| Reagent or Resource | Source | Identifier |
| Antibodies | ||
| Purified CD16/CD32 (2.4G2) | BD Biosciences | Cat#: 553141; RRID: AB_394656 |
| 4-1BB – APC (17B5) | Biolegend | Cat#: 106110; RRID: AB_2564297 |
| Arg-1 – PE/Cy7 (A1exF5) | Invitrogen | Cat#: 25-3697-82; RRID: AB_2734841 |
| CCR2 – BV785 (SA203G11) | Biolegend | Cat#: 150621; RRID: AB_2721565 |
| CD3e – FITC (145–2 C11) CD3e – PE/Cy5 (145–2 C11) CD3e – BV510 (145–2 C11) | Invitrogen Biolegend BD Biosciences | Cat#: 11-0031-85; RRID: AB_464883 Cat#: 100310; RRID: AB_312675 Cat#: 563024; RRID: AB_2737959 |
| CD4 – BUV496 (RM4-5) | BD Biosciences | Cat#: 741050; RRID: AB_2870665 |
| CD8a – BUV395 (53–6.7) | BD Biosciences | Cat#: 565968; RRID: AB_2739421 |
| CD11b – BUV563 (M1/70) CD11b – APC/Fire750 (M1/70) | BD Biosciences Biolegend | Cat#: 741242; RRID: AB_2870793 Cat#: 101262; RRID: AB_2572122 |
| CD11c – BV605 (HL3) CD11c – APC/Fire750 (N418) | BD Biosciences Biolegend | Cat#: 563057; RRID: AB_2737978 Cat#: 117352; RRID: AB_2572124 |
| CD19 – SparkBlue550 (6D5) CD19 – BV510 (1D3) | Biolegend BD Biosciences | Cat#: 115566; RRID: AB_2832389 Cat#: 562956; RRID: AB_2737915 |
| CD24 – BV650 (M1/69) | BD Biosciences | Cat#: 563 545 RRID: AB_2738271 |
| CD25 – BV421 (PC61) | Biolegend | Cat#: 102043; RRID: AB_2562611 |
| CD27 – BUV785 (LG.3A10) | Biolegend | Cat#: 124241; RRID: AB_2800595 |
| CD28 – PE/Cy7 (37.51) | Biolegend | Cat#: 102126; RRID: AB_2617011 |
| CD39 – PE (Duha59) | Biolegend | Cat#: 143804; RRID: AB_11218603 |
| CD44 – BV510 (IM7) CD44 – BV785 (IM7) | Biolegend Biolegend | Cat#: 563114; RRID: AB_2738011 Cat#: 103 059 RRID: AB_2571953 |
| CD45 – AlexaFluor700 (30-F11) | Biolegend | Cat#: 103128; RRID: AB_493715 |
| CD45.1 – AlexaFluor700 (A20) | Biolegend | Cat#: 110724; RRID: AB_493733 |
| CD45.2 – FITC (104) | Biolegend | Cat#: 109 806 RRID: AB_313443 |
| CD47 – APC/Cy7 (miap301) | Biolegend | Cat#: 127 526 RRID: AB_2632862 |
| CD49a – BUV737 (Ha31/8) | BD Biosciences | Cat#: 741776; RRID: AB_2871130 |
| CD54 – FITC (YN1/1.7.4) | ThermoFisher | Cat#: 11-0541-82 RRID: AB_465094 |
| CD62L – BUV805 (MEL-14) | BD Biosciences | Cat#: 741924; RRID: AB_2871237 |
| CD69 – BUV737 (H1.2F3) | BD Biosciences | Cat#: 612793; RRID: AB_2870120 |
| CD86 – BUV496 (PO3) | BD Biosciences | Cat#: 750437; RRID: AB_2874600 |
| CD106 – PE (429) | Biolegend | Cat#: 105 714 RRID: AB_1134164 |
| CD115 – PE/Dazzle594 (AFS98) | Biolegend | Cat#: 135528; RRID: AB_2566523 |
| CD122 – PE/Cy5 (TM-β1) | Biolegend | Cat#: 123220; RRID: AB_2715962 |
