REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rat Anti-CD16/CD32 Monoclonal Antibody, Unconjugated, (Clone 2.4G2)	BD Biosciences	Cat# 553141; RRID:AB_394656
Brilliant Violet 421 anti-mouse CD45	BioLegend	Cat# 103134; RRID:AB_2562559
BUV395 Rat Anti-Mouse CD45 (Clone 30-F11)	BD Biosciences	Cat# 564279; RRID:AB_2651134
FITC anti-mouse CD3	BioLegend	Cat# 100204; RRID:AB_312661
Brilliant Violet 510 anti-mouse CD3	BioLegend	Cat# 100234; RRID:AB_2562555
Brilliant Violet 605 anti-mouse CD3	BioLegend	Cat# 100237; RRID:AB_2562039
Brilliant Violet 650 anti-mouse CD4	BioLegend	Cat# 100555; RRID:AB_2562529
Brilliant Violet 711 anti-mouse CD4	BioLegend	Cat# 100549; RRID:AB_11219396
Brilliant Violet 421 anti-mouse CD4	BioLegend	Cat# 100544; RRID:AB_11219790
Brilliant Violet 785 anti-mouse CD8a	BioLegend	Cat# 100750; RRID:AB_2562610
Brilliant Violet 510 anti-mouse CD8a	BioLegend	Cat# 100752; RRID:AB_2563057
Alexa Fluor 488 anti-mouse CD8a	BioLegend	Cat# 100723; RRID:AB_389304
PE anti-FoxP3	Thermo Fisher	Cat #14-4771-80; RRID: AB_529583
PE anti-FoxP3	BD Biosciences	Cat# 560408; RRID: AB_1645251
APC/Cyanine7 anti-mouse CD25	BioLegend	Cat# 102026; RRID:AB_830745
APC anti-mouse CD25	BioLegend	Cat# 102012; RRID:AB_312861
FITC anti-PD-1	BioLegend	Cat# 135214; RRID: AB_10680238
Brilliant Violet 421 anti-PD-1	BioLegend	Cat# 109121; RRID:AB_2687080
Brilliant Violet 650 anti-mouse/human CD44	BioLegend	Cat# 103049; RRID:AB_2562600
Brilliant Violet 421 anti-mouse CD62L	BioLegend	Cat# 104435; RRID:AB_10900082
FITC anti-mouse Ki-67	BioLegend	Cat# 652409; RRID:AB_2562140
Brilliant Violet 711 anti-mouse/human CD45R/B220	BioLegend	Cat# 103255; RRID:AB_2563491
APC anti-mouse CD69	BioLegend	Cat# 104513; RRID:AB_492844
Alexa Fluor 488 anti-mouse CD69	BioLegend	Cat# 104516; RRID:AB_492845
Pacific Blue anti-human/mouse Granzyme B	BioLegend	Cat# 515407; RRID:AB_2562195
APC anti-mouse IFN-gamma	BioLegend	Cat# 505810; RRID:AB_315404
PE anti-mouse CD11c	BioLegend	Cat# 117307; RRID:AB_313776
APC/Cyanine7 anti-mouse/human CD11b	BioLegend	Cat# 101225; RRID:AB_830641
Brilliant Violet 605 anti-mouse CD103	BioLegend	Cat# 121433; RRID:AB_2629724
Brilliant Violet 785 anti-mouse/rat Xcr1	BioLegend	Cat# 148225; RRID:AB_2783119
FITC anti-mouse I-A/I-E	BioLegend	Cat# 107605; RRID:AB_313320
Alexa Fluor 700 anti-mouse Ly-6G	BioLegend	Cat# 127622; RRID:AB_10643269
PerCP/Cyanine5.5 anti-mouse F4/80	BioLegend	Cat# 123127; RRID:AB_893496
PE/Cyanine7 anti-mouse CD274 (B7-H1, PD-L1)	BioLegend	Cat# 124313; RRID:AB_10639934
APC anti-mouse CD274 (B7-H1, PD-L1)	BioLegend	Cat# 124311; RRID:AB_10612935
Alexa Fluor 647 anti-mouse CD172a (SIRPalpha)	BioLegend	Cat# 144028; RRID:AB_2721301
PerCP/Cyanine5.5 anti-mouse CD45.1	BioLegend	Cat# 110727; RRID:AB_893348
