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. 2022 May 13;25(6):104404. doi: 10.1016/j.isci.2022.104404
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies

Rabbit anti-CX43 Cell Signaling Technology Cat#3512S; RRID: AB_2294590
Rabbit monoclonal anti-VDAC (D73D12) Cell Signaling Technology Cat#4661; RRID: AB_10557420
Rabbit monoclonal anti-RIG-I (D14G6) Cell Signaling Technology Cat#3743; RRID: AB_2269233
Rabbit monoclonal anti-MDA5 (D74 × 104) Cell Signaling Technology Cat#5321; RRID: AB_10694490
Rabbit anti-SOD1 Cell Signaling Technology Cat#2770; RRID: AB_2302392
Rabbit monoclonal anti-MAVS (D5A9E, H) Cell Signaling Technology Cat#24930; RRID: AB_2798889
Rodent specific anti-MAVS (Mouse/Rat) Cell Signaling Technology Cat#4983; RRID: AB_823566
Rabbit monoclonal anti-COX IV (3 × 1011) Cell Signaling Technology Cat#4850; RRID: AB_2085424
Rabbit monoclonal anti-STAT1 (D1K9Y) Cell Signaling Technology Cat#14994; RRID: AB_2737027
Rabbit monoclonal anti-STING (D2P2F) Cell Signaling Technology Cat#13647; RRID: AB_2732796
Rabbit monoclonal anti-TBK1/NAK (D1B4) Cell Signaling Technology Cat#3504; RRID: AB_2255663
Rabbit monoclonal anti-phoshoTBK1/NAK1 (Ser172, D52C2) Cell Signaling Technology Cat#5483; RRID: AB_10693472
Rabbit monoclonal anti-phospho-IRF3 (Ser396, 4D4G) Cell Signaling Technology Cat#4947; RRID: AB_823547
Mouse monoclonal anti-dsDNA [35I9 DNA] Abcam Cat#ab27156; RRID: AB_470907
Rabbit polyclonal anti-DDX41 ABclonal Inc. Cat#A6576; RRID: AB_2767170
Rabbit polyclonal Lamin A/C [KO validated] ABclonal Inc. Cat#A0249; RRID: AB_2757062
Rabbit polyclonal anti-HSP60/HSPD1 ABclonal Inc. Cat#A0969; RRID: AB_2757488
Rabbit polyclonal anti-IRF3 [KO validated] ABclonal Inc. Cat#A11118; RRID: AB_2861504
Rabbit polyclonal anti-PANX1 ABclonal Inc. Cat#A13587; RRID: AB_2760449
Rabbit polyclonal anti-GJC1/CX45 ABclonal Inc. Cat#A7053; RRID: AB_2767608
Rabbit polyclonal anti-cGAS ABclonal Inc. Cat#A8335; RRID: AB_2770305
Rabbit polyclonal anti-phospho-cGAS Y215 ABclonal Inc. Cat#AP0946; RRID: N/A
Mouse monoclonal anti-FLAG (M2) Sigma-Aldrich Cat#F1804; RRID: AB_262044
Mouse monoclonal anti-O4 Sigma-Aldrich Cat#O7139; RRID: AB_477662
Mouse monoclonal anti-CD45 (clone 30-F11) BD Pharmingen Cat#550539; RRID: AB_2174426
Sheep polyclonal anti-ITGB5 R&D Systems Cat#AF3824; RRID: AB_1151977
Mouse monoclonal anti-L1, clone 324 Millipore Sigma Cat#MAB5272; RRID: AB_2133200
Mouse monoclonal anti-DNA:RNA hybrid, clone S9.6 Millipore Sigma Cat#MABE1095; RRID: AB_2861387
Mouse monoclonal anti-NK1.1 Thermo Fisher Scientific Cat#MA1-70100; RRID: AB_2296673
Mouse monoclonal anti-NF-κB p65 (F-6) Santa Cruz Biotechnology Cat#sc-8008; RRID: AB_628017
Mouse monoclonal anti-mtTFA (F6) Santa Cruz Biotechnology Cat#sc-166965; RRID: AB_10610743
Mouse monoclonal anti-Pol II (A10) Santa Cruz Biotechnology Cat#sc-17798; RRID: AB_677355
Rabbit polyclonal anti-TOM20 (FL-145) Santa Cruz Biotechnology Cat#sc-11415; RRID: AB_2207533
Mouse monoclonal anti-GFAP Santa Cruz Biotechnology Cat#sc-33673; RRID: AB_627673
Mouse monoclonal anti-Iba1 Santa Cruz Biotechnology Cat#sc-32725; RRID: AB_667733
Mouse monoclonal anti-CD4 Santa Cruz Biotechnology Cat#sc-19641; RRID: AB_2009035
Mouse monoclonal anti-CD19 Santa Cruz Biotechnology Cat#sc-; RRID: AB_667733
Mouse monoclonal anti-β-Actin (C4) Santa Cruz Biotechnology Cat#sc-47778; RRID: AB_2714189
Mouse monoclonal anti-β-tubulin (G8) Santa Cruz Biotechnology Cat#sc-55529; RRID: AB_2210962
Mouse monoclonal anti-CD68 Santa Cruz Biotechnology Cat#sc-20060; RRID: AB_627158
Mouse monoclonal anti-VP1 Clone 31A2 Mediagnost Cat#M47; RRID: N/A
InVivoMAb anti-mouse IFNAR-1 Bio X Cell Cat#BE0241; RRID: N/A
InVivoMAb anti-mouse CCL2 (MCP-1) Bio X Cell Cat#BE0185; RRID: N/A