| CD163 – BV421 (S15049I) CD163 – APC (S15049I) | Biolegend Biolegend | Cat#: 155309; RRID: AB_2814063 Cat#: 155 306 RRID: AB_2814060 |
| CTLA-4 – BV421 (UC10-4B9) | Biolegend | Cat#: 106312; RRID: AB_2563063 |
| Egr2 – APC (Erongr2) | Invitrogen | Cat#: 17-6691-82; RRID: AB_11151502 |
| Eomes – PE/eFluor610 (Dan11mag) | Invitrogen | Cat#: 61-4875-82; RRID: AB_2574614 |
| F4/80 – PE/Cy5 (BM8) F4/80 – PE (Qa17A29) | Biolegend Biolegend | Cat#: 123112; RRID: AB_893482 Cat#: 157 304 RRID: AB_2832547 |
| FoxP3 – PacificBlue (MF-14) | Biolegend | Cat#: 126410; RRID: AB_2105047 |
| Gata-3 – AlexaFluor488 (TWAJ) | Invitrogen | Cat#: 53-9966-42; RRID: AB_2574493 |
| Granzyme B – PerCP-Cy5.5 (QA16A02) | Biolegend | Cat#: 372212; RRID: AB_2728379 |
| IFNγ – PE/Cy7 (XMG1.2) | BD Biosciences | Cat#: 557649; RRID: AB_396766 |
| IL-2 – PE (JES6-5H4) | Biolegend | Cat#: 503808; RRID: AB_315302 |
| iNOS – AlexaFluor488 (CXNFT) | Biolegend | Cat#: 53-5920-82; RRID: AB_2574423 |
| Ki-67 – BV605 (16A8) | Biolegend | Cat#: 652413; RRID: AB_2562664 |
| KLRG1 – PerCP/Cy5.5 (2F1/KLRG1) | Biolegend | Cat#: 563595; RRID: AB_2738301 |
| Ly6C – PerCP/Cy5.5 (HK1.4) | Biolegend | Cat#: 128012; RRID: AB_1659241 |
| Ly6G – SparkBlue550 (1A8) Ly6G – APC/Fire750 (1A8) | Biolegend Biolegend | Cat#: 127664; RRID: AB_2860671 Cat#: 127652; RRID: AB_2616733 |
| I-A/I-E – PacificBlue (M5/114.15.2) | Biolegend | Cat#: 107620; RRID: AB_493527 |
| NK1.1 – BV650 (PK136) NK1.1 – BV510 (PK136) | BD Biosciences Biolegend | Cat#: 564143; RRID: AB_2738617 Cat#: 108738; RRID: AB_2562217 |
| NKG2A – PE/Cy7 (16A11) | Biolegend | Cat#: 142810; RRID: AB_2728161 |
| OX-40 (CD134) – BV711 (OX-86) | Biolegend | Cat#: 119421; RRID: AB_2687176 |
| PD-1 – BV605 (29F.1A12) | Biolegend | Cat#: 135220; RRID: AB_2562616 |
| PD-L1 – BUV737 (MIH5) | BD Biosciences | Cat#: 741877; RRID: AB_2871203 |
| Qa1b – Biotin (6A8.6F10.1A6) | BD Biosciences | Cat#: 559 829 RRID: AB_397345 |
| RORγT – PE (AFKJS-9) | Invitrogen | Cat#: 12-6988-82; RRID: AB_1834470 |
| Siglec-F – BV711 (E50-2440) | BD Biosciences | Cat#: 740764; RRID: AB_2740427 |
| Siglec-G – BUV615 (SH1) | BD Biosciences | Cat#: 751581; RRID: AB_2875576 |
| Siglec-H – BV650 (440 c) | BD Biosciences | Cat#: 747672; RRID: AB_2744233 |
| SIRPα – APC/Cy7 (P84) | Biolegend | Cat#: 144018; RRID: AB_2629558 |
| T-bet – BV711 (4B10) | Biolegend | Cat#: 644820; RRID: AB_2715766 |
| TCF1/7 – AlexaFluor647 (812145) | R&D Systems | Cat#: FAB8224R; RRID: AB_2888931 |
