Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-TREX1 | Proteintech | Cat# 24876–1-AP RRID:AB_2879772 |
| anti-V5-HRP | Sigma | Cat# V2260–1VL RRID:AB_261857 |
| anti-tubulin | Sigma | Cat# T6199–100μL RRID:AB_477583 |
| anti-RNP | BEI Resources Repository | Cat# NR-3133 |
| anti-dsDNA | Santa Cruz Biotechnology | Cat# sc-58749 RRID:AB_783088 |
| donkey anti-goat 488 AlexaFluor | Invitrogen | Cat# A11055 RRID:AB_2534102 |
| chicken anti-mouse 594 AlexaFluor | Invitrogen | Cat# A21201 RRID:AB_2535787 |
| Bacterial and virus strains | ||
| Influenza A virus A/PR8/34 (H1N1; PR8) | rescued for this study | |
| Influenza A virus A/PR8/34 encoding split NS, TRPPC NS or Rz-TRPPC NS | rescued for this study | |
| Influenza A virus A/PR8/34 encoding a genome-wide TRPPC NS library | rescued for this study | |
| Influenza A virus A/WSN/33 (H1N1; WSN) | rescued for this study | |
| Influenza A chimeric WSN and A/green-winged teal/Ohio/175/1986 (H2N1; S009) | rescued for this study | |
| Influenza A virus A/California/04/2009 (H1N1; CA04) | rescued for this study | |
| Influenza B virus B/Brisbane/60/2008 (B-Victoria lineage; B/Bris) | rescued for this study | |
| Nanoluciferase-expressing PASTN reporter viruses | Tran,et al. 2013, 2015, 202015,90,91 Larson, et al.85 Amato, et al.86 |
|
| VSV-GFP | Schott, et al.92 | |
| human adenovirus 5 | rescued for this study | |
| human adenovirus 5 TRPCCa-SH | rescued for this study | |
| Mach1 competent E. coli | prepared in-house | |
| Biological samples | ||
| Primary normal human bronchial epithelial cells (lot # 21TL347555, Caucasian white male age 55) | Lonza | NCC-2540S |
| Chemicals, peptides, and recombinant proteins | ||
| PneumaCult-ALI medium system | Stem Cell Technologies | Cat# 05001 |
| TPCK-treated trypsin | Sigma | Cat# T1426–50MG |
| diABZI | Cayman Chemical | Cat# 28054 |
| jetPRIME | PolyPlus | Cat# 101000001 |
| Avicel | FMC BioPolymer | Cat# RC-581 |
| TransIT-2020 | Mirus | Cat# mir5406 |
| Trizol | Invitrogen | Cat# 15596018 |
| iTaq SYBR master mix | BioRad | Cat# 1725121 |
| SuperScriptIV | Invitrogen | Cat# 18090050 |
| Critical commercial assays | ||
| MycoAlert | Lonza | Cat# LT07–218 |
| NanoGlo Luciferase Assay | Promega | Cat# N1120 |
| Renilla Luciferase Assay | Promega | Cat# E2810 |
| Luciferase Assay (firefly) | Promega | Cat# E1500 |
| DNeasy Blood and Tissue kits | Qiagen | Cat# 69504 |
| Deposited data | ||
| RNA seq from TRPPC screen viruses | This study | NCBI BioProject PRJNA930886 |
| RNA seq from cells | This study | NCBI BioProject PRJNA930919 |
| Experimental models: Cell lines | ||
| A549 cells | ATCC | Cat# CCL-185 |
| Madin-Darby canine kidney (MDCK) cells | ATCC | Cat# CCL-34 |
| human embryonic kidney 293 (HEK293) cells | ATCC | Cat# CRL-1573 |
| human embryonic kidney 293T (HEK293T) cells | ATCC | Cat# CRL-3216 |
| MDCK-SIAT1-TMPRSS2 cells | Lee, et al.81 | |
| A549 MAVS knockout cells | Rahim, et al.82 | |
| A549 STING knockout cells | Stabell, et al.53 | |
| A549 TREX1 knockout cells | this study | |
| A549 TREX1 knockout cells complemented with WT TREX1 | this study | |
| A549 TREX1 knockout cells complemented with D18N TREX1 | this study | |
| A549-Cre-reporter CRISPR-SAM clone #15 (referred to here as A549-CRISPRa cells) | Heaton, et al.19 | |
| Polyclonal 293T-CRISPRa cells | this study | |
