KEY RESOURCES Table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| InVivoMAb anti-mouse IFNγ clone R4–6A2 | BioXCell | BE0054, RRID: AB_1107692 |
| InVivoMAb rat IgG1 Isotype control, anti-trinitrophenol, clone TNP6A7 | BioXCell | BE0290, RRID: AB_2687813 |
| InVivoMAb anti-mouse CXCL9 (MIG), clone MIG-2F5.5 | BioXCell | BE0309, RRID: AB_2736989 |
| InVivoMAb polyclonal Armenian hamster IgG | BioXCell | BE0091, RRID: AB_1107773 |
| anti-Human CXCR3 Antibody, clone 49801 | R&D Systems | MAB160–100 |
| anti-Human CCR5 Antibody, clone 45531 | R&D Systems | MAB182–100 |
| Ultra-LEAF™ Purified anti-human HLA-A,B,C Antibody | Biolegend | 311427, RRID: AB_2561492 |
| Purified anti-human HLA-DR, DP, DQ Antibody | Biolegend | 361702, RRID: AB_2563139 |
| anti-human IFNα | R&D systems | 21100–2 |
| Purified anti-human IFN-β Antibody | Biolegend | 514002, RRID: AB_2122765 |
| LEAF™ Purified anti-human IFN-γ Antibody | Biolegend | 506513, RRID: AB_315446 |
| anti-mouse CD45-BV650, clone 30F11 | Biolegend | 103151, RRID: AB_2565884 |
| anti-mouse CD3e PECy5.5, clone 145–2C11 | Invitrogen | 35–0031-80, RRID: AB_11218085 |
| anti-mouse CD3 eFluor 660, clone 17A2 | eBioscience | 50–0032-82, RRID: AB_10598657 |
| anti-mouse CD3 eFluor450 | Home made | |
| anti-mouse CD4 PB, clone GK1.5 | Biolegend | 100428, RRID: AB_493647 |
| anti-mouse CD8 BV711, clone 53.6.7 | Biolegend | 100748, RRID: AB_2562100 |
| anti-mouse CD11b PECy7, clone M1/70 | eBioscience | 25–0112-81, RRID: AB_469587 |
| anti-mouse CD11c BV605, clone N418 | Biolegend | 117334, RRID: AB_2562415 |
| anti-mouse CD206 PE/Dazzle™ 594, clone C068C2 | Biolegend | 141732, RRID: AB_2565932 |
| anti- mouse CD16/CD32, clone 2.4G2 | BD Pharmigen | 553142 |
| LIVE/DEAD™ Fixable Aqua Dead Cell Stain | Invitrogen | L34966 |
| anti-human CD45 APC, clone HI30 | Biolegend | 304012, RRID: AB_314400 |
| anti-human CD3 BV510, clone UCHT1 | Biolegend | 300448, RRID: AB_2563468 |
| anti-human CD11b BB515, clone ICRF44 | BD | 564517 |
| anti-human CD14 BV605, clone M5E2 | BD | 564054, RRID: AB_2564142 |
| anti-human CD19 PE, clone HIB19 | Biolegend | 302254 |
| anti-human CD56 PE, clone HCD56 | Biolegend | 318305, RRID: AB_604093 |
| anti-human EPCAM PeCy7, clone 9C4 | Biolegend | 324222, RRID: AB_2561506 |
| Zombie UV | Biolegend | 423108 |
| anti-human CD11c (rabbit monoclonal, clone EP1347Y) | Abcam | ab52632 |
| anti-human CD68 (mouse monoclonal, clone PG-M1) | Dako | M0876 |
| anti-human CD8 (rabbit monoclonal, clone SP16) | Thermo Scientific | MA5–14548 |
| anti-human Keratin | Dako | M3515 |
| anti-human CCL5/RANTES (rabbit polyclonal) | Abcam | ab9679 |
| anti-human CXCL9/MIG (rabbit polyclonal) | Abcam | ab9720 |
| anti-mouse Immunoglobulins/HRP (goat polyclonal) | Dako | P0447 |
| anti-rabbit Immunoglobulins/HRP (goat polyclonal) | Dako | P0448 |
| anti-mouse Cytokeratin 8+18 (clone EP1628Y) | Abcam | ab53280 |
| anti-mouse CD8, clone 4SM15 | eBioscience | 14–0808-82 |
| Bacterial and Virus Strains | ||
| Biological Samples | ||
| Chemicals, Peptides, and Recombinant Proteins | ||
| Recombinant Human IFN-alpha I (alpha 17) Protein | R&D Systems | 11150–1 |
| Animal-Free Recombinant Human IFN-β | Peprotech | AF-300–02B |
| Animal-Free Recombinant Human IFN-γ | Peprotech | AF-300–02 |
| D-luciferin | Biosynth | L-8220 |
| Liberase TL | Roche | 540102001 |
| Dnase I | Sigma Aldrich | D4527 |
| 5’-aza-2’-deoxycitine | Sigma Aldrich | A3656 |
| DZNeP | Selleckchem | S7120 |
| CFSE | Invitrogen | C34554 |
| Critical Commercial Assays | ||
| Mouse RANTES (CCL5) Flex Set | BD | 558345 |
| Human MIG (CXCL9) Flex Set | BD | 558286 |
| Human CXCL10 | BD | 558280 |
| Dynabeads™ Human T-Activator CD3/CD28 for T Cell Expansion and Activation | Invitrogen | 11131D |
| 561 mRNA targets on the nCounter GX Immunology panel (mouse) | NanoString Technologies | NS_IMMUNOLOGY_MM_C2269 |
| Deposited Data | ||