Bacterial and virus strains

CVB3 ATCC Cat#VR-300
HCoV-OC43 ATCC Cat#VR-1558

Chemicals, peptides, and recombinant proteins

RPMI Medium 1640 (1X) Gibco Cat#11875-093
RPMI Medium 1640 D-Glucose (−) Gibco Cat#11879-020
Fetal Bovine serum (FBS) Gibco Cat#12483-020
HEPES (1M) pH 7.5 Gibco Cat#15630-080
2-mercaptoethanol (1000X) Gibco Cat#21985-023
N2-supplement (100X) Thermo Fisher Cat#17502-048
B-27 supplement (50X), serum free Thermo Fisher Cat#17504044
Cyclosporin A (CsA) Sigma-Aldrich Cat#SML1018
Heparin-Binding EGF-Like Growth Factor Sigma-Aldrich Cat#E4643
LFM-A13 Sigma-Aldrich Cat#435300
2′,3′-Dideoxycytidine (ddC) Sigma-Aldrich Cat#D5782
Corn oil Sigma-Aldrich Cat#C8267
Tween-80 Sigma-Aldrich Cat#P4780
Dimethyl sulfoxide Sigma-Aldrich Cat#D8418
Dexamethasone Sigma-Aldrich Cat#D4902
Carbenoxolone disodium salt Sigma-Aldrich Cat#C4790
Brefeldin A Sigma-Aldrich Cat#B5936
Probenecid Sigma-Aldrich Cat#P3000000
DMEM Sigma-Aldrich Cat#D6429
DMEM Ham’s:F12 Mixture Sigma-Aldrich Cat#51445C
Dulbecco’s PBS Sigma-Aldrich Cat#D8662
Penicillin-Streptomycin Sigma-Aldrich Cat#P4333
Sodium pyruvate solution Sigma-Aldrich Cat#S8636
Hematoxylin solution Gill No.2 Sigma-Aldrich Cat#GHS232
Herring testes (HT)-DNA Sigma-Aldrich Cat#D6898
Digitonin Sigma-Aldrich Cat#D141
Tunicamycin Abcam Cat#ab120296
RNase H NEB Cat#0297S
DNase I NEB Cat#M0303S
IFN-β-human recombinant proteins Bio Basic Canada Cat#RC217-16
Image-iT FX Signal Enhancer Invitrogen Cat#I36933
UltraPure™ Ethidium Bromide Invitrogen Cat#15585011
Lipofectamine 2000 Invitrogen Cat#11668027
Lipofectamine RNAiMAX Invitrogen Cat#13778075
Normocin™ Invivogen Cat#ant-nr-1
High molecular weight poly(I:C) Invivogen Cat#tlrl-pic
Protease inhibitor cocktail tablets Roche Cat#05892791001
DNAfectin™ Plus ABM Canada Cat#G2500
TransIT-X2 Dynamic Delivery System Mirus Bio Cat#MIR 6004
TNFR1 Blocking Peptide Fitzgerald Cat#33R-10641
RU.521 Cayman Chemical Cat#31765
C-176 Cayman Chemical Cat#25859
H-151 Cayman Chemical Cat#25857
Fluo-cGAMP BIOLOG Life Science Institute Cat#C195-001
Protein G-SepharoseTM 4 Fast Flow GE Healthcare Biosciences Cat#17-0618

