REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Anti-CD4 antibody	Biolegend	Clone: OKT4
Anti-CD4 antibody	Biolegend	Clone: RPA-T4
Anti-CD8 antibody	Biolegend	Clone: SK1
Anti-CD8 antibody	Biolegend	Clone: HIT8a
Anti-CD3 antibody	Biolegend	Clone: OKT3
Anti-CD3 antibody	Biolegend	Clone: UCHT1
Anti-CD45 antibody	Biolegend	Clone: H130
Anti-CD25 antibody	Biolegend	Clone: BC96
Anti-PD-1 antibody	Biolegend	Clone: EH12.2H7
Anti-CD137 antibody	Biolegend	Clone: 4B4-1
Anti-HLA-DR antibody	Biolegend	Clone: L243
Anti-HLA-BC antibody	Thermo Fisher Scientific	Clone: B1.23.2
Anti-TCRγδ antibody	Biolegend	Clone: B1
Anti-TCR⍺/β	Biolegend	Clone: IP26
Anti-CD19 antibody	Biolegend	Clone: H1B19
Anti-CD14 antibody	Biolegend	Clone: M5E2
Anti-CD38 antibody	Biolegend	Clone: HIT2
Anti-CD69 antibody	Biolegend	Clone: FN50
Anti-APC microbeads	Miltenyi Biotech	Cat#: 130-090-855
Anti-CD3/CD28 microbeads	Thermo Fisher Scientific	Cat#: 11141D
Anti-TMEM161A antibody	abcam	Clone: EPR14369
Chemicals, Peptides, and Recombinant Proteins
Collagenase III	Worthington Biochemical	Cat#: LS004182
DNase I	Worthington Biochemical	Cat#: LS002007
Zombie Aqua	Biolegend	Cat#: 423102
Human TruStain FcX	Biolegend	Cat#: 422302
Live/dead near-IR dye	Thermo Fisher Scientific	Cat#: L34975
AMPure XP beads	Beckman Coulter	Cat#: A63881
Recombinant hIL-2	Peprotech	Cat#: 200-02
Recombinant RNase Inhibitor	Takara Bio	Cat#: 2313A
ERCC RNA Spike-In Mix	Ambion/Life Technologies	Cat#: 4456740
LNA-TSO	Exiqon	Cat#: 500100
Ni-NTA resin	QIAGEN	Cat#: 30210
BirA Biotin-protein ligase	Avidity	Cat#: BirA500
Streptavidin MicroBeads	Miltenyi Biotech	Cat#: 130-048-101
LS Columns	Miltenyi Biotech	Cat#: 130-042-401
Polyethylenimine (PEI)	Millipore-Sigma	Cat#: 408727
Opti-MEM	Thermo Fisher Scientific	Cat#: 31985062
RetroNectin® Recombinant Human Fibronectin Fragment	Takara Bio	Cat#: T100A
FuGENE® 6	Promega	Cat#: E2691
Amicon® Ultra-15 Centrifugal Filter Unit (30 kDa filter)	Millipore-Sigma	Cat#: UFC903024
Streptavidin	Thermo Fisher Scientific	Cat#: 434302
Custom synthetic peptides	Alan Scientific	N/A
Flex-T HLA-A∗02:02 Monomer UVX	Biolegend	Cat#: 280003
Betaine	Millipore-Sigma	Cat#: W422312
Critical Commercial Assays
SMARTScribe Reverse Transcriptase kit	Takara Bio	Cat#: 639538
KAPA Library Quantification kit	Roche	Cat#: KK2602
AATI Fragment Analyzer	Agilent	Cat#: DNF-474-1000
Nextera XT DNA Library Preparation Kit	Illumina	Cat#: FC-131-1096
MiSeq Reagent Kit v2 (300-cycles; yeast screen)	Illumina	Cat#: MS-102-2002
MiSeq Reagent Kit v2 (500-cycles; scTCR-seq)	Illumina	Cat#: MS-102-2003
Chromium Single-Cell V(D)J kit (for TCR)	10x Genomics	Cat#: 1000005; 1000009; 120262; 1000084; 1000080; 1000014; 1000020
Immunoseq assay (Deep)	Adaptive Biotechnologies	Cat#: hsTCRB
RosetteSep human T cell enrichment cocktail	Stem Cell Technologies	Cat#: 15061
KAPA HyperPrep Kit	Roche	Cat#: KK8502
SeqCap EZ MedExome Enrichment Kit	Roche	Cat#: 07676581001
Gibson Assembly Cloning Kit	NEB	Cat#: E5510S
Zymoprep II kit	Zymo Research	Cat#: D2004
In-Fusion Cloning	Takara Bio	Cat#: 638947
Deposited Data
scRNA-seq data (tumor-infiltrating T cells from 10 Stanford lung cancer patients)	This paper	Database: GSE151537 (SuperSeries #GSE151538)
scRNA-seq data (tetramer-sorted T cells from peripheral blood)	This paper	Database: GSE151531 (SuperSeries #GSE151538)
