KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| IRF1 (D5E4) | Cell signaling | RRID: AB_10949108 |
| IRF1 (C-20 x) | Santa Cruz | RRID: AB_631838 |
| IRF3 (D83B9) | Cell signaling | RRID: AB_1904036 |
| IRF5 (10T1) | Abcam | RRID: AB_775785 |
| IRF7 | Cell signaling | RRID: AB_2127551 |
| IRF8 (C-19) | Santa Cruz | RRID: AB_649510 |
| IRF9 (C-20) | Santa Cruz | RRID: AB_2127709 |
| IRF9 (D2T8M) | Cell signaling | RRID: AB_2799885 |
| STAT1 (D1K9Y) | Cell signaling | RRID: AB_2737027 |
| pSTAT1 Y701 (58D6) | Cell signaling | RRID: AB_561284 |
| STAT2 (D9J7L) | Cell signaling | RRID: AB_2799824 |
| STAT2 (B-3) | Santa Cruz | RRID: AB_2810271 |
| pSTAT2 Y689 | Millipore | RRID: AB_2198439 |
| STAT3 (124H6) | Cell signaling | RRID: AB_331757 |
| STAT4 | Santa Cruz | RRID: AB_2810272 |
| STAT5 | Santa Cruz | RRID: AB_1129711 |
| USP18 (D4E7) | Cell signaling | RRID: AB_10614342 |
| ISG15 | Cell signaling | RRID: AB_2126201 |
| β-Actin-HRP (13E5) | Cell signaling | RRID: AB_1903890 |
| GAPDH (14C10) | Cell signaling | RRID: AB_561053 |
| mCXCR3-PE-Cy7 | Biolegend | RRID: AB_2086740 |
| mCD49b-PE | Biolegend | RRID: AB_313414 |
| mCD8a-BV421 | Biolegend | RRID: AB_10897101 |
| mCD4-APC-Cy7 | eBiosciences | RRID: AB_2534398 |
| mCD3-APC | eBiosciences | RRID: AB_11153519 |
| mCD19-BV785 | Biolegend | RRID: AB_11218994 |
| mCD45.2-PerCP-Cy5.5 | Biolegend | RRID: AB_893352 |
| mSiglecF-APC-Cy7 | BD | RRID: AB_2732831 |
| mCD11c-APC | eBiosciences | RRID: AB_469346 |
| mCD11b-PE | Biolegend | RRID: AB_312790 |
| mMHCII-A700 | eBiosciences | RRID: AB_494009 |
| mLy6C-BV421 | Biolegend | RRID: AB_2562177 |
| mLy6G-BV785 | Biolegend | RRID: AB_2566317 |
| Donkey Anti-Mouse IgG (HRP-Conjugated) | Jackson ImmunoResearch | RRID: AB_2340770 |
| Donkey Anti-Rabbit IgG (HRP-Conjugated) | Jackson ImmunoResearch | RRID: AB_10015282 |
| Bacterial and Virus Strains | ||
| VSV-GFP | Gale Lab | Fredericksen and Gale, 2006 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Human IFNβ | PBL Assay Science | 111415–1 |
| Human IFNα2 | Shenandoah Biotechnology | 100–54-20ug |
| Human IFNλ1 | R&D Systems | 1598-IL-025 |
| Human IFNλ2 | R&D Systems | 8417-IL-025 |
| Human IFNλ3 | R&D Systems | 5259-IL-025 |
| Human IFNγ | Shenandoah Biotechnology | 100–77-20ug |
| Recombinant Mouse IFNβ | R&D Systems | 8234-MB/CF |
| Recombinant Mouse IFNλ3 | R&D Systems | 1789-ML/CF |
| Recombinant Mouse IFNγ | R&D Systems | 315–05 |
| muINTEPI medium | InSCREENeX | INS-ME-1005 |
| 4-Thiouridine (4sU) | Cayman Chemical Company | 16373 |
| Streptavidin M280 Dynabeads | Thermo Fisher Scientific | 11205D |
| Rnasin Plus | Fisher Scientific | PRN2615 |
| α-[32P] deoxycytidine triphosphate | Perkin Elmer | BLU513H |
| Klenow Fragment | Invitrogen | 18012021 |
| poly[dI-dC] | Sigma-Aldrich | 10108812001 |
| Mirus Bio TransIT-X2 | Fisher Scientific | MIR6000 |
| Mirus Bio TransIT-TKO | Fisher Scientific | MIR2150 |
| Cell Recovery Solution | Corning | 354253 |
| Critical Commercial Assays | ||
| QuantiTect RT kit | Qiagen | 205314 |
| TaqMan™ Universal Master Mix II, no UNG | Thermo Fisher Scientific | 4440048 |
| NucleoSpin® RNA Clean-up | Clontech | 740948.25 |
| Direct-Zol 96-well kit | Zymo Research | R2056 |
| CellLytic NuCLEAR | Sigma-Aldrich | NXTRACT-1KT |
| TruSeq Stranded mRNA Library Prep Kit | Illumina | 20020594 |
| Qubit™ RNA BR Assay Kit | Thermo Fisher Scientific | Q10210 |
| NucleoSpin® RNA II | Clontech | 740955.25 |
| LEGENDplex Human Proinflammatory Chemokine Panel (13-plex) | Biolegend | 740007 |
| HiScribe™ T7 High Yield RNA Synthesis Kit | New England Biolabs | E2040S |
| RNA 6000 Nano Reagents | Agilent | 5067–1512 |
| Deposited Data | ||
| RNA sequencing Data | GEO | GSE115198 |
