| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rat anti-mouse CD16/CD32 (clone 2.4G2) | BD PharMingen | Cat# 553142; RRID: AB_394657 |
| Rat anti-CD11b-BV711 (clone M1/70) | BioLegend | Cat# 101241; RRID: AB_11218791 |
| Rat anti-CD11b-PE-Cy7 (clone M1/70) | eBioscience | Cat# 25-0112-82; RRID: AB_469588 |
| Rat anti-CD45-V500 (clone 30-F11) | BD Biosciences | Cat# 561487; RRID: AB_10697046 |
| Rat anti-CD45-PerCP-Cy5.5 (clone 30-F11) | eBioscience | Cat# 45-0451-82; RRID: AB_1107002 |
| Rat anti-F4/80-APC-Cy7 (clone BM8) | BioLegend | Cat# 123115; RRID: AB_893493 |
| Rat anti-F4/80-AF647 (clone BM8) | BioLegend | Cat# 123121; RRID: AB_893492 |
| Rat anti-Ly6G-BV605 (clone 1A8) | BioLegend | Cat# 127639; RRID: AB_2565880 |
| Rat anti-Ly6C-AF700 (clone HK1.4) | BioLegend | Cat# 128023; RRID: AB_10640119 |
| Rat anti-F4/80-AF488 (clone BM8) | BioLegend | Cat# 123119; RRID: AB_893491 |
| Rat anti-MRC1-AF647 (clone C068C2) | BioLegend | Cat# 141711; RRID: AB_10900240 |
| Hamster anti-CD11c-PE (clone HL3) | BD Biosciences | Cat# 553802; RRID: AB_395061 |
| Rat anti-CD11b-FITC (clone M1/70) | BD Biosciences | Cat# 553310; RRID: AB_394774 |
| Rat anti-MHC II-AF647 (clone M5/114.15.2) | BioLegend | Cat# 107617; RRID: AB_493526 |
| Rabbit anti-RAB7-AF647 (clone EPR7589) | Abcam | Cat# ab198337; RRID: AB_2783538 |
| Mouse anti-ACTB (clone AC-15) | Sigma | Cat# A1978; RRID: AB_476692 |
| Mouse anti-ALIX (clone 3A9) | Abd Serotec | Cat# MCA2493; RRID: AB_872031 |
| Rabbit anti-CANX | Abcam | Cat# ab22595; RRID: AB_2069006 |
| Mouse anti-CASP9 (clone C9) | Cell Signaling | Cat# 9508; RRID: AB_2068620 |
| Rat biotin anti-CD9 antibody (clone KMC8) | BD Biosciences | Cat# 558749; RRID: AB_397103 |
| Rat anti-CD63 (clone R5G2) | MBL International | Cat# D263-3; RRID: AB_1278815 |
| Rat anti-CD68 (clone FA-11) | GeneTex | Cat# GTX41864; RRID: AB_11176186 |
| Mouse anti-CD81 (clone B-11) | Santa Cruz | Cat# sc-166029; RRID: AB_2275892 |
| Mouse anti-COX1 (clone 5F6/F4) | Abcam | Cat# ab695; RRID: AB_305674 |
| Rat biotin anti-F4/80 (clone BM8) | BioLegend | Cat# 123105; RRID: AB_893499 |
| Rabbit anti-GAPDH (clone 16C10) | Cell Signaling | Cat# 2118; RRID: AB_561053 |
| Rabbit anti-GFP | Thermo Fisher Scientific | Cat# A11122; RRID: AB_221569 |
| Rat anti-GP96 (clone 9G10) | Enzo | Cat# ADI-SPA-850-D; RRID: AB_2039133 |
| Mouse biotin anti-HER2 (clone e2-4001) | Thermo Fisher Scientific | Cat# MA5-13102; RRID: AB_10984470 |
| Goat anti-MRC1 | R&D | Cat# AF2535; RRID: AB_2063012 |
| Rabbit anti-PARP9 | Cell Signaling | Cat# 9542; RRID: AB_2160739 |
| Rabbit anti-Syntenin-1 | Invitrogen | Cat# PA5-28826; RRID: AB_2546302 |
| Rabbit anti-STING (clone D2P2F) | Cell Signaling | Cat# 13647; RRID: AB_2732796 |
| Rabbit anti-TBXAS1 (clone EPR7333(2)) | Abcam | Cat# ab157481; RRID: AB_2783536 |
| Mouse anti-TSG101 (clone 4A10) | Abcam | Cat# ab83; RRID: AB_306450 |
| Rabbit anti-VINCULIN (clone EPR8185) | Abcam | Cat# ab129002; RRID: AB_11144129 |
| Rat biotin anti-CD11b (clone M1/70) | eBioscience | Cat# 13-0112-82; RRID: AB_466359 |
