KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit polyclonal anti-RIG-I | Cell Signaling Technology | 3743S; RRID: AB_2269233 |
| Goat polyclonal IgG anti-actin | Santa Cruz Biotechnology | SC-1616; RRID: AB_630836 |
| IRDye 800CW Goat anti-rabbit IgG | LI-COR | 926–32211; RRID: AB_621843 |
| IRDye 680CW Donkey anti-goat IgG | LI-COR | 926–68074; RRID: AB_10956736 |
| Secondary antibody goat anti-rabbit -Atto647N | Sigma-Aldrich | 50185-1ML-F |
| Bacterial and Virus Strains | ||
| TC83 vaccine strain VEEV-GFP | Dr. Jan Carette | N/A |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Cy3-UTP | GE Healthcare | PA53026 |
| FastAP | ThermoFisher Scientific | EF0652 |
| RNase R | Epicenter | RNR07250 |
| T4 DNA ligase | New England Biolabs | M0202M |
| RNase H | New England Biolabs | M0297L |
| DNase I | Ambion | AM2222 |
| T4 PNK | New England Biolabs | M0201S |
| Ribolock RNase Inhibitor | Life Technologies | EO0384 |
| T4 RNA ligase 1, high concentration | New England Biolabs | M0437M |
| RecJf | New England Biolabs | M0264L |
| Deadenylase | New England Biolabs | M0331S |
| T7 Endonuclease I | New England Biolabs | M0302L |
| TRIzol | Invitrogen | 15596018 |
| Brilliant II SYBR Green qRT-PCR Master Mix | Agilent | 600825 |
| Low molecular weight poly(I:C) | Invivogen | tlrl-picw |
| High molecular weight poly(I:C) | Invivogen | vac-pic |
| Interferon stimulatory DNA | Invivogen | tlrl-isdn |
| Lipofectamine 2000 | Invitrogen | 11668-019 |
| Antibody dilution reagent | ThermoFisher Scientific | 00-3218 |
| DAPI | Vector Labs | H-1200 |
| Annexin V-FITC | BD PharMingen | 556420 |
| Critical Commercial Assays | ||
| mMessage mMachine T7 transcription kit | Ambion | AM1344 |
| MEGAscript T7 transcription kit | Ambion | AM1334 |
| RiboMinus Eukaryote Kit for RNA-Seq | Invitrogen | A1083708 |
| LIVE/DEAD Fixable Blue Dead Cell Stain Kit | ThermoFisher | L23105 |
| Dual-Luciferase Reporter Assay | Promega | E1910 |
| Deposited Data | ||
| Raw and analyzed RNA-seq data | This paper | GEO: GSE81345 |
| ChIRP-MS data | This paper | Table S1 |
| Experimental Models: Cell Lines | ||
| HeLa | ATCC | CCL-2 |
| HEK293T | ATCC | CRL-3216 |
| HaCaT | ATCC | PCS-200-010 |
| RAW 264.7 | ATCC | TIB-71 |
| Wild-type MEF | Kato et al., 2005 | N/A |
| RIG-I KO MEF | Kato et al., 2005 | N/A |
| RIG-I KO HeLa | This paper | N/A |
| Oligonucleotides | ||
| Primers | This paper | Table S2 |
| ChIRP probes | This paper | Table S3 |
| Recombinant DNA | ||
| Plasmid: autocatalytic-splicing linear GFP-IRES | This paper | N/A |
| Plasmid: autocatalytic-splicing circular GFP-IRES | This paper | N/A |
| Plasmid: autocatalytic-splicing linear mCherry | This paper | N/A |
| Plasmid: autocatalytic-splicing circular mCherry | This paper | N/A |
| Plasmid: ZKSCAN1-directed linear GFP-IRES | This paper | N/A |
| Plasmid: ZKSCAN1-directed circular GFP-IRES | This paper | N/A |
| Plasmid: laccase2-directed linear GFP-IRES | This paper | N/A |
| Plasmid: laccase2-directed circular GFP-IRES | This paper | N/A |
| Plasmid: ZKSCAN1-directed linear exon2_intron_exon3 | Liang and Wilusz, 2014 | N/A |
| Plasmid: ZKSCAN1-directed circular exon2_intron_exon3 | Liang and Wilusz, 2014 | N/A |
| Plasmid: MLM3636 | Addgene | 43860 |
| Plasmid: p3s-Cas9HC | Addgene | 43945 |
| Software and Algorithms | ||
| DESeq2 | Love et al., 2014 | N/A |
| Metascape | Tripathi et al., 2015; http://metascape.org | N/A |