REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
anti-p53 (1C12) Mouse mAb	Cell signaling	Cat#2524; RRID:AB_331743
Mouse anti-GAPDH	Millipore	Clone 6C5 Cat#MAB374; RRID:AB_2107445
Peroxidase Affinipure Goat anti-Mouse IgG	Jackson ImmunoResearch Labs	Cat#115-035-003; RRID:AB_10015289
anti-mouse PD-1 (CD279)	BioXCell	29F.1.A12 Cat#: BE0273; RRID: AB_2687796
Rat IgG2a isotype control	BioXCell	2A3, Cat#: BE0089; RRID: AB_1107769
Alexa Fluor700 anti-mouse CD45	Biolegend	Clone 30-F11 Cat#103128; RRID:AB_493715
PerCP/Cy5.5 anti-mouse CD8a	Biolegend	clone 53-6.7 Cat#100734; RRID:AB_2075238
APC/Cy7 anti-mouse CD4	Biolegend	clone GK1.5 Cat#100413; RRID:AB_312698
FITC anti- mouse CD107a (LAMP-1)	Biolegend	clone 1D4B Cat#121605; RRID:AB_572006
Pacific Blue anti-Granzyme B	Biolegend	clone GB11 Cat#515407; RRID:AB_2562195
PE/Cy7 anti- mouse IFN-γ	Biolegend	clone XMG12 Cat #505826; RRID:AB_2295770
Pacific Blue anti-mouse CD8a	Biolegend	Clone 53-6.7 Cat#100728; RRID:AB_493426
PerCP anti-mouse CD4	Biolegend	clone GK1.5 Cat#100431; RRID:AB_893329
FITC anti-mouse CD45	Biolegend	Clone 30-F11 Cat#103108; RRID:AB_312973
PE/Cy7 anti-mouseCD90.2 (Thy-1.2)	Biolegend	Clone 30-H12 Cat#105325; RRID:AB_2303142
PE anti-mouseTCRβ	Biolegend	clone H57-597 Cat#109207; RRID:AB_313430
a-CD8a rat monoclonal antibody	eBioscience	Clone 4SM15 Cat#14-0808-82; RRID:AB_2572861
Biotin Donkey anti Rat IgG (H+L)	Jackson ImmunoResearch	Cat#712-065-153; RRID:AB_2315779
anti-CD3 rabbit monoclonal antibody [SP7]	Abcam	Cat#ab16669; RRID:AB_443425
anti-FoxP3 rat monoclonal antibody (FJK-16 s)	Thermo Fisher Scientific	Cat#14-5773-82; RRID:AB_467576
Cy2 Donkey anti Rabbit IgG (H+L)	Jackson ImmunoResearch	Cat#711-225-152; RRID:AB_2340612
Cy3 Donkey anti Rat IgG (H+L)	Jackson ImmunoResearch	Cat#712-165-153; RRID:AB_2340667
anti-CPD	Cosmo Bio	Cat#CAC-NM-DND-001; RRID:AB_1962813
Cy3 Donkey anti Mouse IgG (H+L)	Jackson ImmunoResearch	Cat#715-165-151; RRID:AB_2315777
anti-H2-Kb	ATCC	Cat#20-8-4 s (HB-11)
anti-H2-Db	In house; generated from hybridoma purchased from ATCC	Cat#28-14-8 s (HB-27)
APC anti-mouse H-2Kb	In house; generated from hybridoma purchased from ATCC	clone AF6-88.5 Cat#116517; RRID:AB_10568693
PE anti-mouse H-2Db	BioLegend	clone KH95 Cat#111507; RRID:AB_313512
APC anti-CD11c	Thermo Fisher Scientific	Clone N418 Cat# 17-0114-81; RRID:AB_469345
Pacific Blue(TM) anti-mouse CD80 antibody	BioLegend	Clone 16-10A1 Cat# 104723; RRID:AB_2076001
PE Anti-Mouse CD86 (B7-2)	Thermo Fisher Scientific	Clone PO3.1 Cat# 12-0861-81; RRID:AB_465764
PE/Cy7 anti-mouse I-Ab (Anti-MHCII)	BioLegend	Clone AF6-120.1 Cat# 116419; RRID:AB_10575904
PerCP-Cyanine5.5 CD197 (CCR7) Monoclonal Antibody (4B12)	Thermo Fisher Scientific	Clone 4B12 Cat# 45-1971-80; RRID:AB_925738
APC Anti-Mouse CD45.1	Thermo Fisher Scientific	Clone A20 Cat# 17-0453-82; RRID:AB_469398
