KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
CD8α - Brilliant Violet 605	BioLegend	Cat#100744
TCRβ - PE-eFluor 610	ThermoFisher	Cat#61–5961-82
CD44 – APC	Tonbo Bioscience	Cat#20–0441-U100
CD62L - APC-eFluor780	ThermoFisher	Cat#47–0621-82
NK1.1 - eFluor 450	ThermoFisher	Cat#48–5941-82
CD4 - PerCP-Cyanine5.5	Tonbo Bioscience	Cat#65–0042-U100
PD-1 - FITC	ThermoFisher	Cat#11–9985-82
CD39 - PerCP-eFluor 710	ThermoFisher	Cat#46–0391-80
CD73 - eFluor 450	ThermoFisher	Cat#48–0731-82
CD9 - PE	BioLegend	Cat#124805
CD38 - APC	ThermoFisher	Cat#17–0381-82
Rabbit anti-TCF1 monoclonal	Cell Signaling Technology	Cat#2203S
anti-mouse CD4	BIOXCELL	Cat#BE0003–1
Bacterial and Virus Strains
LCMV Armstrong and Clone 13	Produced in-house	N/A
Chemicals, Peptides, and Recombinant Proteins
D(b) NP396 LCMV Tetramers	NIH Tetramer Core Facility	N/A
Agencourt AMPure XP - PCR Purification	Beckman Coulter	Cat#A63881
Ghost Dye Live/Dead stain	Tonbo Biosciences	Cat#13–0870-T100
Protein A/G-MNase	Produced in-house	N/A
Complete mini EDTA-free Protease Inhibitor	Sigma-Aldrich	Cat#11836153001
Critical Commercial Assays
eBioscience Foxp3/Transcription Factor Staining Buffer Set	Thermo Fisher	Cat#00–5523-00
MinElute Reaction Cleanup Kit	QIAGEN	Cat#28206
KAPA Hyper Prep Kit	Kapa Biosystems	Cat#KK8504
KAPA UDI adaptor kit	Kapa Biosystems	Cat#KK8727
Deposited Data
scATAC-seq, scRNA-seq, CUT&RUN	This paper	NCBI GEO: GSE164978
ATAC-seq, RNA-seq	NCBI GEO	Accession numbers listed in Table S1
Experimental Models: Organisms/Strains
Spret/EiJ	JAX	001146
CD45.1	JAX	002014
C57BL/6J	JAX	000664
Software and Algorithms
Flowjo	Tree Star	https://www.flowjo.com/https://www.flowjo.com
Prism	GraphPad	https://www.graphpad.com/scientific-software/prism/https://www.graphpad.com/scientific-software/prism/
Illustrator	Adobe	N/A
fastq-dump	NCBI SRA Toolkit	https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_dochttps://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc
Bowtie2	Langmead B, Salzberg SL, 2012	http://bowtie-bio.sourceforge.net/bowtie2http://bowtie-bio.sourceforge.net/bowtie2
SAMtools	Li et al., 2009	http://www.htslib.org/http://www.htslib.org/
MACS2	Zhang et al., 2008	https://github.com/macs3-project/MACShttps://github.com/macs3-project/MACS
IDR	Li et al., 2011	https://github.com/nboley/idrhttps://github.com/nboley/idr
Rsubread	Liao et al., 2019	https://bioconductor.org/packages/release/bioc/html/Rsubread.htmlhttps://bioconductor.org/packages/release/bioc/html/Rsubread.html
deepTools	Ramirez et al., 2016	https://github.com/deeptools/deepToolshttps://github.com/deeptools/deepTools
DESeq2	Love et al., 2014	https://bioconductor.org/packages/release/bioc/html/DESeq2.htmlhttps://bioconductor.org/packages/release/bioc/html/DESeq2.html
gprofiler2	Raudvere et al., 2019	https://cran.r-project.org/web/packages/gprofiler2/index.htmlhttps://cran.r-project.org/web/packages/gprofiler2/index.html
HOMER	Heinz et al., 2010	http://homer.ucsd.edu/homer/http://homer.ucsd.edu/homer/
FIMO	Grant et al., 2011	https://meme-suite.org/meme/doc/fimo.htmlhttps://meme-suite.org/meme/doc/fimo.html
mpath	Wang et al., 2015	https://cran.r-project.org/web/packages/mpath/index.htmlhttps://cran.r-project.org/web/packages/mpath/index.html
HISAT2	Kim et al., 2019	http://daehwankimlab.github.io/hisat2/http://daehwankimlab.github.io/hisat2/
HiC-Pro	Servant et al., 2015	https://github.com/nservant/HiC-Prohttps://github.com/nservant/HiC-Pro
HiC-DC	Carty et al., 2017	https://bitbucket.org/leslielab/hic.dchttps://bitbucket.org/leslielab/hic.dc
cellranger-atac	10X Genomics	https://support.10xgenomics.com/single-cell-atac/software/downloads/latesthttps://support.10xgenomics.com/single-cell-atac/software/downloads/latest
scanpy	Wolf et al., 2018	https://github.com/theislab/scanpyhttps://github.com/theislab/scanpy
GSVA	Hänzelmann et al., 2013	https://www.bioconductor.org/packages/release/bioc/html/GSVA.htmlhttps://www.bioconductor.org/packages/release/bioc/html/GSVA.html
MAGIC	Van Dijk et al., 2018	https://github.com/KrishnaswamyLab/MAGIChttps://github.com/KrishnaswamyLab/MAGIC
STAR	Dobin et al., 2013	https://github.com/alexdobin/STAR
cellranger	10X Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
velocyto	Le Manno et al., 2018	http://velocyto.org/
scvelo	Bergen et al., 2020	https://scvelo.readthedocs.io/