Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER | |||
|---|---|---|---|---|---|
| Antibodies | |||||
| CD103 APC-eFluor780 | eBioscience | Cat#47–1031-82 | |||
| CD103 BV421 | BD Bioscience | Cat#562771 | |||
| CD115 BV605 | BD Bioscience | Cat#743640 | |||
| CD11b PE-Cy7 | BD Bioscience | Cat#561098 | |||
| CD11c PE-Cy5 | BioLegend | Cat#117316 | |||
| CD11c R718 | BD Bioscience | Cat#567076 | |||
| CD127 BV711 | BD Bioscience | Cat#565490 | |||
| CD135 (Flt3) BV421 | BD Bioscience | Cat#562898 | |||
| CD14 APC-Fire750 | BioLegend | Cat#123331 | |||
| CD150 BV786 | BD Bioscience | Cat#567518 | |||
| CD152 (CTLA-4) PE-CF594 | BD Bioscience | Cat#564332 | |||
| CD16/32 - APC | BD Bioscience | Cat#558636 | |||
| CD172a BV711 | BD Bioscience | Cat#740766 | |||
| CD201 (EPCR) APC-eFluor780 | eBioscience | Cat#46–2012-82 | |||
| CD206 PE | BD Bioscience | Cat#568273 | |||
| CD27 BV510 | BD Bioscience | Cat#563605 | |||
| CD279 (PD-1) BV786 | BD Bioscience | Cat#744548 | |||
| CD3 BUV615 | BD Bioscience | Cat#751418 | |||
| CD317/BST-2 BV615 | BD Bioscience | Cat#751038 | |||
| CD34 PE | BioLegend | Cat#152204 | |||
| CD4 BV510 | BD Bioscience | Cat#563106 | |||
| CD44 BUV496 | BD Bioscience | Cat#741057 | |||
| CD45.1 BUV737 | BD Bioscience | Cat#612811 | |||
| CD45.2 BUV395 | BD Bioscience | Cat#564616 | |||
| CD48 - PerCP-Cy5.5 | BioLegend | Cat#103422 | |||
| CD62L - PerCP-Cy5.5 | BD Bioscience | Cat#560513 | |||
| CD69 BV605 | BD Bioscience | Cat#563290 | |||
| CD8 APC | BD Bioscience | Cat#553035 | |||
| CD80 BV650 | BD Bioscience | Cat#563687 | |||
| CD86 BB700 | BD Bioscience | Cat#742145 | |||
| F4/80 BV510 | BD Bioscience | Cat#743280 | |||
| FoxP3 PE-Cy7 | Tonbo | Cat#60–5773-U025 | |||
| GranzymeB eFluor450 | eBioscience | Cat#48–8898-82 | |||
| IFNg FITC | BD Bioscience | Cat#554411 | |||
| Ki67 R718 | BD Bioscience | Cat#566963 | |||
| CD117 (c-KIT) PE-Cy7 | BioLegend | Cat#105814 | |||
| Biotin Mouse Lineage Panel (CD3, NK1.1, B220, Ter-119) | BD Bioscience | Cat#559971 | |||
| BV 510 anti-human Lineage Cocktail (CD3, CD14, CD16, CD19, CD20, CD56) | BioLegend | Cat#348807 | |||
| Ly-6C BV785 | BioLegend | Cat#128041 | |||
| Ly-6G PE-CF594 | BD Bioscience | Cat#562700 | |||
| MHCII (I-A/I-E) BUV615 | BD Bioscience | Cat#751570 | |||
| Perforin PE | BioLegend | Cat#154306 | |||
| SCA1 PE-eFluor610 | eBioscience | Cat#61–5981-82 | |||
| Streptavidin FITC | BD Bioscience | Cat#554060 | |||
| TNFa BV711 | BD Bioscience | Cat#563944 | |||
| XCR1 APC | BioLegend | Cat#148206 | |||
| CD45 BUV395 | BD Bioscience | Cat#563792 | |||
| CD45 BUV661 | BD Bioscience | Cat#612975 | |||
| CD90.2 FITC | Biolegend | Cat#140304 | |||
| NK1.1 FITC | Invitrogen | Cat#11–5941-85 | |||
| CD19 FITC | Invitrogen | Cat#11–0193-82 | |||
| TCRgd FITC | Invitrogen | Cat#11–5711-82 | |||
| CD11b APC-Cy-7 | BD Bioscience | Cat#557657 | |||
| Ly6G Percp Cy5.5 | Biolegend | Cat#127616 | |||
| Ly6c BUV605 | BD Bioscience | Cat#563011 | |||
| MHCII BUV737 | BD Bioscience | Cat#748845 | |||
| Siglec F FITC | Biolegend | Cat#155504 | |||
| CD90.2 BV786 | BD Bioscience | Cat#564365 | |||
| CD11c APCR700 | BD Bioscience | Cat#565872 | |||
| CD34 FITC | Miltenyi | Cat#130–113-178 | |||
| CD49f Pacific Blue | Biolegend | Cat#313620 | |||
| CD90 PE | Biolegend | Cat#328110 | |||
| CD38 PE-Cy7 | Biolegend | Cat#303516 | |||
| CD45RA APC | Biolegend | Cat#304128 | |||
| Anti-mouse TNF | BioXcell | Cat#BE0058 | |||