| TIGIT – PE/Dazzle594 (1G9) | Biolegend | Cat#: 142110; RRID: AB_2566573 |
| Tim-3 – BV785 (RMT3-23) | Biolegend | Cat#: 119725; RRID: AB_2716066 |
| TNF-α – APC/Cy7 (MP6-XT22) | Biolegend | Cat#: 506344; RRID: AB_2565953 |
| XCR1 – PE (ZET) | Biolegend | Cat#: 148204; RRID: AB_2563843 |
| HPV16 E749-57 – APC (RAHYNIVTF) | Peptide synthesis facility of department IHB, LUMC | N/A |
| Rat anti-mouse F4/80 (CI:A3-1) | Sanbio | Cat#: MCA497; RRID: AB_2098196 |
| Rat anti-mouse CD8 (4SM15) | eBioscience | Cat#: 14-0808-82 RRID: AB_2572861 |
| Rabbit anti-rat IgG | Abcam | Cat#: ab6733; RRID: AB_954909 |
| Rabbit anti-mouse CD163 (M-96) | Santacruz | Cat#: sc-33560; RRID: AB_2074556 |
| Goat anti-rabbit IgG | Agilent | Cat#: E0432; RRID: AB_2313609 |
| Goat anti-mouse CD31 (M-20) | Santacruz | Cat#: sc-1506 RRID: AB_2161037 |
| Rabbit anti-Heme Oxygenase 1 (EPR18161-128) | Abcam | Cat#: ab237267 RRID: AB_764541 |
| Rabbit anti-goat IgG | Agilent | Cat#: P0449 RRID: AB_2617143 |
| APC Goat Anti-Rat Ig | BD Biosciences | Cat#: 551 019 RRID: AB_398484 |
| Steptavidin – APC | eBioscience | Cat#: 17-4317-82 |
| Mouse T-Activator CD3/CD28 Dynabeads | ThermoFisher | Cat#: 11–452-D |
| Chemicals, peptides, and recombinant proteins | ||
| Lipofectamine 2000 Transfection Reagent | Invitrogen | Cat#: 11 668 027 |
| Recombinant IFN-γ | Biolegend | Cat#: 575 308 |
| Recombinant IL-2 | Peprotech | Cat#: 212–12 |
| Zombie UV fixable viability kit | Biolegend | Cat#: 423 108 |
| LIVE/DEAD Fixable Aqua Dead Cell Stain Kit | ThermoFisher | Cat#: L34957 |
| Liberase TL Research grade | Roche | Cat#: 05401020001 |
| FoxP3/Transcription Factor Staining Buffer Set | Invitrogen | Cat#: 00-5523-00 |
| HPV16 E743-63 peptide (GQAEPDRAHYNIVTFCCKCDS) | Peptide synthesis facility of department IHB, LUMC | N/A |
| RMA Env-encoded CD4 T cell epitope (EPLTSLTPRCNTAWNRLKL) | Peptide synthesis facility of department IHB, LUMC | N/A |
| RMA Gag-encoded CD8 T cell epitope (CCLCLTVFL) | Peptide synthesis facility of department IHB, LUMC | N/A |
| CpG (ODN 1826) | Invivogen | Cat#: tlrl-1826 |
| Incomplete Freunds Adjuvant (Difco) | BD Biosciences | Cat#: 263 910 |
| PLX3397 275 mg/kg rodent chow diet Control rodent chow diet | Research Diets Inc. Research Diets Inc. | N/A N/A |
| αCD163-DXR liposomes(15) αCD163-Control liposomes(15) | Department of Biomedicine, University of Aarhus | N/A |
| Tin Protoporphyrin IX dichloride | Santa Cruz Biotechnology | Cat#: sc-203452B |
| Entellan mouting medium for microscopy | Sigma Aldrich | Cat#: 107 960 |