Critical commercial assays

CyQuant™ LDH Cytotoxicity kit Thermo Fisher Cat#C20301
POWER SYBR® Green RNA-to-CTTM kit Thermo Fisher Cat#4389986
ATP assay kit Sigma-Aldrich Cat#MAK190
MMP-assay kit Sigma-Aldrich Cat# MAK147-1KT
Universal Mycoplasma detection kit ATCC Cat#30-1012K
QIAGEN Plasmid Plus kit QIAGEN Cat#12941
RNeasy Mini-extraction kit QIAGEN Cat#74104
QIAmp DNA Mini Kit QIAGEN Cat#51304
Mouse ChAT ELISA Kit Antibodies.com Cat#A77879
QuicKey Mouse IgG ELISA Kit Elabscience Cat#E-TSEL-M0003
Mouse IgM ELISA Kit Elabscience Cat#E-EL-M3036
Mouse ANA (Anti-Nuclear Antibody) ELISA MyBioSource Cat#MBS261480
2′3′-cGAMP ELISA Kit Cayman Chemical Cat#501700
VeriKine mouse IFN Beta ELISA Kit, High Sensitivity PBL Assay Science Cat#42410-1

Deposited data

RAW and analyzed data This paper GEO: GSE167974

Experimental models: Cell lines

HeLa ATCC Cat#CCL-2.2; RRID: CVCL_0030
U2-OS ATCC Cat#HTB-96; RRID: CVCL_0042
HEK293T ATCC Cat#CRL-3216; RRID: CVCL_0063
THP-1 ATCC Cat#TIB-202; RRID: CVCL_0006
RAW264.7 ATCC Cat#TIB-71; RRID: CVCL_0493
SH-SY5Y ATCC Cat#CRL-2266; RRID: CVCL_0019
Neuro2a ATCC Cat#CCL-131; RRID: CVCL_0470
SIM-A9 ATCC Cat#CRL-3265; RRID: CVCL_5I31
HASTR/ci35 From Dr. Tomomi Furihata (TUPLS, Japan) Cat#N/A; RRID: CVCL_4U69; (Furihata et al., 2016; Kitamura et al., 2018)
C20 From Dr. David Alvarez-Carbonell (CWRU, USA) Cat#N/A; RRID: N/A; (Garcia-Mesa et al., 2017)
NSC-34 From Dr. Neil R. Cashman (UBC, Canada) Cat#N/A; RRID: CVCL_D356; (Cashman et al., 1992)
MO3.13 From Dr. Neil R. Cashman (UBC, Canada) Cat#N/A; RRID: CVCL_D357; (McLaurin et al., 1995)

Experimental models: Organisms/strains

Wild-type C57BL/6J background mice The Jackson Laboratory Cat#000664
B6.Cg-Tg (SOD1∗G85R)148Dwc/J mice The Jackson Laboratory Cat#008248
B6.Cg-Tg(SOD1∗G93A)1Gur/J mice The Jackson Laboratory Cat#004435
B6.Cg-Tmem173tm1.2Camb/J mice The Jackson Laboratory Cat#025805