| Anti-mouse Ly6G | BioXcell | Cat#BE00775–1 | |||
| Anti-mouse IFNAR1 | BioXcell | Cat#BE0241 | |||
| Anti-mouse IFNγ | BioXcell | Cat#BR0055 | |||
| Anti-mouse CD4 | BioXcell | Cat#BE0003–1 | |||
| Anti-mouse CD8 | BioXcell | Cat#BE0061 | |||
| Bacterial and virus strains | |||||
| BCG Pasteur | This study | NA | |||
| Biological samples | |||||
| PBMCs from patients with NMIBC at Memorial Sloan Kettering Cancer Center(n=8) | This study | NA | |||
| PBMCs from patients with NMIBC at McGill University (n=13) | This study | NA | |||
| Chemicals, peptides, and recombinant proteins | |||||
| G418 | Thermo Fisher | Cat#10–131-035 | |||
| RPMI with 10% FBS and 2mM L-glutamine | Sloan Kettering Institute media preparation facility | NA | |||
| 0.05 Tripsin, 0.02 EDTA in HBSS | Sloan Kettering Institute media preparation facility | NA | |||
| F12 media | Sigma Aldrich | Cat#11–765-062 | |||
| IMDM media | Thermo Fisher | Cat#31980030 | |||
| MethoCult media | StemCell Technologies | Cat#M3434 | |||
| Middlebrook 7H9 broth | Thermo Fisher | Cat#DF0713–17-9 | |||
| Bovine Serum Albumin | Sigma | Cat#3116964001 | |||
| Dextrose | Thermo Fisher | Cat#BP350–1 | |||
| Sodium Chloride | Thermo Fisher | Cat#BP358–10 | |||
| Glycerol | Thermo Fisher | Cat#AAA16205AP | |||
| Tween 80 | Sigma | Cat#P8074 | |||
| Phosphate buffered saline (PBS) | Sloan Kettering Institute media preparation facility | NA | |||
| 7H10 agar | Thermo Fisher | Cat#DF0627174 | |||
| Poly-L-lysine | Sigma | Cat#P4707 | |||
| Cell stimulation cocktail | Thermo Fisher | Cat#00–4975-03 | |||
| Foxp3 fixation/permeabilization buffer | Thermo Fisher | Cat#50–112-8857 | |||
| Fixable blue dead stain kit | Thermo Fisher | Cat#L34962 | |||
| eFluor 506 fixable viability dye | Thermo Fisher | Cat#65–0866-14 | |||
| DAPI | Thermo Fisher | Cat#D1306 | |||
| BUV395-Annexin V | Thermo Fisher | Cat#564871 | |||
| Annexin V binding buffer | Abcam | Cat#ab14084 | |||
| YOYO-1 Dimeric Cyanine Nucleic Acid Stain | Thermo Fisher | Cat#Y3601 | |||
| Insulin-Transferrin-Selenium-Ethanolamine | Thermo Fisher | Cat#51500056 | |||
| Penicillin/streptomycin/glutamine | Thermo Fisher | Cat#10378016 | |||
| HEPES | Thermo Fisher | Cat#15630080 | |||
| MACS buffer | Miltenyi | Cat#130–091-376 | |||
| Mouse recombinant TPO | Thermo Fisher | Cat#315–14 | |||
| Mouse recombinant SCF | Thermo Fisher | Cat#250–03 | |||
| 87% hydrolyzed polyvinyl alcohol | Sigma | Cat#363081 | |||
| Fibronectin Coated 96 well plates | Corning | Cat#354409 | |||
| IL-3 | Thermo Fisher | Cat#213–13 | |||
| CSF-1 | Thermo Fisher | Cat#315–02 | |||
| Beta-mercapto-ethanol | Thermo Fisher | Cat#31350010 | |||
| Lipofectamine 2000 | Thermo Fisher | Cat#11668027 | |||
| Mouse recombinant IFNγ | Thermo Fisher | Cat#315–05 | |||
| Mouse recombinant TNF | Thermo Fisher | Cat#315–01A | |||
| 7-AAD | Thermo Fisher | Cat#A1310 | |||
| Diphtheria toxin | Sigma | Cat#D0564 | |||
| Triton X-100 | Sigma | Cat#T8787 | |||
| Critical commercial assays | |||||
| MycoAlert Plus | Lonza | Cat#LT07–710 | |||
| Mouse T cell isolation kit | Miltenyi | Cat#130–095-130 | |||
| CD34 MicroBead Kit, human | Miltenyi | Cat#130–046-702 | |||
| MACS columns | Miltenyi | Cat#130–042-201 | |||
| Mouse 48-plex ProcartaPlex kit | Thermo Fisher | Cat#EPX480–20834-901 | |||
| RNeasy Mini Kit | Qiagen | Cat#74104 | |||
| RNase-Free DNase Set | Qiagen | Cat#79254 | |||
| Deposited data | |||||
