REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-B220 AF488	BD Biosciences	RA3-6B2
Anti-B220 BV510	BD Biosciences	RA3-6B2
Anti-Bst2 APC	eBiosciences	CD317
Anti-CD115 BV 711	BioLegend	AFS98
Anti-CD11c APC-Cy7	Tonbo Biosciences	N418
Anti-CD127 BV 421	BD Biosciences	SB/199
Anti-CD16/32 (Fc block)	BD Biosciences	2.4G2
Anti-CD172α APC	BD Biosciences	P84
Anti-CD172α PerCP-ef710	eBiosciences	P84
Anti-CD19 A700	Biolegend	6D5
Anti-CD19 PE	BD Biosciences	1D3
Anti-CD24 PE-Cy7	BioLegend	M1/69
Anti-CD27 APC	BD Biosciences	LG.3A10
Anti-CD3 BUV 496	BD Biosciences	145-2c11
Anti-CD3 BUV 395	BD Horizon	145-2C11
Anti-CD4 FITC	BioLegend	RM4-5
Anti-CD4 APC-Cy7	Biolegend	GK1.5
Anti-CD44 APC-Cy7	BD Biosciences	IM7
Anti-CD45 BUV 395	BD Biosciences	30-F11
Anti-CD45 Alexa 488	BD Biosciences	30-F11
Anti-CD45.1 PE-Cy7	Tonbo Biosciences	A20
Anti-CD45.1 PE-Cy7	Biolegend	A20
Anti-CD45R AF488	BD Biosciences	RA3-6B2
Anti-CD8α PerCP-Cy5.5	BioLegend	53-6.7
Anti-CD8α V450	BD Biosciences	53-6.7
Anti-CD8β PerCp-Cy5.5	Biolegend	YT5156.7.7
Anti-ckit BUV 395	BD Biosciences	2B8
Anti-ckit PE-Cy7	BD Biosciences	2B8
Anti-Flt3 PE Texas Red	BD Biosciences	A2F10.1
Anti-FoxP3 BV421	BioLegend	MF-14
Anti-Granzyme B PE	Invitrogen	GB11
Anti-IFN-γ BV421	BioLegend	XMB1.2
Anti-Ly6D PE	BioLegend	49-H4
Anti-MHCII I-A/I-E V450	BioLegend	M5/114.15.2
Anti-MHCII I-A/I-E V500	BD Biosciences	M5/114.15.2
Anti-Sca-1 PE	BD Biosciences	D7
Anti-Sca-1 PE-Cy7	eBiosciences	D7
Anti-SiglecH PerCP-Cy5.5	eBioscience	440c
Anti-TCR-V α2 PE	Invitrogen	B20.1
Anti-TNF-α BV605	BioLegend	MP6-XT22
Biotin-B220	BioLegend	RA3-6B2
Biotin-CD105	eBiosciences	MJ7/18
Biotin-CD11b	BioLegend	M1/70
Biotin-CD19	BD Biosciences	1D3
Biotin-CD3	Tonbo Biosciences	145-2C11
Biotin-Ly6C	BD Biosciences	AL-21
Biotin-Ly6G	BioLegend	1A8
Biotin-NK1.1	BioLegend	PK136
Biotin-Ter119	BioLegend	Ter119
Db-WNV NS4B tetramer Alexa647	NIH Tetramer Core Facility	SSVWNATTA
Db-ZIKV envelope tetramer APC	Chiips Core, Washington University	IGVSNRDFV
Virus Strains
DENV2 strain D2S20	Diamond lab	Makhluf et al., 2013
WNV NY2000 strain 30000259	Diamond lab	Ebel et al., 2001
ZIKV Dakar strain 41671	Diamond lab	N/A
Chemicals, Peptides, and Recombinant Proteins
Ampicillin sodium salt	Sigma-Aldrich	A9518
CFSE	eBiosciences	65-0850-84
Db-NS4B peptide	NIH Tetramer Core Facility	Purtha et al., 2007
Fixable Viability Dye eFluor 506	eBiosciences	65-0866-14
Metronidazole	Sigma-Aldrich	M1547
Neomycin trisulfate salt hydrate	Sigma-Aldrich	N1876
Streptavidin conjugate	ThermoFisher Scientific	Qdot 605
Vancomycin hydrochloride	Sigma-Aldrich	V2002
Critical Commercial Assays
Bio-Plex Pro Mouse cytokine 23-plex assay	Bio-rad	M60009RDPD
FoxP3/transcription factor staining buffer set	eBiosciences	00-5523-00
Pan T cell isolation kit II, mouse	MACS Miltenyi Biotech	130-095-130
Cd8α+ T cell isolation kit, mouse	MACS Milteny Biotech	130-104-075
Deposited Data
Raw data	This paper	ENA: PRJEB15424
Experimental Models: Cell Lines
African green monkey kidney (Vero) cells	ATCC; WHO Reference Cell Bank	Vero 76 clone E6; WHO Vero cells
Baby hamster kidney (BHK) cells	ATCC	BHK-21 clone 15
Aedes albopictus cells	ATCC	C6/36
Experimental Mouse Models:
C57BL6/J	The Jackson Laboratory	000664
Caspase1/11−/−	The Jackson Laboratory	016621
Cd8α−/−	The Jackson Laboratory	002665
cGas−/−	Virgin laboratory	Schoggins et al., 2014
Ifnar1−/−	Michel Aguet	Müller et al., 1994
Ifnarf/f	Ulrich Kalinke	Kamphuis et al., 2006;
LysMCre	The Jackson Laboratory	004781
Ifnlr1−/−	Zymogenetics	Ank et al., 2008
WNV NS4B+/−	Diamond laboratory	Kim et al., 2014
Stat6−/−	The Jackson Laboratory	005977
Sting−/−	The Jackson Laboratory	017537
Tcrβδ−/−	The Jackson Laboratory	002122
Tlr2−/−	The Jackson Laboratory	004650
Tlr5−/−	The Jackson Laboratory	008377
Oligonucleotides
WNV specific primers and probes	IDT	Brien et al., 2013
ZIKV Dakar specific primers and probes	IDT	Govero et al., 2016
V4 region specific 16S rRNA primers (515f/805r)	IDT	N/A
V4 region specific Golay-barcoded 16S rRNA primers (515f/806r)	IDT	N/A
Recombinant DNA
16S rRNA plasmid standard in pCR2.1 TOPO	Diamond laboratory	This paper
Software and Algorithms
FlowJo	Treestar, Inc.	v10.4.1
Prism 7	GraphPad	v7.0a
dada2 R package	Callahan et al., 2016	v.1.5.2
QIIME	Caporaso et al., 2010	v.1.8.0
MSA	Bodenhofer et al., 2015	v.1.8.0
Phangorn	Schliep, 2011	v.2.3.1
PhyloSeq	McMurdie and Holmes, 2013	v.1.23.1
Other
16S rRNA sequence data	This paper	https://www.ebi.ac.uk/ena/data/view/PRJEB15424