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. 2020 Oct 29;183(3):636–649.e18. doi: 10.1016/j.cell.2020.09.020
REAGENT or RESOURCE SOURCE IDENTIFIER
Antibodies

Rabbit monoclonal anti-phospho-TBK1/NAK (Ser172) (D52C2) antibody Cell Signaling Technology Cat# 5483; RRID: AB_10693472
Rabbit monoclonal anti-TBK1/NAK (D1B4) antibody Cell Signaling Technology Cat# 3504; RRID: AB_2255663
Rabbit monoclonal anti-phospho-IRF-3 (Ser396) (D6O1M) antibody Cell Signaling Technology Cat# 29047; RRID: AB_2773013
Rabbit polyclonal anti-IRF-3 (FL-425) antibody Santa Cruz Biotechnology Cat# sc-9082; RRID: AB_2264929
Rabbit monoclonal anti-phospho-NF-κB p65 (Ser536) (93H1) antibody Cell Signaling Technology Cat# 3033; RRID: AB_331284
Rabbit monoclonal anti-NF-κB p65 (C22B4) antibody Cell Signaling Technology Cat# 4764; RRID: AB_823578
Rabbit monoclonal anti-TFAM (D5C8) antibody Cell Signaling Technology Cat# 8076; RRID: AB_10949110
Rabbit monoclonal anti-STING (D2P2F) antibody Cell Signaling Technology Cat# 13647; RRID: AB_2732796
Rabbit monoclonal anti-cleaved Caspase-3 (Asp175) (5A1E) antibody Cell Signaling Technology Cat# 9664; RRID: AB_2070042
Rabbit polyclonal anti-GFP antibody Thermo Fisher Scientific Cat# A-11122; RRID: AB_221569
Rabbit polyclonal anti-TDP-43 antibody Thermo Fisher Scientific Cat# PA5-27221; RRID: AB_2544697
Rabbit polyclonal anti-AGK antibody Atlas Antibodies Cat# HPA020959; RRID: AB_1854206
Rabbit monoclonal anti-Cyclophilin F [EPR11311-121] antibody Abcam Cat# ab231155
Rabbit polyclonal anti-MAVS (Rodent specific) antibody Cell Signaling Technology Cat# 4983; RRID: AB_823566
Rabbit monoclonal anti-Histone H3 (D1H2) antibody Cell Signaling Technology Cat# 4499; RRID: AB_10544537
Rabbit monoclonal anti-GAPDH (14C10) antibody Cell Signaling Technology Cat# 2118; RRID: AB_561053
Mouse monoclonal anti-ATP5A antibody [15H4C4] Abcam Cat# ab14748
Mouse monoclonal anti-PKR (B-10) antibody Santa Cruz Biotechnology Cat# sc-6282; RRID: AB_628150
Mouse monoclonal anti-cGAS (D-9) antibody Santa Cruz Biotechnology Cat# sc-515777; RRID: AB_2734736
Rat monoclonal anti-FLAG (9H1) antibody In-House N/A
Mouse monoclonal anti-β-Actin (C4) antibody Santa Cruz Biotechnology Cat# sc-47778 HRP; RRID: AB_2714189
Mouse monoclonal anti-DNA (AC-30-10) antibody Progen Cat# 61014; RRID: AB_2750935
Rabbit monoclonal anti-TOMM20 [EPR15581-54] Alexa Fluor 647 antibody Abcam Cat# ab209606
Rabbit polyclonal anti-TIMM44 antibody Sigma-Aldrich Cat# HPA043052; RRID: AB_10795713
Goat anti-Rat IgG H&L Alexa Fluor 405 antibody Abcam Cat# ab175671
Goat anti-Mouse IgG (H+L) Cross-Adsorbed Secondary Antibody Alexa Fluor 488 antibody Thermo Fisher Scientific Cat# A-11001; RRID: AB_25344069
Goat anti-Rabbit IgG (H+L) Cross-Adsorbed Secondary Antibody Alexa Fluor 568 antibody Thermo Fisher Scientific Cat# A-11011; RRID: AB_143157
Rabbit polyclonal anti-MNX1 (HB9) antibody Millipore Cat# ABN174; RRID: AB_27322012
Goat polyclonal anti-Choline Acetyltransferase antibody Millipore Cat# AB144P; RRID: AB_2079751
Mouse monoclonal anti-βIII Tubulin (5G8) antibody Promega Cat# G7121; RRID: AB_430874
Rat monoclonal anti-Myc tag [9E10] antibody Abcam Cat# ab206486
Anti-FLAG M2 Affinity Gel antibody Sigma Aldrich Cat# A2220; RRID: AB_10063035

