REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-biotin MACS microbeads	Miltenyi biotec	Cat#130-097-046
CD16/CD32, clone 2.4G2	BioXCell	Cat#BE0307
anti-VSV Indiana G	Absolute Antibody	Cat#Ab01401-2.0
B220, clone RA3-6B2, APC	Tonbo Biosciences	Cat#20-0452-U100
B220, clone RA3-6B2, BUV496	BD Biosciences	Cat#612950
B220, clone RA3-6B2, BV650	Biolegend	Cat#103241
B220, clone RA3-6B2, PE	Biolegend	Cat#103207
Bcl6, clone K112-91, Ax647	BD Biosciences	Cat#624024
CD138, clone 281-2, BV421	Biolegend	Cat#142508
CD138, clone 281-2, BV650	BD Biosciences	Cat#564068
CD19, clone 6D5, BV711	Biolegend	Cat#115555
CD19, clone 6D5, BV605	Biolegend	Cat#115539
CD19, clone 6D5, BV785	Biolegend	Cat#115543
CD25, clone PC61.5, AF488	eBioScience	Cat#53-0251-82
CD3, clone 145-2C11, BUV395	BD Biosciences	Cat#565992
CD3, clone 17A2, APC-Cy7	Biolegend	Cat#100222
CD38, clone 90, AF700	Invitrogen	Cat#56-0381-82
CD4, clone GK1.5, PE-Cy7	Biolegend	Cat#100409
CD4, clone H29.19, PE-Cy5	Biolegend	Cat#130312
CD4, clone RM4-5, Biotin	eBioScience	Cat#13-0042-85
CD4, clone RM4-5, PerCP-Cy5.5	Biolegend	Cat#100540
CD44, clone IM7, BV605	Biolegend	Cat#103047
CD44, clone IM7, FITC	Biolegend	Cat#103005
CD62L, clone MEL-14, BUV395	BD Biosciences	Cat#740218
CD8a, clone 53-6.7, Biotin	eBioScience	Cat#13-0081-85
CD8a, clone 53-6.7, PerCP-Cy5.5	Biolegend	Cat#100734
CD8a, clone 53-6.7, PE-Cy7	Biolegend	Cat#100722
CD8a, clone 53-6.7, PE-Cy5	BD Biosciences	Cat#553034
CD8a, clone 53-6.7, PerCP-Cy5.5	Biolegend	Cat#100734
CXCR5, clone SPRCL5, Biotin	eBioScience	Cat#13-7185-82
F4/80, clone BM8, Biotin	eBioScience	Cat#13-4801-82
F4/80, clone BM8, PE-Cy5	eBioScience	Cat#15-4801-82
F4/80, clone BM8, PE-Cy7	Biolegend	Cat#123114
FAS, clone JO2, BV510	BD Biosciences	Cat#563646
FoxP3, clone FJK-16 s, PE-Cy7	eBioScience	Cat#25-5773-82
GL7, clone GL7, e660	eBioScience	Cat#50-5902-82
GL7, clone GL7, PerCP-Cy5.5	Biolegend	Cat#144610
GL7, clone GL7, AF488	Biolegend	Cat#144612
Gr-1, clone RB6-8C5, PE-Cy5	Biolegend	Cat#108410
IgD, clone 11-26c, e450	eBioScience	Cat#48-5993-82
IgD, clone 11-26c.2a, PE-Cy7	Biolegend	Cat#405720
IgD, clone 11-26c.2a, APC-Cy7	Biolegend	Cat#405716
IgD, clone 11-26c.2a, BV605	Biolegend	Cat#405727
IgG1 isotype control	Bio X Cell	Cat#BE0088
IgM, clone II/41, PerCP-eF710	Invitrogen	Cat#46-5790-82
IgM clone R6-60.2, PE-CF594	BD Biosciences	Cat#562565
IL-6, clone MP5-20F3	Bio X Cell	Cat#BE0046
Live/Dead Aqua	Biolegend	Cat#423101
Mouse IL-6 Uncoated ELISA kit	Invitrogen	Cat#88-7064
PD-1, clone RMP1-30, PE-Cy7	Biolegend	Cat#109110
Ter-199, clone Ter-199, Biotin	Biolegend	Cat#116204
Ter-199, clone Ter-199, PE-Cy7	Biolegend	Cat#116222
Streptavidin-conjugated AF488	Biolegend	Cat#405235
