REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Armenian hamster anti-CD48 (clone HM48-1) neutralizing Ab	BioXcell	Cat# BE0147
Rat anti-CD3 (clone 17A2)	BioLegend	Cat# 100220
Armenian hamster anti-CD3 (clone 145.2C11)	BioLegend	Cat# 100331
Rat anti-CD4 (clone RM4-5)	BioLegend	Cat# 116016
Rat anti-CD4 (clone YTS191) depleting Ab	BioXcell	Cat# BE0119
Rat anti-CD8a (clone 53-6.7)	BioLegend	Cat# 100725
Rat anti-CD11b (clone M1/70)	BioLegend	Cat# 101212
Armenian hamster anti-CD11c (clone N418)	BioLegend	Cat# 117310
Armenian hamster anti-CD28 (clone 37.51)	BioLegend	Cat# 102112
Goat anti-hamster IgG (H+L)	Jackson Immunoresearch	Cat# 127-005-099
Rat anti-CD44 (clone IM7)	BioLegend	Cat# 103028
Rat anti-CD45 (clone 30-F11)	BioLegend	Cat# 103116
Mouse anti-CD45.1 (clone A20)	BioLegend	Cat# 110722
Mouse anti-CD45.2 (clone 104)	BioLegend	Cat# 109822
Rat anti-CD45R/B220 (clone RA3-6B2)	BioLegend	Cat# 103236
Rat anti-CD49b (clone DX5)	BioLegend	Cat# 108909
Rat anti-CD107a (clone 1D4B)	BioLegend	Cat# 121606
Rat anti-CD127 (clone A7R34)	BioLegend	Cat# 135014
Mouse anti-CD244 (clone m2B4 (B6)458.1)	BioLegend	Cat# 133508
Mouse anti-granzyme B (clone GB11)	BioLegend	Cat# 515406
Rat anti-IFN-γ (clone XMG1.2)	BioLegend	Cat# 505829
Rat anti-IL-2 (clone JES6-5H4)	BioLegend	Cat# 503808
Rat anti-IL-10 (clone JES5-2A5) neutralizing Ab	BioXcell	Cat# BE0049
Armenian hamster anti-IFN-a (clone TIF-3C5) neutralizing Ab	Leinco Technologies	Cat# I-1183
Rat anti-IRF4 (clone IRF4.3E4)	BioLegend	Cat# 664406
Mouse anti-TIGIT (clone 1G9)	BioLegend	Cat# 142107
Rat anti-Ki-67 (clone SolA15)	eBioscience	Cat# 12-5698-82
Syrian hamster anti-KLRG1 (clone 2F1/KLRG1)	BioLegend	Cat# 138410
Armenian hamster anti-NKG2D (clone C7)	BioLegend	Cat# 115705
Rat anti-NKp46 (clone 29A1.4)	BioLegend	Cat# 137611
Mouse anti-LAG-3 (clone 11C3C65)	BioLegend	Cat# 369306
Mouse anti-T-bet (clone 4B10)	BioLegend	Cat# 644814
Mouse anti-T-bet (clone 4B10) for ChIP	Santa Cruz Biotechnology	Cat# sc-21749
Mouse anti-TIM-3 (clone B8.2C12)	BioLegend	Cat# 134008
Rat anti-PD-1 (clone RMP1-30)	BioLegend	Cat# 109103
Rat anti-PD-1 (clone 29F.1A12) neutralizing Ab	BioXcell	Cat# BE0273
Rat anti-TNF-α (clone MP6-XT22)	BioLegend	Cat# 506323
Rat anti-Eomes (Dan11mag)	eBioscience	Cat# 25-4875-80
Rabbit anti-TCF-1 (C63D9)	Cell Signaling Technology	Cat# 6709S
Rat anti-TOX (clone TXRX10)	eBioscience	Cat# 12-6502-82
Rat anti-CD3 (clone CD3-12)	Biorad	Cat# MCA1477A488
Biotin-labeled rabbit anti-rat antibody	Dako	Cat# E0468
Mouse anti-Nogo A (clone 11C7)	Oertle et al., 2003	N/A
Rabbit anti-cleaved caspase-3	Cell Signaling Technology	Cat# 9661
Alexa555-labeled-goat anti-mouse	Invitrogen	Cat# A21127