Oligonucleotides

HCoV-OC43 Nucleocapsid (N): F: CGATG
AGGCTATTCCGACTAGGT
R: CCTTCCTGAGCCTTCAATATAGTAACC
Integrated DNA Technologies (IDT) (Hammitt et al., 2011)
CVB3 2A gene: F: GCTTTGCAGACATCCGTGATC
R: CAAGCTGTGTTCCACATAGTCCTTCA
Integrated DNA Technologies (IDT) N/A
CVB3 VP1 gene: F: ACATGGTGCGAAGAGTCTATTGAG
R: TGCTCCGCAGTTAGGATTAGC
Integrated DNA Technologies (IDT) N/A
Murine IFNA4 gene: F: CTGCTACTTGGAATGCAACTC
R: CAGTCTTGCCAGCAAGTTGG
Integrated DNA Technologies (IDT) (Mattei et al., 2013)
Murine IFNB1 gene: F: GCCTTTGCCATCCAAGAGATGC
R: ACACTGTCTGCTGGTGGAGTTC Human IFNB1 gene:
F: CAACTTGCTTGGATTCCTACAAAG R: TATTCAAGCC
TCCCATTCAATTG
Integrated DNA Technologies (IDT) N/A
Murine RSAD2 gene: F: TGGGGATGCTGGTGCCCACT
R: ACCCCGGACCTGTGGCTGTT Human RSAD2 gene:
F: TTGGACATTCTCGCTATCTCCT R: AGTGCTTTGAT
CTGTTCCGTC
Integrated DNA Technologies (IDT) N/A
Murine ISG15 gene: F: CAAGCAGCCAGAAGCAGACT
R: CCCAGCATCTTCACCTTTAGG Human ISG15 gene:
F: CGCAGATCACCCAGAAGATCG R: TTCGTCGCAT
TTGTCCACCA
Integrated DNA Technologies (IDT) N/A
Murine TNF gene: F: GTCCCCAAAGGGATGAGAAGTT
R: GTTTGCTACGACGTGGGCTACA Human TNF gene:
F: CCTCTCTCTAATCAGCCCTCTG R: GAGGACCTGG
GAGTAGATGAG
Integrated DNA Technologies (IDT) N/A
Murine CXCL10 gene: F: GCTGGGATTCACCTCAAGAA
R: CTTGGGGACACCTTTTAGCA Human CXCL10 gene:
F: GTGGCATTCAAGGAGTACCTC R: TGATGGCCTTC
GATTCTGGATT
Integrated DNA Technologies (IDT) N/A
Human CCL3 gene: F: ATGCAGGTCTCCACTGCTGCCCTT
R: GCACTCAGCTCCAGGTCGCTGACAT
Integrated DNA Technologies (IDT) (Chui and Dorovini-Zis, 2010)
Murine CCL5 gene: F: GCTGCTTTGCCTACCTCTCC
R: TCGAGTGACAAACACGACTGC
Integrated DNA Technologies (IDT) N/A
Murine IL-6 gene: F: ACAACCACGGCCTTCCCTAC
R:TCTCATTTCCACGATTTCCCAG Human IL-6 gene:
F: ACTCACCTCTTCAGAACGAATTG R: CCATCTTT
GGAAGGTTCAGGTTG
Integrated DNA Technologies (IDT) N/A
Murine IL-1B gene:F: GCAACTGTTCCTGAACTCAACT
R: ATCTTTTGGGGTCCGTCAACT Human IL-1B gene:
F: CCACAGACCTTCCAGGAGAATG R: GTGCAGTTC
AGTGATCGTACAGG
Integrated DNA Technologies (IDT) N/A
Human NOS2 gene: F: AGGGACAAGCCTACCCCTC
R: CTCATCTCCCGTCAGTTGGT
Integrated DNA Technologies (IDT) N/A
Human IRF7 gene: F: GCTGGACGTGACCATCATGTA
R: GGGCCGTATAGGAACGTGC
Integrated DNA Technologies (IDT) N/A
Human TNFAIP3 gene: F: TTGTCCTCAGTTTCGGGAGAT
R: ACTTCTCGACACCAGTTGAGTT
Integrated DNA Technologies (IDT) N/A
Murine AXL gene: F: ATGGCCGACATTGCCAGTG
R: CGGTAGTAATCCCCGTTGTAGA
Integrated DNA Technologies (IDT) (Zou et al., 2020)
Murine B2M gene: F: ACAGTTCCACCCGCCTCACATT
R: TAGAAAGACCAGTCCTTGCTGAAG
Integrated DNA Technologies (IDT) N/A
Murine AIF1 gene: F: TCTGCCGTCCAAACTTGAAGCC
R: CTCTTCAGCTCTAGGTGGGTCT
Integrated DNA Technologies (IDT) N/A
Human IBA1 gene: F: CCCTCCAAACTGGAAGGCTTCA
R: CTTTAGCTCTAGGTGAGTCTTGG
Integrated DNA Technologies (IDT) N/A
Human CD11B gene: F: GGAACGCCATTGTCTGCTTTCG
R: ATGCTGAGGTCATCCTGGCAGA
Integrated DNA Technologies (IDT) N/A
Murine SLC1A2 gene: F: ACAATATGCCCAAGCAGGTAGA
R: CTTTGGCTCATCGGAGCTGA
Integrated DNA Technologies (IDT) N/A
Murine GFAP gene: F: CGGAGACGCATCACCTCTG
R: AGGGAGTGGAGGAGTCATTCG
Integrated DNA Technologies (IDT) N/A
Murine FGFR3 gene: F: GGAGGACGTGGCTGAAGAC
R: GGAGCTTGATGCCCCCAAT
Integrated DNA Technologies (IDT) N/A
Murine AQP4 gene: F: CTTTCTGGAAGGCAGTCTCAG
R: CCACACCGAGCAAAACAAAGAT
Integrated DNA Technologies (IDT) N/A
