Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-SLIRP antibody | Abcam | Cat# ab51523; RRID: AB_2066704 |
| Mouse monoclonal Beta Tubulin (D3U1W) | Cell Signaling Technology | Cat# 86298; RRID: AB_2715541 |
| Rabbit monoclonal Rab5 | Cell Signaling Technology | Cat# 3547; RRID: AB_2300649 |
| Mouse monoclonal Lamin A/C (E-1) | Santa Cruz Biotechnology | Cat# sc-376248; RRID: AB_10991536 |
| Rabbit monoclonal SAPK/JNK (56G8) | Cell Signaling Technology | Cat# 9258; RRID: AB_10839119 |
| Rabbit polyclonal AIF | Cell Signaling Technology | Cat# 4642; RRID: AB_2224542 |
| Rabbit monoclonal MDA5 (D74E4) | Cell Signaling Technology | Cat# 5321; RRID: AB_10694490 |
| Mouse monoclonal GAPDH (6C5) | Santa Cruz Biotechnology | Cat# sc-32233; RRID: AB_627679 |
| Rabbit monoclonal Phospho-IRF-3 (Ser396) | Cell Signaling Technology | Cat# 4947; RRID: AB_823547 |
| Rabbit monoclonal IRF-3 (D6I4C) | Cell Signaling Technology | Cat# 11904; RRID: AB_2722521 |
| Donkey mouse IgG (H+L) secondary antibody, Alexa Fluor 488 | Invitrogen | Cat# A-21202; RRID: AB_141607 |
| Donkey rabbit IgG (H+L) secondary antibody, Alexa Fluor 488 | Invitrogen | Cat# A-21206; RRID: AB_2535792 |
| Bacterial and virus strains | ||
| Human coronavirus OC43 | Korea Bank for Pathogenic Viruses | KBPV-VR-8 |
| Human influenza A virus PR8 | Gift from Professor Eui-cheol Shin, KAIST | |
| SARS-CoV-2 virus | National Culture Collection for Pathogens, Korea National Institute of Health, Korea | NCCP 43326 |
| Biological samples | ||
| Minor salivary gland biopsy tissue | This study | |
| Chemicals, peptides, and recombinant proteins | ||
| Collagenase type II | Worthington | Cat# LS004176 |
| Penicillin/Streptomycin | Gibco | Cat# 15140122 |
| Lipopolysaccharide (LPS) | Sigma Aldrich | Cat# L2630 |
| Single-strand poly-uridine (ssPolyU) | Invivogen | Cat# tlrlsspu |
| Polyinosinic-polycytidylic acid (Poly I:C) | Sigma Aldrich | Cat# P1530 |
| CpG oligodeoxynucleotides (CpG ODN) | Invivogen | Cat# tlrl-2006 |
| Inhibitor of mitochondrial transcription 1 (IMT1; LDC195943) | This paper | (Bonekamp et al., 2020) |
| Recombinant Human IFN-beta 1A (Mammalian) protein | R&D Systems | Cat# 11415-1 |
| 5’ triphosphate hairpin RNA (3p-hpRNA) | Invivogen | Cat# tlrl-hprna |
| Short synthetic dsRNA (79bp) | This paper | (Zheng et al., 2004) |
| Long synthetic dsRNA (717bp) | This paper | (Kang et al., 2022) |
| Lipofectamine 3000 Transfection Reagent | Invitrogen | Cat# L30000075 |
| Bovine Serum Albumin (BSA) | RMBIO | Cat# BSA-BSH |
| Puromycin | Invivogen | Cat# ant-pr-1 |
| TRIzol | Ambion | Cat# 15596018 |
| TRIzol LS | Ambion | Cat# 10296028 |
| Recombinant Dnase I (RNAse-free) | TaKaRa | Cat# 2270 |
| RevertAid Reverse Transcriptase (200U/μL) | Thermo Scientific | Cat# EP0442 |
| SuperScript IV Reverse Transcriptase | Invitrogen | Cat# 18090200 |
| Primescript RT Master Mix | TaKaRa | Cat# R036A |
| Protease Inhibitor Cocktail Set III, Animal-Free | Calbiochem | Cat# 535140 |
| Phosphatase Inhibitor Cocktail 3 | Sigma Aldrich | Cat# P0044 |
| Triton X-100 | Promega | Cat# H5141 |
| DAPI (4’6-Diamidino-2-Phenylindole, Dihydrochloride) | Invitrogen | Cat# D1306 |
| Pierce™ Protein A UltraLink™ Resin | Thermo Scientific | Cat# 53139 |
| NP-40 | Biosolution | Cat# BN015 |
| Proteinase K, recombinant, PCR Grade | Roche | Cat# 3115879001 |
| Acid-Phenol:Chloroform, pH 4.5 | Invitrogen | Cat# AM9722 |
| Glycoblue Coprecipitant | Invitrogen | Cat# AM9516 |
| SlowFade Diamond Antifade Mountant | Invitrogen | Cat# S36972 |