Goat-anti-mouse Fab fragment	Jackson Immunoresearch	Cat# 115-006-006
Rabbit anti-GFP (clone D5.1)	Cell Signaling Technology	Cat# 2956
Mouse-anti-human CD8 (clone C8/144B)	Dako	Cat# IR62361-2
Alexa647-labeled-donkey anti-rat	Jackson Immunoresearch	Cat# 712-605-153
Rabbit anti-TOX1	AbCam	Cat# ab155768
Bacterial and Virus Strains
Listeria-OVA	Zehn et al., 2009	N/A
Listeria-GP33	Oberle et al., 2016	N/A
pAAV-MBP-eGFP	von Jonquieres et al., 2013	N/A
LCMV-OVA	Kallert et al., 2017	N/A
LCMV-Q4H7	Zehn et al., 2009	N/A
LCMV WT (Armstrong)	Flatz et al., 2006	N/A
LCMV-GP33	Kallert et al., 2017	N/A
Biological Samples
MS lesions	University of Göttingen	N/A
Post ischemic lesion	University of Göttingen	N/A
Chemicals, Peptides, and Recombinant Proteins
DAPI	Molecular Probes	Cat# D1306
CellTracker Red CMPTX	Molecular Probes	Cat# C34552
Green CFSE	BioLegend	Cat# 423801
Collagenase A	Roche	Cat# 11088793001
DNaseI	Roche	Cat# 10104159001
Monensin	BioLegend	Cat# 420701
SIINFEKL peptide	Polypeptide Group	N/A
Recombinant murine IL-12	Peprotech	Cat# 210-12
Recombinant murine IL-15	Peprotech	Cat# 210-15
Critical Commercial Assays
CD8a+ T Cell Isolation Kit, mouse	Miltenyi Biotec	Cat# 130-104-075
AccuCheck Counting Beads	Molecular Probes	Cat# PCB100
Alexa Fluor 488 Tyramide Reagent	Molecular Probes	Cat# B40953
FoxP3/Transcription Factor Staining Buffer Set	eBioscience	Cat# 00-5523-00
Fixation buffer	BioLegend	Cat# 420801
Intracellular Staining Perm Wash Buffer	BioLegend	Cat# 421002
CytoTox 96 NonRadioactive Cytotoxicity Assay	Promega	Cat# G1780
RNeasy Mini Kit	QIAGEN	Cat# 74104
TruSeq ChIP Sample Preparation Kit	Illumina	Cat# IP-202-1012
TruSeq RNA Sample Prep Kit v2	Illumina	Cat# RS-122-2001
Dual Glo Luciferase Assay Kit	Promega	Cat# E2920
Nucleofector kit L	Lonza	Cat# VACA-1005
iScript cDNA synthesis kit	Biorad	Cat# 1708891
iQ SYBR Green Supermix	Biorad	Cat# 1708864
nCounter GX Mouse Inflammation Kit	Nanostring technologies	Cat# XT-GXA-MIN2-24
Deposited Data
RNA-seq OT-1 LCMV-OVA/Lm-OVA	This paper	GEO: GSE93805
RNA-seq OT-1 Tox+/+/Tox−/−	This paper	GEO: GSE93804
ChIP-seq OT-1 Tox+/+/Tox−/−	This paper	GEO: GSE93953
Id2-dependent CTL signature upon HK×31 Influenza infection	Masson et al., 2013	GEO: GSE44140
Notch-1-2-dependent CTL signature upon HK×31 Influenza infection	Backer et al., 2014	E-MTAB-2999
Microarray data T cell exhaustion signature	Doering et al., 2012	GEO: GSE41867
Experimental Models: Cell Lines
MC57G	ATCC	ATCC CRL-2295
EL4	ATCC	ATCC TIB-39
Experimental Models: Organisms/Strains
Mouse: C57BL/6J	Charles River	Stock#: 000664
Mouse: ODC-OVA	Laboratory of Thomas Hunig	N/A