Murine GJB6 gene: F: ACCAGCATAGGGAAGGTGTG
R: TGCAGAGTGTTGCAGACAAAG
Integrated DNA Technologies (IDT) N/A
Murine GJC2 gene: F: TCCACAATCATTCCACCTTCG
R: CAGAAGCGCACATGAGACAG
Integrated DNA Technologies (IDT) N/A
Murine SOX10 gene: F: ACACCTTGGGACACGGTTTTC
R: TAGGTCTTGTTCCTCGGCCAT
Integrated DNA Technologies (IDT) N/A
Murine SIGLEC4A gene: F: CTGCCGCTGTTTTGGATAATGA
R: CATCGGGGAAGTCGAAACGG
Integrated DNA Technologies (IDT) N/A
Murine MOG gene: F: `AGCTGCTTCCTCTCCCTTCTC
R: ACTAAAGCCCGGATGGGATAC
Integrated DNA Technologies (IDT) N/A
Murine MBP gene: F: GGCGGTGACAGACTCCAAG
R: GAAGCTCGTCGGACTCTGAG
Integrated DNA Technologies (IDT) N/A
Murine HB9/MNX1 gene: F: CAGCACCTTCCAACTGGACCAG
R: TTCGGCACTTCCCCAAGAGGTT
Integrated DNA Technologies (IDT) N/A
Murine ISL1 gene: F: GGTCTCTGGAACATCCCACATTGT
R: CTGTTCCTACTCCCCATTCACT
Integrated DNA Technologies (IDT) N/A
Murine CHAT gene: F: GCTTGAATGGAGCGAATCGTTGG
R: CACCAGGACGATGCCATCAAAAG
Integrated DNA Technologies (IDT) N/A
Murine ACTB gene: F: CATTGCTGACAGGATGCAGAAGG
R: TGCTGGAAGGTGGACAGTGAGG Human ACTB gene:
F: ACTGGAACGGTGAAGGTGAC R: GTGGACTTGGGA
GAGGACTG
Integrated DNA Technologies (IDT) N/A
MT-DNA D-LOOP: F: AATCTACCATCCTCCGTGAAACC
R: TCAGTTTAGCTACCCCCAAGTTTAA
Integrated DNA Technologies (IDT) N/A
MT-DNA MT-CO1: F: GACGTAGACACACGAGCATATTTCA
R: AGGACATAGTGGAAGTGAGCTACAAC
Integrated DNA Technologies (IDT) N/A
MT-DNA MT-ND1: F: CCACCTCTAGCCTAGCCGTTTA
R: GGGTCATGATGGCAGGAGTAAT
Integrated DNA Technologies (IDT) N/A
MT-DNA MT-ATP6: F: TAGCCATACACAACACTAAA
GGACGA R: GGGCATTTTTAATCTTAGAGCGAAA
Integrated DNA Technologies (IDT) N/A
Nuclear TERT gene: F: CTAGCTCATGTGTCAAGACCC
TCTT R: GCCAGCACGTTTCTCTCGTT
Integrated DNA Technologies (IDT) N/A
RIG-I/DDX58 sgRNA (Human): 5′-GGATTAT
ATCCGGAAGACCC-3′
Applied Biological Materials Inc. N/A
MDA5/IFIH1 sgRNA (Human): 5′-CGAATTCC
CGAGTCCAACCA-3′
Applied Biological Materials Inc. (Ng et al., 2020)
MAVS sgRNA (Human): 5′-ATTGCGGCAGAT
ATACTTAT-3′
Applied Biological Materials Inc. N/A
GJA1 (CX43) sgRNA (Human): 5′-CTTGTCAA
GGAGTTTGCCTA-3′
Applied Biological Materials Inc. N/A
GJC1 (CX45) sgRNA (Human): 5′-ATCGTCCTT
ACAGCTGTAGG-3′
Applied Biological Materials Inc. N/A
GJD2 (CX36) sgRNA (Human): 5′-AGCACTCCA
CTATGATCGGG-3′
Applied Biological Materials Inc. N/A
PANX1 sgRNA (Human): 5′-AATCGAGATCTC
CTGCGCGA-3′
Applied Biological Materials Inc. N/A
TBK1 sgRNA (Human): 5′-AGAGCACTTCTAA
TCATCTG-3′
Applied Biological Materials Inc. N/A
IRF3 sgRNA (Human): 5′-TTGGAAGCACGG
CCTACGGC-3′
Applied Biological Materials Inc. N/A
TICAM1/TRIF sgRNA (Human): 5′-GTAGGCC
ACGTCCCGCAGCG-3′
Applied Biological Materials Inc. N/A
cGAS/MAB21L3 sgRNA (Human): 5′-ATGGC
CTTTCCGTGCCA-3′
Applied Biological Materials Inc. N/A
STING/TMEM173 sgRNA (Human): 5′-ACGGG
ATGGATGGATGC-3′
Applied Biological Materials Inc. N/A
STAT1 sgRNA (Human): 5′-TCCCATTACAGG
CTCAGTCG-3′
Applied Biological Materials Inc. N/A
TFAM sgRNA (Human): 5′-GCGTTTCTCCG
AAGCATGTG-3′
Applied Biological Materials Inc. N/A
DDX41 sgRNA (Human): 5′-AAGAGCGACAT
GAGCGCGTG-3′
Applied Biological Materials Inc. N/A
siRNAs targeting human PPID gene: ID: s10913, s10914, and s10915 Thermo Fisher Cat#4390824
siRNAs targeting human ZBP1 gene: ID: s37484, and s37485 Thermo Fisher Cat#4390420
siRNAs targeting human IFI16 gene: ID: s7136, and s7137 Thermo Fisher Cat#4392420