Chemicals, Peptides, and Recombinant Proteins
RPMI	Biological Industries	Cat#01-100-1A
FBS	GIBCO	Cat#12657-029
L-glutamine	Biological Industries	Cat#03-020-1B
Penicillin/Streptomycin antibiotics	Invitrogen	Cat#15140163
HEPES	Sigma	Cat#H0887
DMEM	GIBCO	Cat#41965-039
MCDB 153	Sigma	Cat# M7403
L-15 Medium (Leibovitz)	Sigma	Cat#L1518
bovine insulin	Sigma	Cat#I0516
SDS Solution 20%	Bio-Rad	Cat# 161-0418
SYBR Green I	Invitrogen	Cat#S7567
Water, ultra-pure	Biological Industries	Cat#01-866-1A
β-mercaptoethanol	EMD Millipore Corp.	Cat#444203
Dulbecco’s Phosphate Buffered Saline (PBS)	Biological Industries	Cat#02-023-1A
sodium pyruvate	Biological Industries	Cat#03-042-1B
MEM-Eagle Non-essential amino acids solution	Biological Industries	Cat#01-340-1B
Recombinant Mouse Granulocyte Macrophage Colony Stimulating Factor GM-CSF Mouse	PROSPEC	Cat#cyt-222
Lipopolysaccharides (LPS) from E-coli	Sigma	Cat#L26630
Opti-MEM Reduced Serum Medium	GIBCO	Cat#31985-047
CFSE	eBioscience	Cat#65-0850-84
Collagenase D	Roche	Cat# 11088866001
DNase I	Roche	Cat#10104159001
BSA	Sigma	Cat# A9418
HBSS (w/o Ca2+ or Mg++)	Bio-Lab	Cat#004717237500
Collagenase IV	gibco	Cat#17104-019
EGTA	Merck	Cat# 324626.25
polyvinyl alcohol (PVA)	Sigma	Cat# P8136
trypsin	Sigma	Cat# T4549
Optiprep	Sigma	Cat#D1556
Versen	Lonza	Cat#17-711E
Paraformaldehyde (PFA)	Electron Microscopy Sciences	Cat#15710
hematoxylin	Sigma	Cat#GHS316
Hoechst	Invitrogen	Cat#LSH3570
Protease Inhibitors Cocktail	Sigma	Cat#P8340
sodium deoxycholate	Sigma	Cat#D6750
iodoacetamide	Sigma	Cat#I6125
EDTA	Promega	Cat#V4231
PMSF	Sigma	Cat#78830
octyl-β-D glucopyranoside	Sigma	Cat#O8001
Protein-A Resin	A2S	Cat#L00210
FAIFNTEQM synthetic peptide	GenScript Biotech Corp.	N/A
VINENYDYL synthetic peptide	GenScript Biotech Corp.	N/A
SAYEKLYSL synthetic peptide	GenScript Biotech Corp.	N/A
ASLTHVDSL synthetic peptide	GenScript Biotech Corp.	N/A
LANETISTL synthetic peptide	GenScript Biotech Corp.	N/A
VAHIFVIGV synthetic peptide	GenScript Biotech Corp.	N/A
AGLLNSPHFI synthetic peptide	GenScript Biotech Corp.	N/A
HQNVNVENI synthetic peptide	GenScript Biotech Corp.	N/A
QAFDFAYV synthetic peptide	GenScript Biotech Corp.	N/A
FAALLRYSI synthetic peptide	GenScript Biotech Corp.	N/A
SMYLVSKL synthetic peptide	GenScript Biotech Corp.	N/A
Critical Commercial Assays
BD Cytofix/Cytoperm Kit	Thermo Fisher Scientific	Cat#BD 554714
SENSE Total RNA-Seq Library Prep Kit for Illumina),	Lexogen	Cat#LX-009.96 1
DNeasy Blood & Tissue Kit	QIAGEN	Cat# 69504
SureSelectXT Mouse All Exon System	Agilent Technologies	Cat# 5190-4641
Dynabeads mRNA DIRECT Kit	Invitrogen	Cat#61012
SuperSignal WestPicoPLUS Chemiluminescent Suibstrat	Thermo Fisher Scientific	Cat#34580
3,3′-Diaminobenzidine tetrahydrochloride	Sigma	Cat# D5905
Deposited Data
Mouse WES sequencing data	This paper	https://www.ebi.ac.uk/ena; accession number: PRJEB25961, secondary accession: ERP107928.
