Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-Mouse PD1 (Clone RMP1–14) | BioXcell | Bio X Cell Cat# BE0146 (also BE0146–100MG, BE0146–1MG, BE0146–25MG, BE0146–50MG, BE0146–5MG, BP0146–100MG, BP0146–25MG, BP0146–50MG, BP0146–5MG), RRID:AB_10949053 |
| BUV395 Rat Anti-Mouse CD44 | BD Biosciences | 740215, RRID:AB_2739963 |
| BUV496 Rat Anti-Mouse CD45R/B220 | BD Biosciences | 612950, RRID:AB_2870227 |
| BUV563 Rat Anti-Mouse CD4 | BD Biosciences | 612923, RRID:AB_2870208 |
| BUV661 Rat Anti-CD11b | BD Biosciences | 612977, RRID:AB_2870249 |
| BUV737 Rat Anti-Mouse CD127 | BD Biosciences | 612841, RRID:AB_2870163 |
| BUV805 Rat Anti-Mouse CD8a | BD Biosciences | 612898, RRID:AB_2870186 |
| Brilliant Violet 421™ anti-mouse FOXP3 | Biolegend | 126419 |
| BV480 Mouse Anti-Mouse CD45.2 | BD Biosciences | 566073, RRID:AB_2739488 |
| BV605 Hamster Anti-Mouse KLRG1 | BD Biosciences | 564013, RRID:AB_2722497 |
| BV650 Anti-Mouse TCRB | Biolegend | 109251, RRID:AB_2810348 |
| BV711 Anti-Mouse CD366 (Tim-3) | Biolegend | 119727, RRID:AB_2716208 |
| Brilliant Violet 785™ anti-mouse CD62L Antibody | Biolegend | 104440, RRID:AB_2629685 |
| BB700 Ly108 | BD Biosciences | 742272, RRID:AB_2871448 |
| PE Mouse Anti-TCF-7/TCF-1 | BD Biosciences | 564217, RRID:AB_2687845 |
| PECy5 CD69 | Biolegend | 104510, RRID:AB_313113 |
| PECy7 PD1 | Biolegend | 109110, RRID:AB_572017 |
| TOX Antibody, anti-human/mouse, APC, REAfinity™ | Miltenyi | 130–118-335, RRID:AB_2751485 |
| Alexa Fluor® 700 anti-mouse/rat/human CD27 Antibody | Biolegend | 124240, RRID:AB_2810383 |
| Biotin Anti Mouse CX3CR1 | Biolegend | 149018, RRID:AB_2565701 |
| eBioscience™ Foxp3 / Transcription Factor Staining Buffer Set | Thermo Fisher | 00–5523-00 |
| C57BL/6 WT mice | Charles River Laboratories | Stock 027 |
| CTLA4 | BIOXCELL | 9H10 |
| PD1 | BIOXCELL | RMP1–14 |
| CD40 | BIOXCELL | #BE0016–2 |
| HLA-1/MHC-1, Clone: A4 | eBioscience | AB_1210772 |
| B2M Polyclonal | DAKO | AB_812325 |
| Bacterial and virus strains | ||
| Biological samples | ||
| Patient tumor tissue from MSKCC Cohort | MSK | - |
| Patient tumor tissue from Study 06 Cohort | Astra Zeneca | - |
| CT26 RNA samples for RNAseq | Azenta/Genewiz | - |
| CT26 DNA samples for ATACseq | Azenta/Genewiz | - |
| MC38 RNA samples for qPCR | Shattuck Labs | - |
| KP RNA samples for RNAseq | University of Pennsylvania | - |
| LLC1 RNA samples for RNAseq | University of Pennsylvania | - |
| Chemicals, peptides, and recombinant proteins | ||
| Interferon Gamma | R&D Systems | 485-MI-100 |
| Collagenase | StemCell Technologies | 07902 |
| Venor GeM Mycoplasma Detection Kit | Sigma | MP0025 |
| Critical commercial assays | ||
| First Strand cDNA Synthesis Kit | Origene | NP100042 |
| RNeasy Kit | Qiagen | 75144 |
| QIAshredder | Qiagen | 79656 |
| RNase-Free DNase Set | Qiagen | 79254 |
| SsoAdvanced Universal SYBR Green Supermix | Bio-Rad | 1725270 |
| NextSeq 500/550 v2.5 | Illumina | 20024906 |
| TruSeq® Stranded Total RNA Library Prep Human/Mouse/Rat (96 Samples) | Illumina | 20020597 |
| Deposited data | ||
| Raw Exome data from human clinical samples of MSK Study | This paper | dbGaP Study Accession: phs002834.v1.p1 |
| Raw microarray data from human clinical samples of MSK Study | This paper | GEO Accession Number: GSE248249 |
| Raw RNASeq Data from CT26 Mouse Model | This paper | GEO Accession Number: GSE249000 |
| Raw ATACSeq Data from CT26 Mouse Model | This paper | GEO Accession Number: GSE249001 |
