KEY RESOURCES TABLE:
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| InVivoMab rat IgG2a isotype control (clone 2A3) | BioXCell | Cat# BE0089, RRID:AB_1107769 |
| InVivoMab anti-mouse TIM3 (clone RMT3-23) | BioXCell | Cat# BE0115, RRID:AB_10949464 |
| InVivoMab anti-mouse PD-1 (clone 29F.1A12) | BioXCell | Cat# BE0273, RRID:AB_2687796 |
| InVivoMab anti-mouse CTLA-4 (clone 9D9) | BioXCell | Cat# BE0164, RRID:AB_10949609 |
| InVivoMab anti-mouse CD8a (clone 2.43) | BioXCell | Cat# BE0061, RRID:AB_1125541 |
| InVivoMab anti-mouse CD4 (clone GK1.5) | BioXCell | Cat# BE0003–1, RRID:AB_1107636 |
| InVivoMab rat IgG2b isotype control (clone LTF-2) | BioXCell | Cat# BE0090, RRID:AB_1107780 |
| InVivoMab anti-mouse PD-1 (clone RMP1-14) | BioXCell | Cat# BE0146, RRID:AB_10949053 |
| InVivoMab anti-mouse IFNγ (clone R4–6A2) | BioXCell | Cat# BE0054, RRID:AB_1107692 |
| InVivoMab anti-mouse CD8a (clone 53–6.7) | BioXCell | Cat# BE0004–1, RRID:AB_1107671 |
| Human TruStain FcX | Biolegend | Cat# 422302 |
| TruStain FcX anti-mouse CD16/32 (clone 93) | Biolegend | Cat# 101320, RRID:AB_1574975 |
| PE anti-human CD45 (clone HI30) | Biolegend | Cat# 304008, RRID:AB_314396 |
| APC anti-human CD3 (clone UCHT1) | Biolegend | Cat# 300412, RRID:AB_314066 |
| FITC anti-human HLA-A,B,C (clone W6/32) | Biolegend | Cat# 311404, RRID:AB_314873 |
| APC/Cy7 anti-human CD235a (clone HI264) | Biolegend | Cat# 349116, RRID:AB_2650978 |
| PE/Cy5 anti-human CD3 (clone HIT3a) | Biolegend | Cat# 300309, RRID:AB_314045 |
| Brilliant Violet 421 anti-human CD279 (PD-1; clone EH12.2H7) | Biolegend | Cat# 329919, RRID:AB_10900818 |
| PE/Cy7 anti-human CD366 (TIM3; clone F38–2E2) | Biolegend | Cat# 345013, RRID:AB_2561719 |
| APC/Cy7 anti-human CD39 (clone A1) | Biolegend | Cat# 328226, RRID:AB_2571981 |
| Alexa Fluor 700 anti-human CD4 (clone OKT4) | Biolegend | Cat# 317425, RRID:AB_571942 |
| Brilliant Violet 650 anti-human CD8a (clone RPA-T8) | Biolegend | Cat# 301041, RRID:AB_11125174 |
| Alexa Fluor 647 anti-mouse CD39 (clone Duha59) | Biolegend | Cat# 143808, RRID:AB_2563978 |
| Brilliant Violet 605 anti-mouse CD3 (clone 145–2C11) | Biolegend | Cat# 100351, RRID:AB_2565842 |
| Pacific Blue anti-mouse CD3 (clone 145-2C11) | Biolegend | Cat# 100334, RRID:AB_2028475 |
| PE/Cy5 anti-mouse CD8a (clone 53–6.7) | Biolegend | Cat# 100710, RRID:AB_312749 |
| FITC anti-mouse CD8a (clone 53–6.7) | Biolegend | Cat# 100705, RRID:AB_312744 |
| APC/Cy7 anti-mouse CD4 (clone GK1.5) | Biolegend | Cat# 100414, RRID:AB_312699 |
| Brilliant Violet 650 anti-mouse CD45.2 (clone 104) | Biolegend | Cat# 109836, RRID:AB_2563065 |
| FITC anti-mouse CD45.2 (clone 104) | Biolegend | Cat# 109806, RRID:AB_313443 |
| APC anti-mouse CD90.2 (Thy1.2; clone 53–2.1) | Biolegend | Cat# 140312, RRID:AB_10640728 |
| Pacific Blue anti-mouse CD90.2 (thy1.2; clone 30-H12) | Biolegend | Cat# 105324, RRID:AB_2201291 |