| CuratedOvarianData Package | (Ganzfried et al., 2013) | https://bioconductor.org/packages/release/data/experiment/html/curatedOvarianData.html |
| METABRIC | (Curtis et al., 2012) | https://www.ebi.ac.uk/ega/studies/EGAS00000000083 |
| NKI | (van ‘t Veer et al., 2002) | https://doi.org/10.1038/415530a |
| Uppsala | (Calza et al., 2006; Viola et al., 2012) | GSE4922 |
| Stockholm | (Calza et al., 2006) | GSE1456 |
| PETACC-3 | (Popovici et al., 2012) | E-MTAB-990 |
| ALMAC | (Kennedy et al., 2011) | E-MTAB-863, E-MTAB-864 |
| CIT | (Marisa et al., 2013) | GSE39582 |
| DFCI | (Director’s Challenge Consortium for the Molecular Classification of Lung et al., 2008) | GSE68465 |
| HLMCC | (Director’s Challenge Consortium for the Molecular Classification of Lung et al., 2008) | GSE68465 |
| UMCC | (Director’s Challenge Consortium for the Molecular Classification of Lung et al., 2008) | GSE68465 |
| MSKCC | (Director’s Challenge Consortium for the Molecular Classification of Lung et al., 2008) | GSE68465 |
| DKFZ | (Kuner et al., 2009) | GSE10245 |
| Sato | (Sato et al., 2013) | GSE41271 |
| NCCH | (Wilkerson et al., 2010) | GSE1771 |
| Expression Project for Oncology (ExpO) | http://www.intgen.org/, GEO GSE2109 | |
| ConsensusPathDB interface | http://cpdb.molgen.mpg.de | |
| STRING database | http://string-db.org | |
| MSigDB | http://software.broadinstitute.org/gsea/msigdb | |
| Experimental Models: Cell Lines | ||
| ID8 | our own laboratory | |
| OVCAR3 | our own laboratory | |
| OVCAR5 | our own laboratory | |
| A1847 | our own laboratory | |
| A2780/C30 | our own laboratory | |
| OV79 | our own laboratory | |
| Experimental Models: Organisms/Strains | ||
| C57/BL6 mice | Envigo (former Harlan Laboratories) | |
| Oligonucleotides | ||
| CCL5 | Applied Biosystems | Hs00982282_m1 |
| CXCL9 | Applied Biosystems | Hs00171065_m1 |
| CXCL10 | Applied Biosystems | Hs01124251_g1 |
| CD8A | Applied Biosystems | Hs00233520_m1 |
| IFNB1 | Applied Biosystems | Hs01077958_s1 |
| IFNA1 | Applied Biosystems | Hs00256882_s1 |
| IFNG | Applied Biosystems | Hs00989291_m1 |
| GAPDH | Applied Biosystems | Hs03929097_g1 |
| Cd8a | Applied Biosystems | Mm01188922_m1 |
| Ccl5 | Applied Biosystems | Mm01302427_m1 |
| Cxcl9 | Applied Biosystems | Mm00434946_m1 |
| Stat1 | Applied Biosystems | Mm01257286_m1 |
| Cxcl10 | Applied Biosystems | Mm00445235_m1 |
| Cxcr3 | Applied Biosystems | Mm99999054_s1 |
| Gzmk | Applied Biosystems | Mm00492530_m1 |
| Gzmb | Applied Biosystems | Mm00442837_m1 |
| Ifng | Applied Biosystems | Mm01168134_m1 |
| Ifnb1 | Applied Biosystems | Mm00439552_s1 |
| Gapdh | Applied Biosystems | Mm99999915_g1 |
| CD3e | Applied Biosystems | Mm01179194_m1 |
| Cd2 | Applied Biosystems | Mm00488928_m1 |
| Cd53 | Applied Biosystems | Mm00514262_m1 |
| Batf3 | Applied Biosystems | Mm01318274_m1 |
| Gbp2 | Applied Biosystems | Mm00494575_m1 |
| Il2rb | Applied Biosystems | Mm00434268_m1 |
| CCL5 cDNA amplification primer 5’-ACGCGCGATCGCCATGAAGATCTCTGCAGCTGCCCTC -3’ | Microsynth | Custom made |
| CCL5 cDNA amplification primer 5’-ACGCCAATTGTCACTAGCTCATCTCCAAATAGTTGATG -3’ | Microsynth | Custom made |
| Recombinant DNA | ||
| MISSION pLKO.1-puro non-target shRNA control | Sigma | SHC016 |
| CCL5 MISSION shRNA Bacterial Glycerol Stock chemokine (C-C motif) ligand 5 | Sigma | SHCLNG-NM_013653 |
| MSCV Luciferase PGK-hygro construct | Addgene | 18782 |
| MSGV1-puromycin-hPGK | Home made | N/A |
| pMD18-T-CCL5 vector | Sino biological | MG50022-M |
| NYESO-1 plasmid | Home made | |
| NY-ESO-1/CCL5 plasmid | Home made | |
| Software and Algorithms | ||
| R Bioconductor package EdgeR (version 3.6.8) | R Project for Statistical Computing | |
| R Bioconductor package limma (version 3.20.9) | R Project for Statistical Computing | |
| RTCGAToolbox R package | R Project for Statistical Computing | |
| R version 3.3.2 with ggplot2 version 2.2.1 | R Project for Statistical Computing | |
| R version 3.3.2 with pROC version 1.9.1 | R Project for Statistical Computing | |
| Other | ||