| Raw RNASeq Data from LLC1 Mouse Model | This paper | GEO Accession Number: GSE248249 |
| Raw RNASeq Data from KP Mouse Model | This paper | GEO Accession Number: GSE248249 |
| Experimental models: Cell lines | ||
| Mouse CT26 Cell Line | ATCC | ATCC Cat# CRL-2638, RRID: CVCL_7256 |
| Mouse MC38 Cell Lines | License through NCI | RRID: CVCL_B288 |
| Mouse LLC1 Cell Line | ATCC | CRL-1642 |
| Mouse KP Cell Line | N/A | |
| Experimental models: Organisms/strains | ||
| BALB/cJ mice | The Jackson Laboratory | RRID:IMSR_JAX:00 0651 |
| C57BL/6J mice | The Jackson Laboratory | RRID:IMSR_JAX:00 0664 |
| Oligonucleotides | ||
| Rps18 Mouse qPCR Primer Pair | Origene | MP212910 |
| Stat1 Mouse qPCR Primer Pair | Origene | MP215434 |
| Stat2 Mouse qPCR Primer Pair | Origene | MP215435 |
| Tap1 Mouse qPCR Primer Pair | Origene | MP217519 |
| Ifitm2 Mouse qPCR Primer Pair | Origene | MP206690 |
| Ifitm3 Mouse qPCR Primer Pair | Origene | MP206691 |
| Recombinant DNA | ||
| Software and algorithms | ||
| ImageJ | https://imagej.nih.gov/ij/ | |
| Illustrator | https://www.adobe.com | |
| Python2.7 | https://www.python.org/download/releases/2.7/ | |
| R 3.6.1 | https://www.r-project.org | |
| Bioconductor | R | https://www.bioconductor.org/ |
| Deseq2 | Bioconductor | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Trimmomatic v.0.36/v.0.38 | Usadel Lab | http://www.usadellab.org/cms/?page=trimmomatic |
| Affymetrix Expression Console Software | Affymetrix | https://www.thermofisher.com/uk/en/home/technical-resources/technical-reference-library/microarray-analysis-support-center.html |
| ComBat | Bioconductor | https://rdrr.io/bioc/sva/man/ComBat.html |
| limma | Bioconductor | https://bioconductor.org/packages/release/bioc/html/limma.html |
| GSVA package | Bioconductor | https://bioconductor.org/packages/release/bioc/html/GSVA.html |
| PhenoPath | Bioconductor | https://www.bioconductor.org/packages/release/bioc/html/phenopath.html |
| bwa aligner v0.7.17 | Sanger Institute | https://github.com/lh3/bwa |
| MATH | Bioconductor | https://rdrr.io/bioc/maftools/man/math.score.html |
| Oncotator v1 | Broad Institute | https://github.com/broadinstitute/oncotator |
| Sigfit | University of Cambridge | https://github.com/kgori/sigfit |
| dNdScv | Sanger Institute | https://www.sanger.ac.uk/tool/dndscv/ |
| PhyloWGS | Morris Lab | https://github.com/morrislab/phylowgs |
| NetMHC 3.4 | Immune Epitope Database and Analysis Resource | http://tools.iedb.org/mhci/download/ |
| GSEA R package version 1.2 | Broad Institute | https://rdrr.io/github/GSEA-MSigDB/GSEA_R/ |
| FlowSOM | FlowJo, LLC | https://bioconductor.org/packages/release/bioc/html/FlowSOM.html |
| MACS2 2.1.2 | Python bioconda | https://pypi.org/project/MACS2/ |
| Homer v4.11.1 | University of California, San Diego | http://homer.ucsd.edu/homer/ |
| STAR aligner v2.4.0k/v.2.5.2b | Cold Spring Harbor Laboratory, | https://code.google.com/archive/p/rna-star/ |
| Bio.pairwise2 package | Biopython | https://biopython.org/docs/1.75/api/Bio.pairwise2.html |
| CIBERSORT | Stanford University | https://cibersortx.stanford.edu |
| GATK v.4.0.2.1 | Broad Institute | https://github.com/broadinstitute/gatk |
| Pyclone-VI | University of British Columbia | https://github.com/Roth-Lab/pyclone-vi |
| snpEff.v4.3t | Wayne State University | https://pcingola.github.io/SnpEff/ |
| OMIQ | Dotmatics | https://www.dotmatics.com/solutions/omiq |
| Other | ||
| BioRad CFX Opus 96 and CFX touch 96 | Bio-Rad | - |