Mouse CD8+ T cell RNaseq data	This paper	https://github.com/bioinf-dev/Wolf_et_al_Cell_2019/blob/master/Other/RNAseq_mouse_CD8Tcell_TPM.txt
Processed data and code used for Figures 1, 2, 3, and 7	This paper (Figures 1, 2, and 3). For Figure 7Snyder et al., 2014, Riaz et al., 2017, Hugo et al., 2016; and Van Allen et al., 2015	https://github.com/bioinf-dev/Wolf_et_al_Cell_2019
MS spectra of the identified neoantigenes and synthetic peptides	This paper	https://github.com/bioinf-dev/Wolf_et_al_Cell_2019/blob/master/Other/Spectra.pdf
Experimental Models: Cell Lines
Murine melanoma B2905	Laboratory of Prof. Merlino	N/A
B16F10.9	Laboratory of Prof. Eisenbach	N/A
RMA-s	Laboratory of Prof. Eisenbach	RRID:CVCL_2180
Experimental Models: Organisms/Strains
C57BL/6JOlaHst	Envigo	N/A
NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ (NSG)	The Jackson Laboratory	Cat#JAX:005557 RRID:IMSR_JAX:005557
B6.129S4-Cd80tm1ShrCd86tm2Shr/J (CD80/86 −/− Double KO)	Laboratory of Prof. Jung	Cat# JAX:003610 RRID:IMSR_JAX:003610
Software and Algorithms
FlowJo software	Tree Star	N/A
Prism	GraphPad	N/A
ImageLab 5.1 software	BioRad	N/A
FIJI	ImageJ	Schindelin et al., 2012
CHAT v1.0	Snyder et al., 2014	https://cran.r-project.org/src/contrib/Archive/CHAT/
deconstructSigs v1.8.0	Rosenthal et al., 2016	https://www.rdocumentation.org/packages/deconstructSigs/versions/1.8.0
NetMHC v4.0	Nielsen et al., 2003	http://www.cbs.dtu.dk/services/NetMHC/
SciClone v1.1.0	Miller et al., 2014	https://www.rdocumentation.org/packages/sciClone/versions/1.1.0/topics/sciClone
Maxqaunt v1.5.3.8	Cox and Mann, 2008	http://coxdocs.org/doku.php?id=maxquant:start
samtools v1.8	Li et al., 2009	http://www.htslib.org/
Trimomatic v0.36	Bolger et al., 2014	http://www.usadellab.org/cms/index.php?page=trimmomatic
Salmon v0.9.2	Patro et al., 2017	https://salmon.readthedocs.io/en/latest/building.html
GATK v3.6	McKenna et al., 2010	https://software.broadinstitute.org/gatk/
CNVkit	Talevich et al., 2016	https://cnvkit.readthedocs.io/en/stable/
CloneEvol	Talevich et al., 2016	https://github.com/hdng/clonevol
BWA	Li and Durbin, 2010	http://bio-bwa.sourceforge.net/
vcf2maf	N/A	https://github.com/mskcc/vcf2maf
bcftools v1.3	Li et al., 2009	https://github.com/samtools/bcftools
Rstudio v1.1.423	N/A	https://www.rstudio.com/products/rstudio/
R ‘survival’ package v2.43-3.	Therneau and Grambsch, 2000	https://cran.r-project.org/web/packages/survival/index.html
R ‘entropy’ package v1.2.1	Hausser and Strimmer, 2009	https://cran.r-project.org/web/packages/entropy/index.html
R ‘ggsurvplot’ function	Kassambara et al., 2017	https://cran.r-project.org/web/packages/survminer/index.html