PE anti-mouse CD45.2	BioLegend	Cat# 109807; RRID:AB_313444
Brilliant Violet 421 Statl (pY701)	BD Biosciences	Cat# 562985; RRID:AB_2737932
Alexa Fluor 647 anti-Stat3, phospho (Tyr705) (Clone 4)	BD Biosciences	Cat# 557815; RRID:AB_647144
Alexa Fluor 647 Stat4 (pY693)	BD Biosciences	Cat# 558137; RRID:AB_397052
Alexa Fluor 488 Stat5 (pY694)	BD Biosciences	Cat# 612598; RRID:AB_399881
PE anti-mouse H-2Kb	BioLegend	Cat# 116507; RRID:AB_313734
APC anti-mouse H-2Db	Thermo Fisher	Cat# 17-5999-82; RRID:AB_2573252
Alexa Fluor 647 anti-human IgG Fc	BioLegend	Cat# 410713; RRID:AB_2728443
Alexa Fluor 647 Rat IgG2a isotype control	BioLegend	Cat# 400526; RRID:AB_2864284
InVivoMAb mouse IgG1 isotype control	Bio X Cell	Cat# BE0083; RRID:AB_1107784
InVivoMAb anti-TGF-β	Bio X Cell	Cat# BE0057; RRID:AB_1107757
InVivoPlus anti-mouse CD4	Bio X Cell	Cat# BE0003-1; RRID:AB_1107636
InVivoPlus anti-mouse CD8a	Bio X Cell	Cat# BP0117; RRID:AB_10950145
rat IgG2b Isotype control	Bio X Cell	Cat# BE0090; RRID:AB_1107780
InVivoPlus anti-mouse NK1.1	Bio X Cell	Cat# BE0036; RRID:AB_1107737
InVivoPlus mouse IgG2a isotype control	Bio X Cell	Cat# BE0085; RRID:AB_1107771
Anti-PD-L1 (E1L3N)	CellSignaling	Cat # 13684; RRID: AB_2687655
Biological samples
Human Malignant Melanoma Tissue Microarray	US Biomax	Cat # ME2082c
Human HNSCC Tissue Microarray	Stanford Healthcare	This paper
Chemicals, peptides, and recombinant proteins
StemPro Accutase	Thermo Fisher	Cat # A1110501
Lipofectamine 2000	Thermo Fisher	Cat # 11668019
Hygromycin B	Thermo Fisher	Cat # 10687010
Polybrene	Sigma	Cat # TR-1003-G
NP40	Sigma	Cat # 11332473001
Digitonin	Promega	Cat # G9441
Tagment DNA Enzyme	Illumina	Cat # 20034197
Collagenase 4	Worthington	Cat # LS004189
LIVE/DEAD Fixable Blue Dead Cell Stain	Thermo Fisher	Cat # L34962
LIVE/DEAD Fixable Near-IR Dead Cell Stain Kit	Thermo Fisher	Cat # L10119
eBioscience FoxP3 Fixation/Permeabilization	Thermo Fisher	Cat # 00-5521-00
DAPI	Thermo Fisher	Cat # D3571
NKG2D-Fc Chimera	R&D Systems	Cat # 139-NK-050
BV421 MHC-ll-Ova tetramer	NIH Tetramer Facility	I-A(b) AAHAEINEA
BV421 MHC-II Cntrl tetramer	NIH Tetramer Facility	I-A(b) PVSKMRMATPLLMQA
Recombinant mouse IFN-α	PBL Assay Science	Cat# 12100-1
Recombinant mouse IFN-γ	Biolegend	Cat # 575306
Fixation Buffer	BD Biosciences	Cat # 554655
Phosflow Perm Buffer III	BD Biosciences	Cat # 558050
Brilliant Stain Buffer Plus	BD Biosciences	Cat # 566385
Recombinant Human TGF-β	Peprotech	Cat# 100-21
Diptheria Toxin	Sigma	Cat # D0564
CellTrace CFSE	Thermo Fisher	Cat # C34554
CellTrace Violet	Thermo Fisher	Cat # C34571
Calcein-AM	Thermo Fisher	Cat # C3100MP
Tissue-Tek Optimal Cutting Temperature Compound	VWR	Cat # 25608-930
Dako Dual Endogenous Enzyme Block	Agilent	Cat # S2003