Biological Samples

Human post-mortem spinal cord tissues (sALS and MS) Victorian Brain Bank Table S1

Chemicals, Peptides, and Recombinant Proteins

FuGENE HD Transfection Reagent Promega Cat# E2311
Lipofectamine 2000 Transfection Reagent Thermo Fisher Scientific Cat# 11668030
Ethidium bromide Sigma-Aldrich Cat# E8751; CAS 1239-45-8
Uridine Sigma-Aldrich Cat# U3003; CAS 58-96-8
Geneticin Selective Antibiotic (G418 Sulfate) Thermo Fisher Scientific Cat# 11811023; CAS 108321-42-2
Doxycycline hyclate Sigma-Aldrich Cat# D9891; CAS 24390-14-5
Blasticidin InvivoGen Cat# ant-bl-1
Poly(dA:dT) InvivoGen Cat# tlrl-patn; CAS 86828-69-5
Deoxyribonucleic acid sodium salt from herring testes (HT-DNA) Sigma-Aldrich Cat# D6898; CAS 438545-06-3
2′3′-c-di-AM(PS)2(Rp, Rp) InvivoGen Cat# tlrl-nacda2r; CAS 1638750-95-4
ABT-737 Active Biochemicals Cat# A-1002; CAS 852808-04-9
MitoSOX™ Red Thermo Fisher Scientific Cat# M36008
Tetramethylrhodamine methyl ester perchlorate (TMRM) Thermo Fisher Scientific Cat# T5428; CAS 115532-50-8
Cyclosporin A Sigma-Aldrich Cat# C3662; CAS 59865-13-3
RU.521 (cGAS inhibitor) M. Ascano Laboratory Vincent et al., 2017
H-151 (STING inhibitor) Life Chemicals Haag et al., 2018
Mitoquinol Cayman Chemical Cat# 89950; CAS 845959-55-9
MitoTEMPO (hydrate) Cayman Chemical Cat# 16621; CAS 1569257-94-8
TDP-43 inhibitor peptide PM1 (YGRKKRRQRRRAQFPGACGL) This paper Wang et al., 2016
TDP-43 control peptide CM1 (YGRKKRRQRRRAAQGFGCPL) This paper Wang et al., 2016
Primocin InvivoGen Cat# ant-pm-1
Y-27632 (RHO/ROCK pathway inhibitor) STEMCELL Technologies Cat# 72304; CAS 129830-38-2
CHIR99021 (GSK3 inhibitor) STEMCELL Technologies Cat# 72054; CAS 252917-06-9
Dorsomorphin (BMP and AMPK inhibitor) STEMCELL Technologies Cat# 72102; CAS 866405-64-3
SB431542 Hydrate (Activin/BMP/TGF-b pathway inhibitor) STEMCELL Technologies Cat# 72234; CAS 301836-41-9
All trans-Retinal Sigma-Aldrich Cat# R2500; CAS 116-31-4
Purmorphamine (Hedgehog pathway activator) STEMCELL Technologies Cat# 72202; CAS 483367-10-8
L-Ascorbic acid Sigma-Aldrich Cat# A4403; CAS 50-81-7
Valproic Acid (Sodium Salt) STEMCELL Technologies Cat# 72292; CAS 1069-66-5
Compound E STEMCELL Technologies Cat# 73954; CAS 209986-17-4
Paraformaldehyde 16% aqueous solution ProSciTech Cat# C004; CAS 30525-89-4
Glutaraldehyde solution Sigma-Aldrich Cat# 340855; CAS 111-30-8
VBIT-4 (VDAC1 oligomerization inhibitor) MedChemExpress Cat# HY-129122; CAS 2086257-77-2
Digitonin Sigma-Aldrich Cat# D141; CAS 11024-24-1
cOmplete Protease Inhibitor Cocktail Roche Biochemicals Cat# 11836145001
IGF1 recombinant human protein Thermo Fisher Scientific Cat# PHG0078
RPMI-1640 In-House N/A
Dulbecco’s Modified Eagle Medium (DMEM) Thermo Fisher Scientific Cat# 11965092
DME/KELSO Medium In-House N/A
Hank’s Balanced Salt Solution (HBSS) Thermo Fisher Scientific Cat# 14170112
Matrigel hESC-Qualified Matrix Corning Cat# 354277
mTeSR™1 STEMCELL Technologies Cat# 85850
ReLeSR STEMCELL Technologies Cat# 05872
KnockOut DMEM/F-12 Thermo Fisher Scientific Cat# 12660012
Neurobasal Medium Thermo Fisher Scientific Cat# 21103049
N-2 Supplement (100X) Thermo Fisher Scientific Cat# 17502048
B-27 Supplement (50X) Thermo Fisher Scientific Cat# 17504044
Accutase cell detachment solution STEMCELL Technologies Cat# 07920
TrypLE Express Enzyme Thermo Fisher Scientific Cat# 12604013
Normal Goat Serum (10%) Thermo Fisher Scientific Cat# 50062Z

