REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
CD3 Antibody, clone UCHT1, fluorophore AF532	Invitrogen	Cat# 58-0038-42; RRID: AB_11218675
CD4 Antibody, clone SK3, fluorophore BUV805	BD	Cat# 612888; RRID: AB_2870177
CD8 Antibody, clone RPA-T8, fluorophore BV570	Biolegend	Cat# 301038; RRID: AB_10933259
CD14 Antibody, clone MφP9, fluorophore BB700	BD	Cat# 566465; RRID: AB_2739737
CD19 Antibody, clone SJ25C1, fluorophore BB700	BD	Cat# 566396; RRID: AB_2744310
CCR7 (CD197) Antibody, clone GO43H7, fluorophore BV605	BD	Cat# 353223; RRID: AB_11124325
CD45RA Antibody, clone HI100, fluorophore BUV563	BD	Cat# 612927; RRID: AB_2870212
CXCR3 Antibody, clone G025H7, fluorophore Pacific blue	Biolegend	Cat# 353724; RRID: AB_2561441
CXCR5 Antibody, clone RF8B2, fluorophore BV480	BD	Cat# 566142; RRID: AB_2739540
Tbet Antibody, clone 4B10, fluorophore BV785	Biolegend	Cat# 644835; RRID: AB_2721566
PD1 (CD279) Antibody, clone MIH4, fluorophore AF488	Invitrogen	Cat# 53-9969-42; RRID: AB_2762480
Lag3 Antibody, clone 11C3C65, fluorophore BV421	Biolegend	Cat# 369314; RRID: AB_2629797
FoxP3 Antibody, clone PCH101, fluorophore PE-Cy5	Invitrogen	Cat# 15-4776-42; RRID: AB_1963595
Tim3 Antibody, clone 7D3, fluorophore BV650	BD	Cat# 565564; RRID: AB_2722547
GZMK Antibody, clone G3H69, fluorophore PerCP-eF710	Invitrogen	Cat# 46-8897-42; RRID: AB_2573854
Tox Antibody, clone TXRX10, fluorophore PE	Invitrogen	Cat# 12-6502-82; RRID: AB_10855034
Eomes Antibody, clone WD1928, fluorophore PE-eF610	Invitrogen	Cat# 61-4877-42; RRID: AB_2574616
GZMB Antibody, clone QA16A092, fluorophore APC-Fire750	Biolegend	Cat# 372210; RRID: AB_2728376
CD28 Antibody, clone CD28.2, fluorophore BUV737	BD	Cat# 612815; RRID: AB_2870140
CD56 Antibody, clone NCAM16.2, fluorophore BUV395	BD	Cat# 563555; RRID: AB_2687886
CCR6 Antibody, clone 11A9, fluorophore BUV496	BD	Cat# 612948; RRID: AB_2833076
Ki67 Antibody, clone B56, fluorophore AF700	BD	Cat# 561277; RRID: AB_10611571
CCR4 Antibody, clone 1G1, fluorophore BUV615	BD	Cat# 613000; RRID: AB_2870269
TCF7 Antibody, clone C63D9, fluorophore PE-Cy7	Cell Signaling Technology	Cat# 90511S; RRID: AB_3086656
HLA-DR Antibody, clone L243, fluorophore BV711	BD	Cat# 752490; RRID: AB_2917483
CD7 Antibody, clone M-T701, fluorophore APC	BD	Cat# 653312; RRID: AB_2870352
CD3 Antibody, clone Sk7, fluorophore AF488	Biolegend	Cat# 344810; RRID: AB_10576234
CD4 Antibody, clone, fluorophore AF700	Invitrogen	Cat# 56-0048-82; RRID: AB_657741
CD8 Antibody, clone SK1, fluorophore BV570	Biolegend	Cat# 344755; RRID: AB_2810546
CD19 Antibody, clone HIB19, fluorophore BV421	Biolegend	Cat# 302234; RRID: AB_10897802
CD56 Antibody, clone NCAM16.2, fluorophore PE-Cy7	BD	Cat# 335809; RRID: AB_399984
CM2B4 Clone	Santa Cruz	136172; RRID: AB_2013156
Anti-HLA-I antibody, EMR8-5 clone	MBL International	D367-3; RRID: AB_3086657
