KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Rabbit monoclonal anti-phospho-PKR Thr446 | Abcam | Cat# ab32036; RRID: AB_777310 |
| Rabbit anti-RNase L antibody | Abcam | Cat# ab191392; RRID: AB_2916269 |
| Rabbit polyclonal anti-XRN1 | Bethyl Laboratories | Cat# A300-443A; RRID: AB_2219047 |
| Rabbit monoclonal anti-ISG15 | Cell Signaling Technology | Cat# 2758; RRID: AB_2126200 |
| Rabbit monoclonal anti-G3BP1 | Cell Signaling Technology | Cat# 17798; RRID: AB_2884888 |
| Rabbit polyclonal anti-MAVS | Cell Signaling Technology | Cat# 3993; RRID: AB_823565 |
| Rabbit monoclonal anti-MDA5 | Cell Signaling Technology | Cat# 5321; RRID: AB_10694490 |
| Rabbit polyclonal anti-total PKR | Cell Signaling Technology | Cat# 3072; RRID: AB_2277600 |
| Rabbit monoclonal anti-phospho-STAT1 (Tyr701) | Cell Signaling Technology | Cat# 9167; RRID: AB_561284 |
| Rabbit polyclonal anti-total STAT1 | Cell Signaling Technology | Cat# 9172; RRID: AB_2198300 |
| Rabbit polyclonal anti-XRN1 | Cell Signaling Technology | Cat# 70205; RRID: AB_2799779 |
| Mouse monoclonal anti-β-actin | Santa Cruz Biotechnology | Cat# sc-47778; RRID: AB_626632 |
| Goat anti-mouse IRDye 680LT | LI-COR Biosciences | Cat# 926-68020; RRID: AB_10706161 |
| Goat anti-rabbit IRDye 800CW | LI-COR Biosciences | Cat# 926-32211; RRID: AB_621843 |
| Alexa Fluor® 647 AffiniPure Donkey anti-Rabbit IgG | Jackson ImmunoResearch Laboratories | Cat# 711-605-152; RRID: AB_2492288 |
| Chemicals, peptides, and recombinant proteins | ||
| Blasticidin | Thermo Fisher Scientific | Cat# A1113903 |
| cOmplete™ Mini Protease Inhibitor Cocktail Tablets | Roche Diagnostics | Cat# 4693124001 |
| Human IFN-Beta 1a, mammalian | PBL Assay Science | Cat# 114151 |
| Laemmli SDS Sample Buffer, reducing (6X) | Thermo Fisher Scientific | Cat# AAJ61337-AC |
| Polybrene | Santa Cruz Biotechnology | Cat# sc-134220 |
| PhosSTOP™ | Roche Diagnostics | Cat# 4906837001 |
| Puromycin | Thermo Fisher Scientific | Cat# A1113803 |
| Restore PLUS Western Blot Stripping Buffer | Thermo Fisher Scientific | Cat# PI46430 |
| RIPA Buffer | Sigma Aldrich | Cat#R0278 |
| Ruxolitinib | Selleck Chemicals | Cat#S1378 |
| Critical commercial assays | ||
| Pierce BCA Protein Assay Kit | Thermo Fisher Scientific | Cat# 23225 |
| CalPhos™ Mammalian Transfection Kit | Takara Bio | Cat# 631312 |
| CellTiter-Glo® Luminescent Cell Viability Assay | Promega | Cat# PAG7572 |
| NEBNext rRNA Depletion Kit | New England Biolabs | Cat#E6310 |
| NEBNext Ultra II Directional RNA Library Prep Kit | New England Biolabs | Cat#E7760 |
| QIAseq FastSelect -rRNA HMR Kit | Qiagen | Cat# 334375 |
| RNeasy Plus Kit | Qiagen | Cat# 74134 |
| Deposited data | ||
| Raw data from bulk RNA-sequencing | This manuscript | NCBI Gene Expression Omnibus (GEO) Accession Number GEO: GSE248036 |
| Experimental models: Cell lines | ||
| A549 (Control, XRN1 single KO, PKR single KO, and XRN1/PKR double KO) | This manuscript | N/A |
| NCI-H1299 (Control, XRN1 single KO, PKR single KO, and XRN1/PKR double KO) | This manuscript | N/A |
| Oligonucleotides | ||
| sgRNA sequences for CRISPR-Cas9-mediated gene knockout | See Table S5 | N/A |
| Recombinant DNA | ||
| plentiCRISPRv2 with puromycin resistance | Addgene | Cat# 98290; RRID: Addgene_98290 |
| plentiCRISPRv2 with blasticidin resistance | Cloned in-house, adapted from Addgene plasmid | N/A |
| plentiCRISPRv2 expressing two sgRNAs with puromycin resistance | Cloned in-house, adapted from Addgene plasmid | N/A |
| pLEX307 | Addgene | Cat# 41392; RRID: Addgene_41392 |
| pMD2.G | Broad Institute of Harvard and MIT | N/A |
| psPAX2 | Broad Institute of Harvard and MIT | N/A |
| pLNHA-C1-HsXRN1 (XRN1 ORF) | Addgene | Cat# 66596; RRID: Addgene_66596 |
| XRN1 D208A ORF, resistant to XRN1 sgRNA targeting | Cloned in-house, adapted from Addgene plasmid | N/A |
| XRN1 E176G ORF, resistant to XRN1 sgRNA targeting | Cloned in-house, adapted from Addgene plasmid | N/A |
| Software and algorithms | ||
| Custom code for identification of complementary sense/anti-sense RNA pairs | This manuscript | https://doi.org/10.5281/zenodo.7971843 |