REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Sulfo-tag conjugated anti-human IgG	Meso Scale Discovery	Cat#D21ADF-3
Sulfo- conjugated anti-human IgM	Meso Scale Discovery	Cat#D21ADD-3
Sulfo-tag conjugated anti-human IgA	Meso Scale Discovery	Cat#D21ADE-3
ACE2 calibration reagent	Meso Scale Discovery	Cat#C01ADG-2
Reference Standard 1	Meso Scale Discovery	Cat#C00ADK-2
Anti-CD20 (clone SP32), for CODEX	Abcam	Cat#ab236434
Anti-CD3 (clone EP449E), for CODEX	Akoya Biosciences	Cat#4450027
Anti-CD21 (clone EP3093), for CODEX	Akoya Biosciences	Cat#4450027
Anti-BCL6 (clone IG191E/A8), for CODEX	Biolegend	Cat#648301; RRID: AB_2274637
Anti-CD20 (clone L26), for IHC	Dako	Cat#M0755; RRID: AB_2282030
Anti-CD3 (clone 2GV6), for IHC	Ventana	Cat#790-4341; RRID: AB_2335978
Anti-CD21 (clone EP3093), for IHC	Ventana	Cat#760-4438
Anti-BCL6 (clone GL191E/A8), for IHC	Ventana	Cat#760-4241; RRID: AB_2335965
Anti-PD-1 (clone NAT105), for IHC	Cell-Marque	Cat#315M-96; RRID: AB_1160829
Anti-CovNP T62 (polyclonal)	Sino Biological	Cat#40143-T62; RRID: AB_2892769
Anti-SARS-CoV-2 spike (clone 1A9)	GeneTex	Cat#GTX632604; RRID: AB_2864418
Biological samples
Plasma and saliva samples from 59 individuals vaccinated with BNT162b2 vaccine	This paper	N/A
Plasma samples from 196 individuals vaccinated with BNT162b2, ChAdOx1-S, Gam-COVID-Vac, BBIBP-CorV vaccines	ND Dashdorj, Ulaanbaatar, Mongolia	http://www.onomfoundation.org
Plasma samples from 188 patients infected with SARS-CoV-2	This paper	N/A
Plasma samples from 50 individuals infected with SARS-CoV-2 variants	This paper	N/A
37 plasma and 20 saliva samples from healthy human control individuals	Sean N. Parker Center for Allergy & Asthma Research	https://med.stanford.edu/allergyandasthma.html
Seven post-mortem peribronchial lymph nodes from patients who died of COVID-19	Banner Health	https://www.bannerhealth.com/
Three post-mortem peribronchial lymph nodes from pre-pandemic control patients	Banner Health	https://www.bannerhealth.com/
Seven axillary lymph node core needle biopsies from individuals vaccinated with BNT162b2 or mRNA-1273	This paper	N/A
Three axillary lymph node core needle biopsies from unvaccinated individuals	This paper	N/A
Chemicals, peptides, and recombinant proteins
Sulfo-tag conjugated human ACE2 protein	Meso Scale Discovery	Cat#D21ADG-3
MSD GOLD Read Buffer B	Meso Scale Discovery	Cat#R60AM-2
RNAscope Probe-V-nCoV2019-S	Advanced cell diagnostics	Cat#848561
RNAscope Probe S-encoding-mRNA-1273-C1 (targeting 101-1488 of Spike-encoding_contig_assembled_from_Moderna_mRNA-1273_vaccine)	Advanced cell diagnostics	Cat#1104251-C1
RNAscope Probe S-encoding-BNT-162b2-C1 (targeting 101-1143 of Spike-encoding_contig_assembled_from_BioNTech/Pfizer_BNT-162b2_vaccine)	Advanced cell diagnostics	Cat#1104241-C1
RNA ISH Positive Control Probe PPIB	Advanced cell diagnostics	Cat#RS7755
SARS-CoV-2 Spike protein	ATUM, custom	N/A
Bond Aspirating Probe Cleaning Solution	Leica Microsystems	Cat#CS9100