Anti-Cytokeratin 20, Clone Ks20.8	Agilent	GA77761-2; RRID: AB_3086658
Anti-CD8, Clone C8/144B	Agilent	GA62361-2; RRID: AB_3073940
Anti-CD3, clone SP7	Invitrogen	MA1-90582; RRID: AB_1956722
Anti-HLA-DR, clone EP96	Bio SB	BSB 6793; RRID: AB_3086660
Anti-CD56, clone 123.C3	Bio SB	BSB 5267; RRID: AB_3086661
Anti-PD-L1	Cell Signaling Technology	13684; RRID: AB_2687655
Biological samples
Neoadjuvant Nivolumab PBMC	Bristol Myers Squibb	NCT02488759
MCC Tumor and PBMC samples	Nghiem lab repository, University of Washington	IRB Protocol 6585, Fred Hutch Cancer Center
Chemicals, peptides, and recombinant proteins
Peptides (See Tables S1, S3, and S6)	Genscript, Piscataway, NJ	Custom
Human Serum	Valley Biomedical	HS1004
RPMI 1640	Corning	15-040-CV
DMSO	Millipore Sigma	20–139
Remel phytohemagglutinin-purified mitogen	Thermofisher	R30852801
human recombinant IL-15	R&D systems	BT-015-025
natural interleukin IL-2	Hemagen	906011
MHC-I tetramers	International Histocompatibility Working Group, Fred Hutch Cancer Center, Seattle WA	Custom
DNAse I	Worthington Biochemical	LS002139
dasatinib	Selleck Chem	S1021
LIVE/DEAD™ Fixable Blue Dead Cell Stain Kit	Invitrogen	L23105
autoMACS® Running Buffer	Miltenyi	130-091-221
eBioscience™ Foxp3/Transcription Factor Staining Buffer Set	Invitrogen	00-5523-00
AbC™ Total Antibody Compensation Bead Kit	Invitrogen	A10497
ArC™ Amine Reactive Compensation Bead Kit	Invitrogen	A10346
Fixable Viability Stain 780	BD	565388
MHC-I dextramers	Immudex	Custiom
Critical commercial assays
Chromium i7 Multiplex Kit, 96 rxns	10× Genomics	120262
Chromium Single Cell 5′ Library & Gel Bead Kit	10× Genomics	1000014
Chromium Single Cell 5′ Library Construction Kit	10× Genomics	1000020
Chromium Single Cell V(D)J Enrichment Kit, Human T cell	10× Genomics	1000005
Chromium Single Cell 5′ Feature Barcode Library Kit	10× Genomics	1000080
Chromium i7 Multiplex Kit N Set A	10× Genomics	1000084
Chromium Next GEM Chip G Single Cell Kit	10× Genomics	1000127
Chromium Next GEM Single Cell 5′ Library and Gel Bead Kit v1.1	10× Genomics	1000167
QIAamp DNA FFPE tissue kit	Qiagen	56404
QIAamp DNA Blood Mini Kit	Qiagen	51104
Deposited data
CITEseq data	This study	GSE227054
Alpha-beta TCRseq	This study	GSE227708
CITEseq data, Patient A	This study	GSE227709
Eberhardt et al. scRNAseq dataset	Eberhardt et al. 2021	GSE180268
Caushi et al. scRNAseq dataset	Caushi et al. 2021	GSE173351
Experimental models: Cell lines
Cos-7 cells	ATCC	Cat#CRL-1651
Software and algorithms
CellRanger	10× Genomics	V3.10
R	CRAN	v.4.1.2
FlowJo	FlowJo	v.10.8.1
scater	CRAN	v.1.22.
Seurat	CRAN	v.4.3.
ggplot2	CRAN	3.4.0)
SCENIC	CRAN	v.1.2.4
UCell	CRAN	v.1.99.1
slingshot	CRAN	v.2.2.1
clustree	CRAN	v.0.5.
scran	CRAN	v.1.22.1
batchelor	CRAN	v1.10.0
scuttle	CRAN	v.1.4.0
DropletUtils	CRAN	v.1.14.2
scds	CRAN	v.1.10.0
phenograph	CRAN	v.0.99.1
uwot	CRAN	v.0.1.14
survminer	CRAN	v0.4.
netMHCpan	DTU Health Tech	v4.0