| Experimental Models: Cell Lines | ||
| PH5CH8 | RRID: CVCL_VL00 | |
| HuH7 | RRID: CVCL_0336 | |
| A549 | ATCC CCL-158 | RRID: CVCL_0023 |
| 2fTGH | Kind gift from George Stark | RRID: CVCL_0115 |
| U3A | Kind gift from George Stark | RRID: CVCL_9469 |
| U6A | Kind gift from George Stark | RRID: CVCL_D316 |
| muINTEPI | InSCREENeX | INS-CI-1007 |
| Experimental Models: Organisms/Strains | ||
| C57BL/6J | Jackson Laboratory | RRID: IMSR_JAX:000664 |
| C57BL/6 Irf1 -/- | Michael S Diamond, Washington University, St. Louis, MO | |
| Oligonucleotides | ||
| EMSA IRF1-Prom 5'-GCCTGATTTCCCCGAAATGACGGCAC-3' |
Integrated DNA Technologies | |
| EMSA ISG15-STAT 5'-GGCTTCAGTTTCGGTTTCCCTTTCCCGAGGCATGCC-3' |
Integrated DNA Technologies | |
| STAT1 siRNA | Dharmacon | M-003543–01 |
| STAT2 siRNA | Thermo Fisher Scientific | s13530 |
| IRF9 siRNA | Dharmacon | M-020858–02 |
| IRF1 siRNA | Thermo Fisher Scientific | 115266 |
| Negative Control siRNA | Thermo Fisher Scientific | AM4613 |
| STAT2 gRNA sense 5'-AAAGGACGAAACACCGTGTGGACATTCGACAGTACTGTTTTAGAGCTAGAAATAGCAAG-3' |
Integrated DNA Technologies | This paper |
| STAT2 gRNA antisense 5'-CTTGCTATTTCTAGCTCTAAAACAGTACTGTCGAATGTCCACACGGTGTTTCGTCCTTT-3' |
Integrated DNA Technologies | This paper |
| ISG15 | Life Technologies | Hs01921425_s1 |
| MX1 | Life Technologies | Hs00895608_m1 |
| OAS1 | Life Technologies | Hs00973637_m1 |
| CXCL9 | Life Technologies | Hs00171065_m1 |
| CXCL10 | Life Technologies | Hs00171042_m1 |
| CXCL11 | Life Technologies | Hs00171138_m1 |
| IFNLR1 | Life Technologies | Hs00417120_m1 |
| IRF1 | Life Technologies | Hs00971959_m1 |
| STAT1 | Life Technologies | Hs01013996_m1 |
| STAT2 | Life Technologies | Hs01013123_m1 |
| IRF9 | Life Technologies | Hs00196051_m1 |
| CIITA | Life Technologies | Hs00172106_m1 |
| TNFSF10 | Life Technologies | Hs00921974_m1 |
| IL10R2 | Life Technologies | Hs001175123_m1 |
| HPRT1 | Integrated DNA Technologies | Hs.PT.58v.45621572 |
| Cxcl9 | Life Technologies | Mm00434946_m1 |
| Cxcl10 | Life Technologies | Hs00171042_m1 |
| Oas1a | Life Technologies | Mm00836412_m1 |
| Isg15 | Life Technologies | Mm01705338_s1 |
| Ciita | Life Technologies | Mm00482914_m1 |
| Ifnlr1 | Life Technologies | Mm00558035_m1 |
| Actin | Integrated DNA Technologies | Mm.PT.58.33257376.gs |
| Gapdh | Life Technologies | Mm99999915_g1 |
| mChmp2a Forward 5'-AGACGCCAGAGGAACTACTTC-3' |
Integrated DNA Technologies | |
| mChmp2a Reverse 5'-ACCAGGTCTTTTGCCATGATTC-3' |
Integrated DNA Technologies | |
| IAV NP Forward 5'-CGTTCTCCATCAGTCTCCATC-3' |
Integrated DNA Technologies | |
| IAV NP Reverse 5'-GAGTGACATCAAAATCATGGCG-3' |
Integrated DNA Technologies | |
| Recombinant DNA | ||
| pGL2-IRF1-luc | Deb et al., 2001 | |
| pGL4/Full length (FL)-CXCL10-luc | Clarke et al., 2010; Spurrell et al., 2005 | |
| pGL4/ISRECXCL10-luc | Clarke et al., 2010; Spurrell et al., 2005 | |
| pcDNA3.1/HisA/huIRF1 | Forero et al., 2014 | |
| IRF7–2D Flag | Gale Lab, University of Washington | |
| pcDNA-6xHis-p48 | Gale Lab, University of Washington | |
| Retro_STAT1_gRNA_Double BB_CMV | Gift from Veit Hornung | |
| Retro_IRF1_gRNA_Double BB_CMV | Gift from Veit Hornung | |
| pRRL-MND-STAT2–2A-Puro | This paper | |
| psPAX-2 | Gift from Didier Trono | RRID: Addgene_12259 |
| pCMV-VSV-G | Gift from Bob Weinberg | RRID: Addgene _8454 |
| pGL3-Basic | Promega | E1751 |
| Software and Algorithms | ||
| ImageJ | https://imagej.nih.gov/ij/ | RRID:SCR_003070 |
| GraphPad Prism 8 | GraphPad Software, Inc | RRID: SCR_002798 |
| R Studio 1.1.442 | Rstudio, Inc | RRID: SCR_000432 |
| FlowJo Software | Threestar, Inc | RRID: SCR_008520 |
| Ingenuity Pathway Analysis | Qiagen | RRID: SCR_008653 |
| iGenomes | Illumina | |
| Other | ||