| APC anti-mouse TNFα (clone MP6-XT22) | Biolegend | Cat# 506307, RRID:AB_315428 |
| PE anti-mouse IL-2 (clone JES6–5H4) | Biolegend | Cat# 503807, RRID:AB_315301 |
| FITC anti-mouse IFNγ (clone XMG1.2) | Biolegend | Cat# 505805, RRID:AB_315399 |
| PE anti-mouse Perforin (clone S16009A) | Biolegend | Cat# 154305, RRID:AB_2721638 |
| APC anti-human/mouse Granzyme B (clone QA16A02) | Biolegend | Cat# 372203, RRID:AB_2687027 |
| Anti-IFNγ FITC, human antibody (clone 45–15) | Miltenyi Biotec | Cat# 130-097-936, RRID:AB_2661059 |
| Anti-IL-2-PE, human antibody (clone N7.48 A) | Miltenyi Biotec | Cat# 130-099-391, RRID:AB_2661066 |
| Anti-TNFα-APC, human antibody (clone cA2) | Miltenyi Biotec | Cat# 130-099-197, RRID:AB_2661079 |
| LEAF Purified anti-human CD3 (clone OKT3) | Biolegend | Cat# 317303, RRID:AB_571924 |
| LEAF Purified anti-human CD28 (clone CD28.2) | Biolegend | Cat# 302913, RRID:AB_314315 |
| LEAF Purified anti-mouse CD3 (clone 145-2C11) | Biolegend | Cat# 100314, RRID:AB_312679 |
| LEAF Purified anti-mouse CD28 (clone 37.51) | Biolegend | Cat# 102112, RRID:AB_312877 |
| Purified anti-human CD8a (clone C8/144B) | Biolegend | Cat# 372902, RRID:AB_2650657 |
| TCF1 (C63D9) Rabbit mAb | Cell Signaling Technology | Cat# 2203, RRID:AB_2199302 |
| Beta 2 Microglobulin antibody | Abcam | Cat# ab27588, RRID:AB_471058 |
| Melanoma Triple Cocktail Primary Antibody (clone HMB45+A103+T311) | Ventana (Roche) | Cat# 790–4677 |
| Biological Samples | ||
| Patient samples used in this study are detailed in tables S1, S3 and S5 | ||
| Chemicals, Peptides, and Recombinant Proteins | ||
| POM-1 (polyoxometalate-1) 5mg/kg/day (ChemCruz; sc-203205) | Santa Cruz Biotechnology | Cat# sc-203205 |
| Zombie green fixable viability dye | Biolegend | Cat# 423111 |
| Zombie violet fixable viability dye | Biolegend | Cat# 423114 |
| CFSE cell division tracker kit | Biolegend | Cat# 423801 |
| Critical Commercial Assays | ||
| Tumor Dissociation Kit, Human | Miltenyi Biotec | Cat# 130-095-929 |
| Transcription Factor Buffer Set | BD Biosciences | Cat# 562574 |
| Fixation/Permeabilization Solution Kit | BD Biosciences | Cat# 555028 |
| Qubit dsDNA HS assay kit | Invitrogen | Cat# Q32854 |
| High sensitivity DNA kit | Agilent | Cat# 5067–4626 |
| Nextera XT Library Prep kit | illumina | Cat# FC-131–1096 |
| OPAL 4-color multiplex manual IHC kit | PerkinElmer | Cat# NEL800001KT |
| 3D culture chips | AIM Biotech | Cat# DAX-1 |
| CellTiter-Glo Luminescent Cell Viability Assay | Promega | Cat# G7571 |
| Nextera DNA Library prep kit | illumina | Cat# FC-121–1031 |
| Allprep DNA/RNA Mini kit | Qiagen | Cat# 80204 |
| Deposited Data | ||
| Raw data for single cell RNA sequencing and Whole Exome sequencing (this paper) | dbGAP | phs001680.v1.p1 https://www.ncbi.nlm.nih.gov/proiects/gap/cgi-bin/study.cgi?studyid=phs001680.v1.p1 |
| Processed data for single cell RNA | GEO | GSE120575 |