| A549 cells overexpressing TREX1 or TREX1-D18N | this study | |
| WT or TREX1 knockout A549 ISRE reporter cells lines | this study | |
| Experimental models: Organisms/strains | ||
| Oligonucleotides | ||
| See Supplemental Table 3 | ||
| Recombinant DNA | ||
| Plasmid: pNL1.2[NlucP] | Promega | Cat# N1011 |
| Plasmid: TRPPCa reporter plasmid p9X-NL1.2 | this study | |
| Plasmid: human SAM CRISPRa sgRNA library | Addgene | Cat# 1000000078 |
| Plasmid: Expression plasmids for RNP components (A/WSN/33 PB2, PB1, PA, and NP) | Mehle and Dounda84 | |
| Plasmid: A/PuertoRico/8/34 pHW190-pHW198 | a kind gift from S. Schultz-Cherry | |
| Plasmid: pHW-Split-NS for PR8, CA07 and B/Bris | this study | |
| Plasmid: pHW-TRPPC-NS, including non-targeting and gene-specific versions | this study | |
| Plasmid: pHW-Rz-TRPPC-NS, including non-targeting and gene-specific versions | this study | |
| Plasmid: Expression plasmids for RNP components for A/California/07/2009 (H1N1; CA07) | Amato, et al.86 | |
| Plasmid: Expression plasmids for RNP components for B/Brisbane/60/2008 (B/Bris) | Tran, et al.; Larons, et al.15,85 | |
| Plasmid: TRPPCi reporter plasmids | this study | |
| Plasmid: CRISPRi expression constructs for VP16-Gal4 transactivator | Yeo, et al.29 | |
| Plasmid: CRISPRi expression constructs for dCas9-KRAB-MeCP2 repressor | Yeo, et al.29 | |
| Plasmid: Adenobuilder system plasmids | Miciak, et al.87 | |
| Plasmid: pAd5-B6 TRPCCa-SH | this study | |
| Plasmid: pAd5 TRPCCi-CH | this study | |
| Plasmid: pHAGE2–EF1ɑInt–TMPRSS2–IRES–mCherry-W | Lee, et al.81 | |
| Plasmid: GFP-TREX1 | Addgene | Cat# 27219 |
| Plasmid: TREX1-D18N | Addgene | Cat# 27220 |
| Plasmid: psPAX2 | Addgene | Cat# 12260 |
| Plasmid: pCMV-VSV-G | Addgene | Cat# 8454 |
| Plasmid: pLenti dCAS-VP64_Blast | Addgene | Cat# 61524 |
| Plasmid: pLenti MS2-P65-HSF1_Hygro | Addgene | Cat# 61426 |
| Plasmid: UCOE-SFFV backbone | Addgene | Cat# 122205 |
| Plasmid: pSFFV-TREX1-V5–2A-BSD | this study | |
| Plasmid: pSSFV-TREX1-D18N-V5–2A-BSD | this study | |
| Plasmid: pCMV(CAT)T7-SB100 | Addgene | Cat# 34879 |
| Plasmid: pSBbi-BB backbone | Addgene | Cat# 60521 |
| Plasmid: ISG54 promoter driving Nluc-2A-GFP cloned into pSBbi-BB | this study | |
| Software and algorithms | ||
| FastQC v.0.11.5 | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ | |
| BBMap (v38.49) suite | Bushnell; Bushnell et al.97,98 | https://sourceforge.net/projects/bbmap/ |
| bowtie2 (v2.3.5.1) | Langmead, et al.99 | https://github.com/BenLangmead/bowtie2 |
| Python (v3.7.3) | https://www.python.org/downloads/release/python-373/ | |
| MAGeCK (v0.4) | Li,e t al.100 | https://sourceforge.net/projects/mageck/ |
| ShinyGO | Ge, et al.101 | http://bioinformatics.sdstate.edu/go/ |
| ImageJ (v1.53) | https://imagej.nih.gov/ij/download.html | |
| Trim Galore (v0.4.4) | Krueger103 | https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ |
| STAR (v2.5.3a) | Dobin, et al.104 | https://github.com/alexdobin/STAR |
| HTSeq (v0.9.1) | Anders, et al.105 | https://htseq.readthedocs.io/ |
| R (v4.1.1) | https://cran.r-project.org/bin/windows/base/old/ | |
| DESeq2 (v1.34.0) | Love, et al.106 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| GraphPad Prism (v9.4.1) | GraphPad Software Inc. | https://www.graphpad.com/ |
| Adobe Illustrator (27.0.1) | Adobe Inc. | https://adobe.com/products/illustrator |
| Other | ||