| Rat biotin IgG2a, κ isotype control (clone RTK2758) | BioLegend | Cat# 400503; RRID: AB_2783537 |
| Mouse-hamster chimeric IgG1 anti-mouse CSF1R (clone 2G2) | Roche | N/A |
| Mouse IgG1 (clone MOPC-21) | BioXCell | Cat# BE0083; RRID: AB_1107784 |
| Rabbit anti-TBXAS1 | Abcam | Cat# ab187176; RRID: AB_2800358 |
| CD3-APC (clone 17A2) | BioLegend | Cat# 100235; RRID: AB_2561455 |
| CD8a-APC/Cy7 (clone 53-6.7) | BioLegend | Cat# 100713; RRID: AB_312752 |
| CD4-APC/eFluor780 (clone GK1.5) | eBioscience | Cat# 47-0041-82; RRID: AB_11218896 |
| CD40-PE (clone: 3/23) | BD Biosciences | Cat# 561846; RRID: AB_10896482 |
| CD86-PerCP-Cy5.5 (clone GL-1) | BioLegend | Cat# 105027; RRID: AB_893420 |
| CD80-FITC (clone 16-10A1) | BioLegend | Cat# 104705; RRID: AB_313126 |
| MHC II-AF647 (clone M5/114.15.2) | BioLegend | Cat# 107617; RRID: AB_493526 |
| CD11c-PacBlue (clone N418) | BioLegend | Cat# 117321; RRID: AB_755987 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Recombinant murine IFN-γ | Peprotech | Cat# 315-05 |
| Recombinant murine IL-4 | Peprotech | Cat# 214-14 |
| Collagenase IV | Life Technologies | Cat# 17104019 |
| Dispase | Life Technologies | Cat# 17105041 |
| DNase I | Life Technologies | Cat# 18047019 |
| Red blood cell lysis buffer Hybri-Max™ | Sigma | Cat# R7757 |
| Poly-L-lysine | Sigma | Cat# P6282 |
| DAPI | Sigma | Cat# D9542 |
| Protease inhibitor cocktail cOmplete™ | Roche | Cat# 11697498001 |
| Halt™ protease and phosphatase inhibitors | Thermo Fisher Scientific | Cat# 1861281 |
| RIPA buffer | Sigma | Cat# R0278 |
| Uranyl acetate | Electron Microscopy Sciences | Cat# 22400 |
| DiOC18(7) (DiR) | Thermo Fisher Scientific | Cat# D12731 |
| PKH67 | Sigma | Cat# MINI67-1KT |
| PKH26 | Sigma | Cat# MINI26-1KT |
| Calcium ionophore A23187 | Sigma | Cat# C7522 |
| Prostaglandin E2 | Cayman Chemical | Cat# 14010 |
| Prostaglandin F2α | Cayman Chemical | Cat# 16010 |
| OVA257-264 SIINFEKL peptide | GenScript | Cat# RP10611 |
| Recombinant murine IL-2 | Peprotech | Cat# 212-12 |
| Recombinant murine GM-CSF | Peprotech | Cat# 315-03 |
| Recombinant murine M-CSF | Peprotech | Cat# 315-02 |
| Critical Commercial Assays | ||
| LIVE/DEAD Fixable Violet Dead Cell Stain Kit | Thermo Fisher Scientific | Cat# L34963 |
| BCA protein assay reagent Kit | Thermo Fisher Scientific | Cat# 23225 |
| Exosome-Streptavidin Isolation/Detection Reagent | Thermo Fisher Scientific | Cat# 10608D |
| PGE2 ELISA kit | Enzo | ADI-901-001 |
| TXB2 ELISA kit | Enzo | ADI-901-002 |
| EasySep Mouse CD8+ T Cell Isolation Kit | STEMCELL | Cat# 19853 |
| Dynabeads Mouse T-Activator CD3/CD28 | Thermo Fisher Scientific | Cat# 11456D |
| EasySep Mouse CD4+ T Cell Isolation Kit | STEMCELL | Cat# 19852 |
| RNeasy RNA Isolation Mini Kit | QIAGEN | Cat# 74104 |
| TaqMan MicroRNA Reverse Transcription Kit | Thermo Fisher Scientific | Cat# 4366596 |
| TaqMan Universal PCR Master Mix | Thermo Fisher Scientific | Cat# 4304437 |
| CellTrace Violet Cell Proliferation Kit | Thermo Fisher Scientific | Cat# C34571 |
| LIVE/DEAD Fixable Red Dead Cell Stain Kit | Thermo Fisher Scientific | Cat# L34971 |