Dako Protein Block	Agilent	Cat # X0909
Critical commercial assays
DNA Clean and Concentrator-5 Kit	Zymo	Cat # D4013
NEBNext 2X Master Mix	New England Biolabs	Cat # M0541S
Lib Quant Kit	Kapa Biosystems	Cat # KK5621
SPHERO AccuCount Fluorescent Particles	Spherotech	Cat # ACFP-50-5
MojoSort Mouse Naïve CD4+ T Cell Isolation Kit	BioLegend	Cat # 480040
anti-CD3/CD28 Dynabeads	Thermo Fisher	Cat # 11456D
EasySep Mouse CD8+ T cell Isolation Kit	StemCell	Cat # 19853
EasySep Mouse NK Cell Isolation Kit	StemCell	Cat # 19855
ImmPRESS-AP Anti-Rabbit IgG (alkaline phosphatase) Polymer Detection Kit	Vector Laboratories	Cat # MP-5401
ImmPACT Vector Red Alkaline Phosphatase (AP) Substrate	Vector Laboratories	Cat # SK-5105
RNEasy Plus Mini	Qiagen	Cat # 74034
QIAshredder	Qiagen	Cat # 79654
DNEasy Blood and Tissue	Qiagen	Cat # 69504
Deposited data
Human HNSCC RNA-seq	This paper	GSE113839
Interferome v2 database	Rusinova et al., 2013	www.interferome.org
Mouse RNA-seq, ATAC-seq, and scRNA-seq	This paper	GSE117529
Mouse WES	This paper	PRJNA820881
Experimental models: Cell lines
B16-F0	ATCC	CRL-6322
B16-F10	ATCC	CRL-6475
LN Lines	This paper	N/A
LMP	Tseng et al., 2010 (our lab)	N/A
MOC2	Judd et al., 2012 (gift from John Sunwoo)	N/A
MC38	Gift from Cornelis J.M. Melief	N/A
Experimental models: Organisms/strains
C57BL/6J	Jackson Laboratories	#000664
B6129SF1/J	Jackson Laboratories	#101043
B6(Cg)-Rag2tm1.1Cgn/J	Jackson Laboratories	#008449
B6.129S4-Il2rgtm1Wjl/J	Jackson Laboratories	#003174
B6.FVB-Tg(MMTV-PyVT)634Mul/LellJ	Jackson Laboratories	#022974
NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ	Jackson Laboratories	#005557
B6.Cg-Tg(TcraTcrb)425Cbn/J	Jackson Laboratories	#004194
B6.129S2-Ltatm1Dch/J	Jackson Laboratories	#002258
B6.Cg-Tg(Tyr-cre/ERT2)13Bos Braftm1Mmcm Ptentm1Hwu/BosJ	Jackson Laboratories	#013590
B6.Cg-Foxp3tm2Tch/J	Jackson Laboratories	#006772
B6.129(Cg)-Foxp3tm3(DTR/GFP)Ayr/J	Jackson Laboratories	#016958
C57BL/6-Tg(TcraTcrb)110OMjb/J	Jackson Laboratories	#003831
B6;129S-Gt(ROSA)26Sortm1.1(CAG-COX8A/Dendra2)Dcc/J	Jackson Laboratories	#018397
B6.SJL-Ptprca Pepcb/BoyJ	Jackson Laboratories	#002014
Oligonucleotides
See Table S4
Recombinant DNA
lentiCRISPR v2	Sanjana et al., 2014	Addgene plasmid #52961
pSpCas9(BB)-2A-GFP (PX458)	Ran et al., 2013	Addgene plasmid #48138
mWasabi-N1	Ai et al., 2008	Addgene plasmid #54765
tdTomato-N1	Shaner et al., 2004	Addgene plasmid #54642
pCI-neo-cOVA	Yang et al., 2010	Addgene plasmid #25097
pLVX-IRES-Hyg	Clontech	Cat # 632185
psPAX2	Didier Trono	Addgene plasmid #12260
pCMV-VSV-G	Stewart et al., 2003	Addgene plasmid #8454
Software and algorithms
Trimmomatic (v0.36)	Bolger at al., 2014	https://github.com/usadellab/Trimmomatic
FastQC (v0.11.3)	Babraham Institute	https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