Mouse: MOGiCre-GP	This paper	Generated at Cyagen Biosciences
Mouse: Tox−/−	Laboratory of Jonathan Kaye	N/A
Mouse: OT-1	Charles River	Stock#: 003831
Mouse: P14Tcf7−/−	Laboratory of Daniel Pinschewer	N/A
Oligonucleotides
Id2 PrimePCR SYBR Green Assay	Bio-Rad	Cat# qMmuCED0044963
Mm_Gapdh_3_SG QuantiTect Primer Assay	QIAGEN	Cat# QT01658692
Il12p35: forward primer 5′-CATCAACGCAGCACTTCAGAA-3′; reverse primer 5′-TCGATGGCCACCAGCAT-3′	Microsynth	N/A
Ifna: forward primer 5′-CGGAATTCTCTCCTGCCTGAAGGAC-3′; reverse primer 5′-AAGGGTACCACACAGTGATCCTGTGGAA-3′	Microsynth	N/A
Il10: forward primer 5′-GGTTGCCAAGCCTTATCGGA-3′; reverse primer 5′-ACCTGCTCCACTGCCTTGCT-3′	Microsynth	N/A
Tox ChIP PCR (−0.5 kb upstream of start codon): forward primer 5′-GGGGTACTGGGCGTTTTATT-3′; reverse primer 5′-GATCTTGATCTCCCCTGCAA-3′	Microsynth	N/A
Tox ChIP PCR (-1.1 kb upstream of start codon): forward primer 5′-AGGGACCCCAGTTGATCTCT-3′; reverse primer 5′-AGCACCCCTGGAGTCTTTTT-3′	Microsynth	N/A
Tox ChIP PCR (-1.6 kb upstream of start codon): forward primer 5′-GGGTGGGCAATGTTTACCTT-3′; reverse primer 5′-TGACGCCAGAAACAGATACCT-3′	Microsynth	N/A
ShRNA targeting sequence for Eomes: 5′ -TCAGGAGGAACTAATCTCTTCT-3′	This paper	N/A
ShRNA targeting sequence for Cd4: 5′-AAACGATCCTTTCTCCCATGCC-3′	Laboratory of Matthew Pipkin	Chen et al., 2014
ShRNA targeting sequence for Tox: 5′-TATAGACCTGTTTCTGTTCTTC-3′	This paper	N/A
Recombinant DNA
pMSCV IRES-GFP	Addgene	N/A
pMSCV Eomes-IRES-GFP	Laboratory of Gabrielle Belz	Mackay et al., 2015
pMSCV T-bet-IRES-GFP	Laboratory of Gabrielle Belz	Joshi et al., 2007
pGL3-Enhancer	Promega	N/A
pGL3-Enhancer-Tox-promoter	This paper	N/A
pGL4.74 (encoding Renilla luciferase)	Promega	N/A
pMSCV miR30 backbone	Laboratory of Matthew Pipkin	Chen et al., 2014
Software and Algorithms
Imaris 5.7.2 ×64	Bitplane	N/A
OsiriX 8	OsiriX	N/A
Definiens Developer 2.5	Definiens	N/A
FlowJo 10.2	TreeStar	N/A
R language and environment for statistical computing and graphics	https://www.r-project.org	N/A
STAR	https://github.com/alexdobin/STAR	N/A
SAMtools	http://samtools.sourceforge.net/	N/A
HTSeq	http://www-huber.embl.de/users/anders/HTSeq/	N/A
Bioconductor and packages	https://www.bioconductor.org	N/A
Bowtie	http://bowtie-bio.sourceforge.net/index.shtml	N/A
MACS2	https://pypi.python.org/pypi/MACS2	N/A
geNorm	https://genorm.cmgg.be	N/A
Pannoramic Viewer software	3DHistech	N/A
Other
HiSeq 2000	Illumina	N/A
HiSeq 2500	Illumina	N/A
AutoMACS	Miltenyi Biotec	N/A
SpectraMax L reader	Molecular devices	N/A
Pannoramic Digital Slide Scanner 250 FLASH II	3DHistech	N/A
Gallios cytometer	Beckman-Coulter	N/A
BD FACSAria II Cell Sorter	BD Biosciences	N/A
CFX 96 instrument	Bio-Rad	N/A