Bond Dewax Solution	Leica Microsystems	Cat#AR9222
Bond Epitope Retrieval 2	Leica Microsystems	Cat#AR9640
Bond Epitope Retrieval 1	Leica Microsystems	Cat#AR9961
Bond Enzyme Pre-treatment Kit	Leica Microsystems	Cat#AR9551
Bond Mixing Stations	Leica Microsystems	Cat#S21.1971
Bond Open Containers, 30mL	Leica Microsystems	Cat#OP309700
Bond Open Containers, 7mL	Leica Microsystems	Cat#OP79193
Bond Polymer Refine Kit	Leica Microsystems	Cat#DS9800
Bond Primary Antibody Diluent	Leica Microsystems	Cat#AR9352
Bond Slide Labs and Ribbon	Leica Microsystems	Cat#S21.4564
Bond Titration Kit	Leica Microsystems	Cat#OPT9049
Bond Titration Container	Leica Microsystems	Cat#OTP9719
Bond Universal Covertiles	Leica Microsystems	Cat#S21.4611
Bond Wash Solution	Leica Microsystems	Cat#AR9590
Hematoxylin II	Ventana	Cat#790-2208
Bluing, 760-2037EZ Prep Solution (10X)	Ventana	Cat#950-102
OptiView Detection Kit	Ventana	Cat#760-700
Protease 1	Ventana	Cat#760-2018
Protease 2	Ventana	Cat#760-2019
Reaction Buffer (10X)	Ventana	Cat#950-300
SSC Solution	Ventana	Cat#950-110
Ultra CC1 Solution	Ventana	Cat#950-224
Ultra LCS Solution	Ventana	Cat#650-210
UltraView Universal DAB Detection Kit	Ventana	Cat#760-500
Vantage Clear Overlay	Ventana	Cat#1749400
Dako Target Retrieval at pH9	Aligent	Cat#S2368
Hydrogen Peroxide 30% (diluted to 3%)	Thermo-Fisher	Cat#H325500
Normal Horse Serum 2.5%	Victor Labs	Cat#S-2012
ImmPress HRP Universal Secondary Antibody	Victor Labs	Cat#MP-7500
Dako Liquid DAB+ Substrate Chromogen System	Aligent	Cat#K3468
Critical commercial assays
V-PLEX Coronavirus Panel 2 (IgG) Kit	Meso Scale Discovery	Cat#K15369U
V-PLEX Coronavirus Panel 2 (IgM) Kit	Meso Scale Discovery	Cat#K15370U
V-PLEX Coronavirus Panel 2 (IgA) Kit	Meso Scale Discovery	Cat#K15371U
V-PLEX SARS-CoV-2 Panel 9 (IgG) Kit	Meso Scale Discovery	Cat#K15448U
V-PLEX SARS-CoV-2 Panel 11 (IgG) Kit	Meso Scale Discovery	Cat#K15455U
V-PLEX SARS-CoV-2 Panel 11 (ACE2) Kit	Meso Scale Discovery	Cat#K15458U
V-PLEX SARS-CoV-2 Panel 20 (IgG) Kit	Meso Scale Discovery	Cat#K15551U
S-PLEX SARS-CoV-2 Spike Kit	Meso Scale Discovery	Cat#K150ADJS
RNAScope 2.5 HD Assay-RED kit	Advanced cell diagnostics	Cat#322350
Deposited data
Electrochemiluminescence data	This paper; Mendeley Data	https://doi.org/10.17632/j8r94pfrj6.1
Original code	This paper; Github	https://github.com/boyd-lab/covid-infection-vs-vaccination
Original code	This paper; Zenodo	https://doi.org/10.5281/zenodo.5854880
Virus neutralization antibody data from individuals vaccinated with BNT162b2	Arunachalam et al. (2021)	DOI:10.1038/s41586-021-03791-x
Software and algorithms
R version 4.0.5 base packages	The R Foundation	https://www.rstudio.com/products/rstudio/download/
R version 4.0.5 ggplot2 package	The R Foundation	https://cran.r-project.org/web/packages/ggplot2/index.html
QuPath version 0.2.3	Bankhead et al. (2017)	PMID: 29203879 https://qupath.github.io/
Python version 3.7.10	Python Software Foundation	https://www.python.org
CODEX® MAV	Akoya Biosciences	https://help.codex.bio