| PAP pen for immunostaining | Merck Millipore | Cat#: Z377821 |
| Microscope slides, SuperFrost Plus | VWR | Cat#: 631–0108 |
| Hirschmann Glass covers | ThermoFisher | Cat#: 10 329 241 |
| Hydrogen peroxide 30% | Merck Millipore | Cat#: 107 209 |
| Methanol>98.5% | VWR Chemicals | Cat#: 20 903.415 |
| Trypsin powder | Merck | Cat#: 85 450C |
| Calcium Chloride | Merck | Cat#: 793 639 |
| Tri-sodium Citrate Dihydrate | Merck | Cat#: 106 448 |
| SuperBlock (PBS) Blocking Buffer | ThermoFisher | Cat#: 37 515 |
| Bovine Serum Albumin (BSA) | Sigma Aldrich | Cat#: A3912 |
| Tween 20 | Merck | Cat#: 8221840500 |
| VECTASTAIN Elite ABC-HRP Kit | Vectorlabs | Cat#: PK-6100; RRID: AB_2336819 |
| Mayer’s haematoxylin staining | Merck | Cat#: 1092490500 |
| DAB+ Substrate Chromogen System (Dako Omnis) | Agilent | Cat#: GV825 |
| Masson’s Trichrome Stain Kit | Polysciences | Cat#: 25 088 |
| Machery-Nagel NucleoSpin RNA, Mini Kit For RNA Purification | Bioké | Cat#: 740 955.50 |
| NEBNext Single Cell/Low Input RNA Library Prep Kit for Illumina | New England Biolabs Inc. | Cat#: E6420S |
| Agilent DNF-474 HS NGS Fragment Kit | Agilent | Cat#: DNF-474–0500 |
| Deposited data | ||
| Bulk RNAseq | Available on acceptation | N/A |
| Experimental models: Cell lines | ||
| TC-1 | Provided by Prof. T.C. Wu (John Hopkins University, Baltimore, U.S.A.) | RRID: CVCL_4699 |
| RMA | Provided by Prof. K. Kärre (Karolinska Institute, Stockholm, Sweden) | RRID: CVCL_J385 |
| KPC3 | (76) | RRID: CVCL_A9ZK |
| Experimental models: Organisms/strains | ||
| Mouse C57BL/6J | Charles River Laboratories France | N/A |
| Mouse TCR transgenic gp10025-33/H-2Db bred to express congenic marker CD45.1 (Ly5.1) | Provided by Dr. N.P. Restifo (NIH, Bethesda, USA) | N/A |
| Software and algorithms | ||
| FlowJo V.10 | Treestar | RRID: SCR_008520; https://www.flowjo.com/solutions/flowjo |
| OMIQ | Omiq Inc. | https://www.omiq.ai/ |
| GraphPad Prism V.9 | GraphPad | RRID: SCR_002798; http://www.graphpad.com/ |
| ImageJ | ImageJ | RRID: SCR_003070; https://imagej.net/ |
| R V.4.1.0 | R | RRID: SCR_001905; http://www.r-project.org/ |
| R studio V.1.4.1717 | R Studio | https://www.rstudio.com/ |
| REViGO tool | REViGO | RRID: SCR_005825; http://revigo.irb.hr/ |
| Cytoscape V.3.8.2 | Cytoscape | RRID: SCR_003032; http://cytoscape.org/ |
| BioRender | BioRender | RRID: SCR_018361; http://biorender.com/ |
| Cellxgene MoMac_VERSE v2021 | cellxgene | RRID: SCR_021059; https://macroverse.gustaveroussy.fr/2021_MoMac_VERSE/ |