KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| CD45 (Clone 30-F11) | Fluidigm | Cat#3089005B; RRID: AB_2651152 |
| Ki67 (Clone SolA15) | Invitrogen | Cat#14-5698-82; RRID: AB_10854564 |
| CD90.2/Thy-1.2 (Clone 30-H12) | Biolegend | Cat#105333; RRID: AB_2563765 |
| Ly-6G (Clone 1A8) | Biolegend | Cat#127602; RRID: AB_1089180 |
| CD69 (Clone H1.2F3) | Invitrogen | Cat#14-0691-82; RRID: AB_467325 |
| CD4 (Clone RM4-5) | Biolegend | Cat#116018; RRID: AB_2650936 |
| F4/80 (Clone BM8) | Biolegend | Cat#123102; RRID: AB_893506 |
| Eomes (Clone Dan11mag) | Invitrogen | Cat#14-4875-82, RRID:AB_11042577 |
| CD11b (Mac-1) (Clone m1/70) | Fluidigm | Cat#3148003B; RRID: AB_2814738 |
| CD62L (L-selectin) (Clone MEL-14) | Biolegend | Cat#104416; RRID: AB_313101 |
| Ly-6C (Clone HK1.4) | Biolegend | Cat#128002; RRID: AB_1134214 |
| CD25 (IL-2R) (Clone 3C7) | Biolegend | Cat#101913; RRID: AB_2562798 |
| CD3e (Clone 145-2C11) | Biolegend | Cat#100314; RRID: AB_312679 |
| TER119 (Clone TER119) | Biolegend | Cat#116214; RRID: AB_313715 |
| CD152 (CTLA-4) (Clone UC10-4B9) | Biolegend | Cat#106308; RRID: AB_2087654 |
| CD14 (Clone Sa14-2) | Biolegend | Cat#123302; RRID: AB_940592 |
| FoxP3 (Clone FJK-16s) | Invitrogen | Cat#14-5773-82; RRID: AB_467576 |
| CD279 (PD-1) (Clone 29F.1A12) | Biolegend | Cat#135202; RRID: AB_1877121 |
| iNOS (Clone CXNFT) | Fluidigm | Cat#3161011B |
| CD366 (Tim-3) (Clone RMT3-23) | Fluidigm | Cat#3162029; RRID: AB_2687841 |
| CD197 (CCR7) (Clone 4B12) | eBiosciences | Cat#16-1971-85; RRID: AB_494123 |
| CD182 (Clone SA044G4) | Biolegend | Cat#149302; RRID: AB_2565277 |
| CD19 (Clone 6D5) | Biolegend | Cat#115514; RRID: AB_313649 |
| CD335 (NKp46) (Clone 29A1.4) | Fluidigm | Cat#3167008B |
| CD8a (Clone 53-6.7) | Biolegend | Cat#100716; RRID: AB_312755 |
| T-bet (Clone 4B10) | Biolegend | Cat#644802; RRID: AB_1595503 |
| CD192 (Clone 475301R) | R&D | Cat#MAB55381R |
| Granzyme B (Clone GB11) | Fluidigm | Cat#3171002B; RRID: AB_2687652 |
| CD44 (Clone 1M7) | Biolegend | Cat#103014; RRID: AB_312965 |
| I-A/I-E (Clone M5/114.15.2) | Biolegend | Cat#107610; RRID: AB_313325 |
| CD278 (ICOS) (Clone 7E.17G9) | Invitrogen | Cat#14-9942-85; RRID: AB_468633 |
| CD11c (Clone N418) | Fluidigm | Cat#3209005B; RRID: AB_2811244 |
| CD16/CD32 (Clone 93, for blocking buffer) | eBioscience | Cat#14-0161-86; RRID: AB_467135 |
| CD8a (Clone 53-6.7) | Biolegend | Cat#100737; RRID: AB_10897101 |
| CD45 (Clone 30-F11) | Biolegend | Cat#103138; RRID: AB_2563061 |
| PerCP-anti-TER119 | Biolegend | Cat#116225; RRID: AB_893637 |
| inVivoMAb anti-mouse PD-L1 (B7-H1) | BioXcell | Cat#BE0101; RRID: AB_10949073 |
| inVivoMAb anti-mouse CD8α (Clone YTS169.4, in vivo antibody) | BioXcell | Cat#BE0117; RRID: AB_10950145 |
| Anti-Mouse CD279 (PD-1) (Clone RMP1-14) - Purified In vivo GOLD™ Functional Grade | Leinco Technologies, Inc. | Cat#P362; RRID: AB_2737557 |
| InVivoPlus anti-mouse CTLA-4 (CD152, Clone 9H10) | BioXcell | Cat#BE0131; RRID: AB_10950184 |
| phospho-p44/42 MAPK (Erk1/2) (Thr202/Tyr204) | Cell Signaling | Cat#4370; RRID: AB_2315112 |
| Goat Anti-Rabbit IgG (H+L) Highly Cross-adsorbed Antibody, Alexa Fluor555 | Life Technologies | Cat#A-21429; RRID: AB_2535850 |
| Bacterial and virus strains | ||
| NEB® Stable Competent E. coli | New England BioLabs | Cat#C3040I |