| IFN-γ ELISA kit | Thermo Fisher Scientific | Catalog# BMS606 |
| Deposited Data | ||
| Raw RNA sequencing data of in vivo-derived tumor-associated macrophages (Squadrito et al., 2012) | NCBI Gene Expression Omnibus | GEO: GSE34903 |
| Unprocessed blots | Mendeley Data | https://doi.org/10.17632/zj43mmthr8.1 |
| Experimental Models: Cell Lines | ||
| Cancer cell line: MC38 | P. Romero (Lausanne, Switzerland) | RRID:CVCL_B288 |
| Cancer cell line: MC38 expressing the human HER2 | M. De Palma (Lausanne, Switzerland) (Squadrito et al., 2018) | N/A |
| Cancer cell line: E0771 | J. Huelsken (Lausanne, Switzerland) | RRID:CVCL_GR23 |
| Experimental Models: Organisms/Strains | ||
| Mouse: WT C57BL/6J | Charles River Laboratories | Stock# 000664 RRID:IMSR JAX:000664 |
| Mouse: B6.Cg-Tg(Wap-ERBB2)229Wzw/J | The Jackson Laboratory | Stock# 010562 RRID:IMSR_JAX:010562 |
| Mouse: C57BL/6/ROSAmT/mG mice | Muzumdar et al., 2007 | N/A |
| Mouse: C57BL/6/LysM.Cre | Clausen et al., 1999 | N/A |
| Mouse: C57BL/6/LysM.Cre/ROSAmT/mG | Baer et al., 2016 | N/A |
| Mouse: C57BL/6-Tg(TcraTcrb)1100Mjb/J | Charles River Laboratory | Stock #003831 RRID:IMSR JAX:003831 |
| Mouse: Balb/cByJ | The Jackson Laboratory | Stock #001026 RRID:IMSR_JAX:001026 |
| Oligonucleotides | ||
| hsa-miR-21 | Thermo Fisher Scientific | Assay ID 000397 |
| U6 ssRN | Thermo Fisher Scientific | Assay ID 001973 |
| hsa-miR-16 | Thermo Fisher Scientific | Assay ID 000391 |
| mmu-miR-511-3 | Thermo Fisher Scientific | Assay ID 463069_mat |
| hsa-let-7a | Thermo Fisher Scientific | Assay ID 000377 |
| Software and Algorithms | ||
| Scaffold™ Version 4.8.7 | Proteome Software | www.proteomesoftware.com, RRID:SCR_014345 |
| MassHunter Version B.07.00 | Agilent | https://www.agilent.com, RRID:SCR_015040 |
| Circos Table Viewer Version 0.63-9 | Krzywinski et al., 2009 | http://mkweb.bcgsc.ca/tableviewer/ |
| Graphpad Prism Version 7 | GraphPad Prism | RRID:SCR_002798 |
| FlowJo v.10.4.2 | FlowJo, LLC | RRID:SCR_008520 |
| Molecular Signature Database (MSigDB) | Liberzon et al., 2011 | RRID:SCR_016863 |
| Immuno-Navigator | Vandenbon et al., 2016 | https://genomics.virus.kyoto-u.ac.jp/immuno-navigator/ |
| R package version 1.0.10 | Raivo Kolde | https://cran.r-project.org/web/packages/pheatmap/index.html, RRID:SCR_003005 |
| String | Szklarczyk et al., 2017 | RRID:SCR_005223 |
| Gene Set Enrichment Analysis (GSEA) | Subramanian et al., 2005 | http://software.broadinstitute.org/gsea/index.jsp, RRID:SCR_003199 |
| ARCHS4 database | Lachmann et al., 2018 | https://amp.pharm.mssm.edu/archs4/, RRID:SCR_015683 |
| EdgeR Bioconductor package | Robinson et al., 2010 | RRID:SCR_012802 |
| Fgsea Bioconductor package | Sergushichev 2016 | https://bioconductor.org/packages/release/bioc/html/fgsea.html |
| PRECOG | Gentles et al., 2015 | https://precog.stanford.edu |
| NTA software version 3.0 | Malvern | RRID:SCR_014239 |
| SDS software version 2.4 | Thermo Fisher Scientific | https://www.thermofisher.com/us/en/home.html |
| FIJI ImageJ Version 2.0 | NIH | https://fiji.sc; RRID: SCR_002285 |
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