V 10.7 software	Tree Star	https://www.flowjo.com/
Other
Dead Cell Removal Microbeads	Miltenyi Biotec	Cat #130-090-101
BioMag Plus Streptavidin	Bangs Labs	Cat #BP628