| Third generation lentivirus | Dr. Lo | N/A |
| Biological samples | ||
| Chemicals, peptides, and recombinant proteins | ||
| Trametinib | LC Laboratories | Cat#T-8123 |
| RP-832c | Riptide Bioscience | PMID: 32051227 |
| Vemurafenib | LC Laboratories | Cat#V-2800 |
| Cell-ID Cisplatin | Fluidigm | Cat#201064 |
| Cell-ID Intercalator Ir | Fluidigm | Cat#201192B |
| 7-AAD | BD Pharmigen | Cat#51-68981E |
| Blasticidin | Sigma-Aldrich | Cat#SBR00022 |
| Prolong Diamond Antifade Mountant with DAPI | ThermoFisher Scientific | Cat#P36962 |
| Critical commercial assays | ||
| 20-Plex Pd Barcoding Kit | Fluidigm | Cat#201060 |
| mirVana™ miRNA Isolation Kit, with phenol | Thermo Fisher Scientific | Cat#AM1560 |
| AllPrep DNA/RNA Mini Kit | Qiagen | Cat#80204 |
| MycoAlert™ Mycoplasma Detection Kit | Lonza | Cat#LT07-418 |
| MycoAlert™ Assay Control Set | Lonza | Cat#LT07-518 |
| Tumor Dissociation Kit | Miltenyi Biotec | Cat#130-095-929 |
| Single Cell 5′ Library and Gel Bead Kit v1.1 | 10X Genomics | Cat#1000167 |
| Enrichment Kit for Mouse T Cells | 10X Genomics | Cat#1000071 |
| QIAGEN QIAseq Immune Repertoire RNA Library Kit - T cell Receptor Panel | Qiagen | Cat#333705 |
| QIAseq Library Quant Array Kit | Qiagen | Cat#333304 |
| Foxp3 Transcription Factor Staining Buffer Set | eBioscience | Cat#00-5523-00 |
| Deposited data | ||
| scRNA-sequencing data of melanoma mouse model | This Paper | GSE177902 |
| scTCR-sequencing data of melanoma mouse model | This Paper | GSE177902 |
| Bulk TCR-sequencing data of melanoma mouse model | This Paper | GSE177902 |
| Mass cytometry data of mouse immune cells (BrafV600E melanoma model) | This Paper | FR-FCM-Z43Z |
| Mass cytometry data of mouse immune cells (Nf1−/− melanoma) | This Paper | FR-FCM-Z4YR |
| Mass cytometry data of mouse immune cells (KrasG12C colorectal carcinoma) | This Paper | FR-FCM-Z42V |
| Experimental models: Cell lines | ||
| Mouse cell line; NIL | Dr. Norman E. Sharpless and adapted by Dr. Roger S. Lo | PMID: 25252692 |
| Mouse cell line; NILER1-4 | Dr. Roger S. Lo | PMID: 33318037 |
| Mouse cell line; mSKMel-254 | Dr. David B. Solit and adapted by Dr. Roger S. Lo | This paper |
| Mouse cell line; YUMM1.7ER | Dr. Marcus W. Bosenberg | PMID: 27287723 |
| Mouse cell line; CT26 | ATCC | PMID: 33318037 |
| Mouse cell line; KPC (KP4662) | Dr. Robert Vonderheide | PMID: 27642636 |
| Mouse cell line; YUMM1.7ER-luciferase | Dr. Roger S. Lo | This paper |
| Experimental models: Organisms/strains | ||
| C57BL/6J; C57BL/6N mice | UCLA: Radiation-Oncology breeding colony | C57BL/6J/NROC |
| BALB/C mice | UCLA: Radiation-Oncology breeding colony | BALB/c ROC |
| C57BL/6J mice | Jackson Laboratory | Cat# 000664 |
| Oligonucleotides | ||
| Recombinant DNA | ||
| pLV-EF1a-IRES-Blast | Addgene | Cat#85133; RRID: Addgene_85133 |
| Software and algorithms | ||
| Cytofkit | Bioconductor | Version: 3.7 |
| R software | CRAN | Version: 3.5.1 |
| GraphPad Prism | https://swcstore.oit.ucla.edu/secure/browse_vendors.php | Version: 7 |
| Cytobank | https://www.cytobank.org/ | |
| Cell Ranger | 10x Genomics | Version: 2.1.0 |
| Seurat | CRAN | Version: 3.0.2 |
| STARTRAC | GitHub | Version: 0.1.0 |
| tcR | CRAN | Version: 2.2.4.1 |
| Living Image | PerkinElmer | Version: 4.7.2 Version |
| Other | ||