Streptavidin-conjugated AF647	Biolegend	Cat#405237
Streptavidin-conjugated BV421	Biolegend	Cat#405225
HRP conjugated anti-mouse secondary	Jackson Immunoresearch	Cat#715-035-150
HRP conjugated anti-mouse IgG1	Abcam	Cat#98693
HRP conjugated anti-mouse IgG2a	Abcam	Cat#98698
HRP conjugated anti-mouse IgG2b	Abcam	Cat#98703
HRP conjugated anti-mouse IgA	Abcam	Cat#97235
Chemicals and recombinant proteins
Addavax	Invivogen	Cat#vac-adx-10
BD Brilliant Buffer	BD Biosciences	Cat#563794
ACK Lysing buffer	Lonza	Cat#10-548E
Cellulose	Sigma-Aldrich	Cat#11363-250G
CleanCap	Trilink	Cat#N-7413
CoMplete protease inhibitor cocktail	Sigma-Aldrich	Cat#11697498001
EZ-Link Micro Sulfo-NHS-Biotinylation Kit	Thermo Fisher Scientific	Cat#21925
Fixable Viability Dye eFluor 780	eBioScience	Cat#65-0865-14
FoxP3/Transcription Factor Staining Buffer Set	eBioScience	Cat#00-5523-00
Illumina MiSeq Reagent kit	Illumina	Cat#MS-102-3003
Lightning-Link® Rapid Alexa Fluor 647	Novus Biologicals	Cat#336-0005
Lightning-Link® R-Phycoerythrin (R-PE)	Novus Biologicals	Cat#703-0010
Luminex 32-Plex	Millipore-Sigma	Cat#MCYTOMAG-70K
N1-methylpseudouridine-triphosphate	Trilink	Cat#N-1081
Miltenyi LD columns	Miltenyi biotec	Cat#130-042-901
M-Per lysis buffer	Thermo Fisher Scientific	Cat#78501
Pierce BCA protein assay kit	Thermo Fisher Scientific	Cat#23227
Pierce microBCA protein assay kit	Thermo Fisher Scientific	Cat#23235
PR8 HA recombinant protein	Sino Biological	Cat#11684-V08H1
QIAGEN Gentra DNA purification kit	QIAGEN	Cat#158689
Recombinant RBD	Florian Krammer	N/A
SARS-CoV-2 RBD	Sino Biological	Cat#40592-VNAH
SARS-CoV-2 RBD	GenScript	Cat#Z03501
KPL TMB 2-Component Microwell Peroxidase Substrate	Seracare	Cat#5120-0050
Whole turkey blood	Lampire Biological Products	Cat# 7209401
Deposited data
BCR sequencing data	Sequence Read Archive	BioProject: PRJNA669143
Experimental models: Organisms/strains
Myd88tm1.1Defr (Myd88−/−) mouse	Jackson Lab	Cat#009088
Mavsstm1zjc (Mavs−/−) mouse	Jackson Lab	Cat#008634
Il6tm1Kopf (Il6−/−) mouse	Jackson Lab	Cat#002650
C57BL/6 mouse	Jackson Lab	Cat#000664
B6129SF2 mouse	Jackson Lab	Cat#101045
BALB/c mouse	Jackson Lab	Cat#000651
Experimental models: Cell lines
HEK293T/17 cell	ATCC	CRL11268
Vero E6 cell stably expressing TMPRSS2	Dr. Stefan Pohlmann	N/A
Recombinant DNA
SARS-CoV-2 receptor binding domain (RBD)	GenBank	MN908947.3
Influenza A/Puerto Rico/8-MC/1934(H1N1) HA	GenBank	CY083950.1
Softwares and algorithms
S6 FluoroSpot Analyzer CTL	Immunospot	N/A
FlowJo v10.3	FlowJo LLC	N/A
FACSDIVA	BD Biosciences	N/A
GraphPad Prism	GraphPad	N/A
pRESTO version 0.5.10	Vander Heiden et al., 2014	https://presto.readthedocs.io
ImmuneDB v0.29.9	Rosenfeld et al., 2018	https://immunedb.readthedocs.io