KEY RESOURCES TABLE

REAGENT or RESOURCE	SOURCE	IDENTIFIER
Antibodies
Rat monoclonal Anti-CD3	Bio Rad	MCA1477
Rabbit monoclonal Anti-CD8	Abcam	Ab101500
Rabbit monoclonal Anti-CD45	Cell Signaling Technology	13917
Rabbit monoclonal. Anti-PDL1	Abcam	B228462
Mouse monoclonal Anti PD-1	Abcam	Ab52587
Rabbit polyclonal Anti-cytokeratin, wide spectrum	DAKO	Z0622
Bacterial and Virus Strains
Biological Samples
Chemicals, Peptides, and Recombinant Proteins
Critical Commercial Assays
Library Amplification Readymix: with KAPA HiFi DNA Polymerase	Kapa Biosystems, Inc.,	Cat# KK2612
Agencourt AMPure XP beads	Beckman Coulter	A63882
SeqCap EZ HGSC VCRome, 96 Reactions	Roche NimbleGen	Cat# (06465676001)
xGen Blocking Oligos	Integrated DNA technologies	Cat# 1016184, Cat#1016186
TruSeq RNA Exome (previously marketed as TruSeq RNA Library Prep for Enrichment (Cat. No. 20020189), TruSeq RNA Enrichment (Cat. No. 20020490), Exome Panel (Cat. No. 20020183)	Illumina	20020490
TruSeq Rapid SBS Kit-HS (200 cycles)	Illumina	FC-402-4001
TruSeq SBS kit v3-HS (200 cycles)	Illumina	FC-401-3001
HiSeq Rapid SBS Kit v2 (200 cycles)	Illumina	FC-402-4021
XT_HS_IO360_CSO + Standard	NanoString	115000222
Low RNA Input Kit	NanoString	1220000219
XT_IO360 Primers	NanoString	115000219
Deposited Data
TCGA data sets	TCGA legacy archive	https://portal.gdc.cancer.gov/legacy-archive/
RNAseq BAM files	This paper	Phs001145.v1.p1 at https://www.ncbi.nlm.nih.gov/gap/ and EXCEPTIONAL_RESPONDERS-ER at https://portal.gdc.cancer.gov/
DNA BAM files	This paper	Phs001145.v1.p1 at https://www.ncbi.nlm.nih.gov/gap/ and EXCEPTIONAL_RESPONDERS-ER at https://portal.gdc.cancer.gov/
Mutation tables for SNV and indels, and for CNA	This paper	Phs001145.v1.p1 at https://www.ncbi.nlm.nih.gov/gap/ and EXCEPTIONAL_RESPONDERS-ER at https://portal.gdc.cancer.gov/
DNA Methylation IDAT files	This paper	Phs001145.v1.p1 at https://www.ncbi.nlm.nih.gov/gap/ and EXCEPTIONAL_RESPONDERS-ER at https://portal.gdc.cancer.gov/
NanoString expression tables	This Paper	Phs001145.v1.p1 at https://www.ncbi.nlm.nih.gov/gap/ and EXCEPTIONAL_RESPONDERS-ER at https://portal.gdc.cancer.gov/
Immunohistochemistry immune cell type quantification (see also Supplementary Table 4)	This paper	Phs001145.v1.p1 at https://www.ncbi.nlm.nih.gov/gap/ and EXCEPTIONAL_RESPONDERS-ER at https://portal.gdc.cancer.gov/
Clinical information	This paper	Phs001145.v1.p1 at https://www.ncbi.nlm.nih.gov/gap/ and EXCEPTIONAL_RESPONDERS-ER at https://portal.gdc.cancer.gov/
Experimental Models: Cell Lines
Experimental Models: Organisms/Strains
Oligonucleotides
RNAscope 2.5 LS Probe - Hs-IFNG-C3	Advanced Cell Diagnostics	Cat# 310508-C3
Recombinant DNA
Software and Algorithms
R v3.6. 2006	R Development Core Team	https://www.r-project.org
function HotellingsT2 in R package ICSNP, v1.1-1	Nordhausen K, Sirkia S, Oja H, Tyler DE, 2018	https://CRAN.R-project.org/package=ICSNP
functions anova, lm, p.adjust, and t.test in the R package stats (incorporated into base R, v3.6)	R Development Core Team	https://www.r-project.org
function gls in R package nlme, v3.1-137	Pinheiro J, Bates D, DebRoy S, Sarkar D, R Development Core Team, 2018	https://CRAN.R-project.org/package=nlme
Function RUVr in RUVseq package v1.22.0	PMID: 25150836	https://www.bioconductor.org/packages/release/bioc/html/RUVSeq.html
Function varianceStabilizingTransformation in DESeq2 Bioconductor package v1.28.1	PMID: 25516281	https://bioconductor.org/packages/release/bioc/html/DESeq2.html
Function betweenLaneNormalization in EDAseq Bioconductor package v2.22.0	PMID: 22177264	https://bioconductor.org/packages/release/bioc/html/EDASeq.html
SeSAMe v1.3.2	PMID: 30085201	https://www.bioconductor.org/packages/release/bioc/html/sesame.html
Other