| sequencing (this paper) | http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE120575 | |
| Bulk RNA expression data Van Allen cohort | (Van Allen et al., 2015) | dbGap accession number: phs000452.v2.p1 |
| Bulk RNA expression data Riaz cohort | (Riaz et al., 2017) | GEO accession number: GSE91061 |
| Single cell sequencing data Tirosh cohort | (Tirosh et al., 2016) | GEO accession number: GSE72056 |
| Experimental Models: Cell Lines | ||
| B16-F10 | Mikael Pittet | N/A |
| CT26 | Umar Mahamood | N/A |
| Experimental Models: Organisms/Strains | ||
| C57BL/6J | Jackson Laboratory | Cat# JAX:000664; RRID:IMSR_JAX:000664 |
| BALB/cJ | Jackson Laboratory | Cat# JAX:000651; RRID:IMSR_JAX:000651 |
| Oligonucleotides | ||
| RT primer (DNA oligo) | IDT | 5’-AAGCAGTGGTATCAACGCAGAGTACT30VN-3’ |
| TSO primer (RNA oligo with LNA) | Exigon | 5’-AAGCAGTGGTATCAACGCAGAGTACATrGrG+G-3’ |
| ISPCR primer (DNA oligo) | IDT | 5’-AAGCAGTGGTATCAACGCAGAGT-3’ |
| Recombinant DNA | ||
| FUGW | David Baltimore | Cat# 14883; addgene |
| psPAX2 | Didier Trono | Cat# 12260; addgene |
| pMD2.G | Didier Trono | Cat# 12259; addgene |
| Software and Algorithms | ||
| STAR | (Dobin et al., 2013) | https://github.com/alexdobin/STAR |
| RSEM | (Li and Dewey, 2011) | https://github.com/deweylab/RSEM |
| t-SNE | (Maaten and Hinton, 2008) | https://lvdmaaten.github.io/tsne/ |
| Matlab | MATLAB and Statistics Toolbox Release 2016b, The MathWorks, Inc., Natick, Massachusetts, United States. | https://www.mathworks.com/products/matlab.html |
| Monocle v. 2.5.4 | (Qiu et al., 2017) | http://cole-trapnell-lab.github.io/monocle-release/ |
| MixCr | (Bolotin et al., 2015) | https://github.com/milaboratory/mixcr |
| Bowtie 2.2.1 | (Langmead and Salzberg, 2012) | http://bowtie-bio.sourceforge.net/index.shtml |
| Samtools 1.3 | (Li et al., 2009) | http://samtools.sourceforge.net/ |
| ContEst | (Cibulskis et al., 2011) | https://www.broadinstitute.org/node/358411 |
| MuTect | (Cibulskis et al., 2013) | https://www.broadinstitute.org/node/358411 |
| oxoG filtering | (Costello et al., 2013) | |
| NovoAlign | Novocraft | www.novocraft.com |
| Oncotator | (Ramos et al., 2015) | https://portals.broadinstitute.org/oncotator/ |
| GOMER | (Granek and Clarke, 2005) | http://people.duke.edu/~josh/biophysicsweb/GOMER/index.html |
| CIS-BP database | (Weirauch et al., 2014) | http://cisbp.ccbr.utoronto.ca/ |
| HOMER version 4.9 | (Heinz et al., 2010) | http://homer.ucsd.edu/homer/download.html |
| edgeR 3.14.0 | (Robinson et al., 2010) | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| FlowJo 10.4.2 | FlowJo | https://www.flowjo.com/solutions/flowjo/downloads/previous-versions |
| CellProfiler 2.2.0 | (Carpenter et al., 2006) | http://cellprofiler.org/previous_releases/ |
| GraphPad PRISM 7.0c | GraphPad Software | https://www.graphpad.com/scientific-software/prism/ |