| Paraformaldehyde | Sigma Aldrich | Cat# P6148 |
| RedSafe Nucleic Acid Staining Solution | iNtRON Biotechnology | Cat# 21141 |
| Polybrene | Sigma Aldrich | Cat# TR-1003-G |
| Critical commercial assays | ||
| Subcellular Protein fractionation Kit for Cultured Cells | Thermo Scientific | Cat# 78840 |
| SensiFAST SYBR Lo-ROX Kit | Bioline | Cat# BIO-94020 |
| PowerSYBR Green | Applied Biosystems | Cat# 4367659 |
| RNeasy Mini Kit | Qiagen | Cat# 74104 |
| High Capacity cDNA Kit | Applied Biosystems | Cat# 4368814 |
| PowerSYBR Green PCR Master Mix | Applied Biosystems | Cat# 4367660 |
| RNAscope Multiplex Fluorescent Reagent Kit | ACD bio | Cat# 323270 |
| RNAscope ™ Probe-Hs-MT-ND5-sense | ACD bio | Cat# 539321 |
| RNAscope ™ Probe-Hs-MT-ND5-C2 | ACD bio | Cat# 539451-C2 |
| Quick-DNA miniprep plus kit | Zymo | Cat# D4069 |
| Deposited data | ||
| Raw data files for Poly I:C transfection in HCT116 cells | This paper | GEO: GSE248259 |
| Raw data files for monocytes of SjD and SLE patients | Lee et al., 2022 | |
| Raw data files for PBMCs of RA patients | Jiang et al., 2021 | GEO: GSE169082 |
| Raw data files for Peripheral blood EV of SPMS patients | Ascension AM et al., 2024 | GEO: GSE255317 |
| Raw data files for fibroblast of AGS patients | Lim Y et al., 2015 | GEO: GSE27353 |
| GENCODE Human v34 | GENCODE |
https://doi.org/10.1101/gr.135350.111; https://www.gencodegenes.org |
| Experimental models: Cell lines | ||
| HCT116 | American Type Culture Collection | Cat# CCL-247; RRID: CVCL_0291 |
| A549 | American Type Culture Collection | Cat# CCL-185; RRID: CVCL_0023 |
| PC3 | Korean Cell line Bank | Cat# 21435; RRID: CVCL_0035 |
| HEK-293T | American Type Culture Collection | Cat# CRL-3216; RRID: CVCL_0063 |
| Calu3 | Korean Cell line Bank | Cat# 30055; RRID: CVCL_0609 |
| A549-ACE2 | Gift from Benjamin tenOver, New York University | |
| Oligonucleotides | ||
| Random primers | Thermo Scientific | Cat# 48190-011 |
| See Supplemental Table 1 for the list of siRNAs | Bioneer | N/A |
| See Supplemental Table 2 for the list of shRNAs | This paper | N/A |
| See Supplemental Table 3 for the list of primer sequences for strand specific reverse transcription | This paper | N/A |
| See Supplemental Table 4 for the list of primer sequences for RT-qPCR | This paper | N/A |
| See Supplemental Table 5 for the list of primer sequences for strand-specific qPCR | This paper | N/A |
| Recombinant DNA | ||
| pLKO.1 | Gift from Professor JinJu Han, KAIST | |
| pMD2.G | Addgene | Cat# 12259 |
| psPAX2 | Addgene | Cat# 12260 |
| Software and algorithms | ||
| HISAT2 v2.1.0 | Kim et al., 2019 |
https://doi.org/10.1038/s41587-019-0201-4; http://daehwankimlab.github.io/hisat2/ |
| Samtools V1.10 | Li et al., 2009 |
https://doi:10.1093/bioinformatics/btp352; https://samtools.sourceforge.net/ |
| DEseq2 v1.34.0 | Love et al., 2014 |
https://doi.org/10.1186/s13059-014-0550-8; http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html |
| FastQC v0.11.9 | Andrews, 2010 | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| STAR v2.7.9 | Dobin et al., 2013 | https://doi.org/10.1093/bioinformatics/bts635 |
| Other | ||
| Roswell Park Memorial Institute media 1640 (RPMI 1640) | Welgene | Cat# LM011-01 |
| Fetal Bovine Serum (FBS) | Welgene | Cat# S-101-01 |
| Dulbecco’s modified eagle medium (DMEM) | Welgene | Cat# LM001-05 |
| 0.05 % Trypsin-EDTA | Welgene | Cat# LS015-01 |
| Dulbecco’s Phosphate Buffered Saline (DPBS) | Corning | Cat# 21-031-CV |