Recombinant DNA

p125-Luciferase reporter (IFN-β) From Dr. Takashi Fujita (Kyoto University, Japan) (Yoneyama et al., 1998)
p55C1B-Luciferase reporter (IRF3) From Dr. Takashi Fujita (Kyoto University, Japan) (Narita et al., 2014)
p55A2-Luciferase reporter (NF-κB) From Dr. Takashi Fujita (Kyoto University, Japan) (Narita et al., 2014)
pEF-Tak-Flag-MAVS From Dr. Takashi Fujita (Kyoto University, Japan) (Onoguchi et al., 2010)
pEF-Flag-IRF3 5D From Dr. Takashi Fujita (Kyoto University, Japan) (Mori et al., 2004)
pcDNA-Flag-cGAS WT, ΔcGAMP, ΔDNA, K394E, and Y215E. From Dr. Nelson O. Gekara (Stockholm University, Sweden) (Jiang et al., 2019)
pEGFP-SOD1-WT, G93A, and G85R From Dr. Neil R. Cashman (UBC, Canada) (Pokrishevsky et al., 2017)
pcDNA-Flag-SOD1-WT, A4V, G37R, H46R, E100G, G93A, G85R, V148G, V148I, and G127X From Dr. Christine Vande Velde (Université deMontréal, Canada) (Semmler et al., 2020)
pGL4.32 (luc2P/NF-κB-RE/Hygro) Promega Cat#E8491
pRL-TK Renilla Luciferase Control reporter vector Promega Cat#E2231

Software and algorithms

Prism version 8.0 GraphPad https://www.graphpad.com/
Microsoft Office Home and Student 2019 Microsoft Corporation https://www.microsoft.com/microsoft-365
Adobe Illustrator 2020 Adobe Inc. http://www.adobe.com