Human reference genome NCBI build 37, GRCh38	Genome Reference Consortium	https://genome.ucsc.edu/cgi-bin/hgTables
Bulk CDR3β sequences (n = 178 HLA-typed NSCLC patients, MDACC)	(Reuben et al., 2020); IMMUNOSEQ ANALYZER (Adaptive Biotechnologies)	https://clients.adaptivebiotech.com
HLA tetramer-derived CDR3β sequences	(Shugay et al., 2018)	https://vdjdb.cdr3.net
Reference CDR3β sequences for GLIPH2	(Huang et al., 2020)	http://50.255.35.37:8080/tools
Bulk RNA-seq data from tumors (pan-lung cancer)	The Cancer Genome Atlas	https://portal.gdc.cancer.gov
GSEA hallmark gene sets	Broad Institute	http://www.gsea-msigdb.org/gsea/downloads.jsp
The UniProt Archive (UniParc)	The UniProt consortium	https://www.uniprot.org/downloads
Emerson CDR3β dataset	(Emerson et al., 2017)	https://clients.adaptivebiotech.com
TRACERx CDR3β sequences	(Joshi et al., 2019)	https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA544699
Experimental Models: Cell Lines
Jurkat 76 cells	S.-A. Xue, University of College London	N/A
T2 cells	ATCC	Cat#: CRL-1992; RRID: CVCL_2211
HLA-A∗02+ 293T cells	S. Feldman, Stanford University	N/A
293T HEK cells	ATCC	Cat#: CRL-11268
H1395 cells	ATCC	Cat#: CRL-5868; RRID: CVCL_1467
Sf9 cells	ATCC	Cat#: CRL-1711
Hi5 cells	Thermo Fisher Scientific	Cat#: BTI-TN-5B1-4
Recombinant DNA
Custom gBlocks dsDNA fragments	IDT	N/A
pAcGP67a vector	BD Biosciences	N/A
Bestbac 2.0	Expression systems	Cat#: 91-002
Yeast A∗02 display library constructs	K.C. Garcia, Stanford University	N/A
Soluble TCR baculoviral constructs	K.C. Garcia, Stanford University	N/A
EF1a-MCS-GFP-PGK-puro lentiviral vector	(Witwicka et al., 2015)	Addgene#: 73582
MSGV1 retroviral vector	S. Rosenberg, NIH	N/A
gag-pol plasmid (Δ8.9)	M.M. Winslow, Stanford University	N/A
pMD.G plasmid (VSV-G)	M.M. Winslow, Stanford University	N/A
Lenti-TMEM161A plasmid	GeneCopoeia	Cat#: EX-A1961-Lv241
Software and Algorithms
GLIPH2 algorithm	(Huang et al., 2020)	http://50.255.35.37:8080
R version 4.0.2	CRAN	https://www.r-project.org/; RRID: SCR_001905
star/2.7.1a	(Dobin et al., 2013)	https://github.com/alexdobin/STAR; RRID: SCR_015899
samtools/1.4	(Li et al., 2009)	http://www.htslib.org; RRID: SCR_002105
python/2.7.3	Python Software Foundation	https://www.python.org; RRID: SCR_008394
htseq-count (HTSeq 0.5.4p5)	(Anders et al., 2015)	https://htseq.readthedocs.io/; RRID: SCR_011867
GSEA v2.2.2	Broad Institute; (Subramanian et al., 2005)	RRID: SCR_003199
GSVA/1.34.0	(Hänzelmann et al., 2013)	https://www.bioconductor.org/packages/release/bioc/html/GSVA.html
FIJI/2.0.0-rc-69/1.52p	(Schindelin et al., 2012)	https://imagej.net/Fiji; RRID: SCR_002285
TraCeR algorithm	(Stubbington et al., 2016)	https://github.com/Teichlab/tracer
HighV-QUEST	international ImMunoGeneTics information system (IMGT)	http://www.imgt.org/; RRID: SCR_018196
FlowJo software	FlowJo, LLC	https://www.flowjo.com; RRID: SCR_008520
varscan2/2.4.3	(Koboldt et al., 2012)	http://varscan.sourceforge.net; RRID: SCR_006849
gatk-3.7/MuTect2	Broad Institute; (Cibulskis et al., 2013)	RRID: SCR_000559
Strelka/2.9.10	Illumina; (Saunders et al., 2012)	RRID: SCR_005109
Seurat/3.1.4	Bioconductor	RRID: SCR_016341
Monocle/2.10.1	Bioconductor	RRID: SCR_018685
netMHCpan/4.0	(Jurtz et al., 2017; Reynisson et al., 2020)	RRID: SCR_018182
BLASTP	National Center for Biotechnology Information (NCBI); (Johnson et al., 2008)	RRID: SCR_001010