| Human PBMC single cell Multiomics cohort 1 sequencing code | This study | https://zenodo.org/records/14046727 | |||
| Human PBMC single cell Multiomics cohort 2 sequencing code | This study | https://zenodo.org/records/14046727 | |||
| Mouse bone marrow ATAC-sequencing code | This study | https://zenodo.org/records/14046727 | |||
| Mouse bone marrow single cell RNA sequencing code | This study | https://zenodo.org/records/14046727 | |||
| Mouse tumor CD45+ single cell RNA sequencing code | This study | https://zenodo.org/records/14046727 | |||
| Human PBMC single cell Multiomics cohort 1 sequencing Raw Data | This study | GEO Accession Number: GSE295309 | |||
| Human PBMC single cell Multiomics cohort 2 sequencing Raw Data | This study | GEO Accession Number: GSE295309 | |||
| Mouse bone marrow ATAC-sequencing Raw Data | This study | GEO Accession Number: GSE295309 | |||
| Mouse bone marrow single cell RNA sequencing Raw Data | This study | GEO Accession Number: GSE295309 | |||
| Mouse tumor CD45+ single cell RNA sequencing Raw Data | This study | GEO Accession Number: GSE295309 | |||
| Experimental models: Cell lines | |||||
| MB49-luciferase | Yi Luo, University of Iowa | NA | |||
| B16 | Taha Merghoub | NA | |||
| MB49 TNFR1KO | This study | NA | |||
| MB49-luciferase YFP | This study | NA | |||
| Experimental models: Organisms/strains | |||||
| C57BL/6J | The Jackson Laboratory | Cat#6664 | |||
| B6 CD45.1 | The Jackson Laboratory | Cat#2014 | |||
| OT-I | The Jackson Laboratory | Cat#3831 | |||
| OT-II | The Jackson Laboratory | Cat#4194 | |||
| ZBTB46-DTR | The Jackson Laboratory | Cat#19506 | |||
| Oligonucleotides | |||||
| TNFR1 gRNA CGGGCCTCCACCGGGGATAT | IDT | NA | |||
| pknB_F GGACCAGAGCCAACGATGATG | IDT | NA | |||
| pknB_R AAACTGACTGCCGCCGGATTC | IDT | NA | |||
| Recombinant DNA | |||||
| pSpCas9(BB)-2A-GFP (PX458) | Addgene | Cat#48138 | |||
| Software and algorithms | |||||
| R studio | Posit | RRID:SCR_000432 | |||
| Prism | GraphPad | RRID:SCR_002798 | |||
| Flowjo | BD Bioscience | RRID:SCR_008520 | |||
| FACS DiVa | BD Bioscience | RRID:SCR_001456 | |||
| SpectroFlo | Cytek | RRID:SCR_025494 | |||
| Cell ranger ARC 2.02 | 10x Genomics | RRID:SCR_023897 | |||
| Scanpy 1.9.3 | NumFOCUS | RRID:SCR_018139 | |||
| ArchR 1.01 | Greenleaf Lab | https://www.archrproject.com/ | |||
| PhenoGraph | Pe’er Lab | RRID:SCR_016919 | |||
| EnrichR | Ma’ayan Lab | RRID:SCR_001575 | |||
| DeSeq2 v1.40.2 | Bioconductor | RRID:SCR_015687 | |||
| MAST | Bioconductor | RRID:SCR_016340 | |||
| Seurat | Satija Lab | RRID:SCR_016341 | |||
| Signac | Satija Lab | RRID:SCR_021158 | |||
| ChromVAR | Greenleaf lab | RRID:SCR_026570 | |||
| Cutadapt | OMICtools | RRID:SCR_011841 | |||
| Genrich | John M. Gaspar | https://github.com/jsh58/Genrich | |||
| Homer2 | NITRC | RRID:SCR_009586 | |||
| Bowtie2 | Debian | RRID:SCR_016368 | |||
| Samtools | OMICtools | RRID:SCR_002105 | |||
| Picard | OMICtools | RRID:SCR_006525 | |||
| Other | |||||
| LSRFortessa flow cytometer | BD biosciences | NA | |||
| Aurora full spectrum analyzer | Cytek | NA | |||
| FACSymphony S6 sorter | BD biosciences | NA | |||
| FACSAria cell sorter | BD biosciences | ||||
| NovaSeq 6000 Sequencing System | Illumina | NA | |||
| Polyurethane I.V. Catheter 24G x 3/4” | Santa Cruz | Cat#sc-360126 | |||
| 3mL syringe | StemCell Technologies | Cat#28240 | |||
| 6-well plate | StemCell Technologies | Cat#27370 | |||