Salmon (v0.7.2)	Patro et al., 2017	https://combine-lab.github.io/salmon/
Rstudio (v1.0.143 – v1.1.463)	RStudio, Inc	https://rstudio.com/
DESeq2 (v1.14.1 and v1.28.1)	Love et al., 2014	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
GSEA (v3.0)	Mootha et al., 2003; Subramanian et al., 2005	https://www.gsea-msigdb.org/
HGNC Comparison of Orthology Predictions	HUGO Gene Nomenclature Committee	https://www.aenenames.ora/cai-bin/hcoo
Gene Ontology	Ashburner wt al., 2000; Gene Ontology Consortium	http://www.geneontology.org/
GraphPad Prism (v7.04 – v9.1.0)	Graphpad Software, LLC	N/A
FlowJo (v10.0.8)	TreeStar	N/A
ggplot2 (v2.2.1)	Wickham, 2016	https://ggplot2.tidyverse.org/
R stats package (v3.3.2)	R Foundation	http://www.r-project.org/
FSA package (v0.8.20)	R Foundation	http://www.r-project.org/
AGeNT Surecall Trimmer (v4.0.1)	Agilent	N/A
Burrows-Wheeler Aligner (bwa-mem) (v0.7.12)	Li et al., 2009 #1	http://bio-bwa.sourceforge.net/
SAMtools (v1.6 and v1.8)	Li et al., 2009 #2	https://github.com/samtools/
Picard (v2.17.0)	Broad Institute	https://broadinstitute.github.io/picard/
MuTect2 (GATK v4.0.0.0)	Broad Institute	https://gatk.broadinstitute.org/hc/enus/articles/360037593851-Mutect2
SnpEff (v4.3)	Cingolani et al., 2012	http://pcingola.github.io/SnpEff/
NetMHCpan (v4.0)	Jurtz et al., 2017	https://services.healthtech.dtu.dk/cgi-bin/sw_request
MuPeXI (v1.2.0)	Bjerregaard et al., 2017	https://github.com/ambj/MuPeXI
Variant Effect Predictor (v87.27)	McLaren et al., 2016	https://github.com/Ensembl/ensembl-vep
Circos (v0.69.4)	Krzywinski et al., 2009	http://circos.ca/
hisat2	Kim et al., 2019	http://daehwankimlab.github.io/hisat2/
MACS2	Zhang et al., 2008	https://pypi.org/project/MACS2/
Integrative Genomics Viewer (v2.5.3)	Broad Institute	https://software.broadinstitute.org/software/igv/
ChromVAR	Schep et al., 2017	https://greenleaflab.github.io/chromVAR/
HOMER	Heinz et al., 2010	http://homer.ucsd.edu/homer/
Cell Ranger (v3.1.0)	10X Genomics	https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest
Seurat (v4.0)	Hao et al, 2021	https://satijalab.org/seurat/
R (v4.0.2)	R Foundation	http://www.r-project.org/
Scikit-image	van der Walt et al., 2014	https://scikit-image.org/
OpenCV	Bradski, et al., 2000	https://pypi.org/project/opencv-python/
BD FACS Diva (v8.0.2)	Becton Dickinson	N/A
Zeiss ZEN 2012 (Blue Edition)	Zeiss	N/A
Nikon NIS-Elements D (v4.30.02)	Nikon	N/A
Adobe Photoshop CS6	Adobe System	N/A
Adobe Illustrator CS6	Adobe System	N/A
Other
Zeis LSM 700 confocal microscope	Zeiss	N/A
FACSAria II	Becton Dickinson	N/A
SMZ1000 Stereo Dissection Microscope	Nikon	N/A
IVIS Spectrum Imager	Caliper Life Sciences	N/A
LSR II	Becton Dickinson	N/A
LSRFortessa X-20	Becton Dickinson	N/A