Critical Commercial Assays

QuikChange Lightning Mutagenesis Kit Agilent Technologies Cat# 210513
Lactate Dehydrogenase Activity Assay Kit Sigma-Aldrich Cat# MAK066
VeriKine-HS Mouse Interferon Beta Serum ELISA Kit PBL Assay Science Cat# 42410-1
VeriKine-HS Human Interferon Beta Serum ELISA Kit PBL Assay Science Cat# 41415-1
Human CXCL10/IP-10 Quantikine ELISA kit R&D Sysytems Cat# SIP100
2′3′-cGAMP ELISA Kit Cayman Chemical Cat# 501700

Deposited Data

Original blots This paper Mendeley Data: https://doi:10.17632/kx9v83c65r.1

Experimental Models: Cell Lines

Human embryonic kidney (HEK) 293T ATCC CRL-3216
AGKFlp-In control HEK293T Diana Stojanovski Laboratory Kang et al., 2017
AGK−/− HEK293T Diana Stojanovski Laboratory Kang et al., 2017
AGK−/− +WT HEK293T Diana Stojanovski Laboratory Kang et al., 2017
AGK−/− +G126E-3XFLAG HEK293T Diana Stojanovski Laboratory Kang et al., 2017
THP-1 human monocytic cells (sex: male, age: 1) ATCC TIB-202
THP-1 Cas9-mCherry cells This paper N/A
THP-1 pSLIK-neo cells This paper N/A
THP-1 pSLIK-TDP-43 WT cells This paper N/A
THP-1 pSLIK-TDP-43 Q331K cells This paper N/A
THP-1 STINGCRISPR−/− cells This paper N/A
THP-1 STINGCRISPR−/− pSLIK-neo cells This paper N/A
THP-1 STINGCRISPR−/− pSLIK-TDP-43 WT cells This paper N/A
THP-1 STINGCRISPR−/− pSLIK-TDP-43 Q331K cells This paper N/A
WT Immortalized mouse embryonic fibroblasts (MEFs) (sex: ND) This paper N/A
MAVS−/− MEFs (sex: ND) Sandra Nicholson Laboratory Nguyen et al., 2017
cGAS−/− MEFs (sex: ND) Benjamin Kile Laboratory White et al., 2014
STING−/− MEFs (sex: ND) Benjamin Kile Laboratory White et al., 2014
Bak−/−/Bax−/− MEFs (sex: ND) Benjamin Kile Laboratory White et al., 2014
Vdac1−/−/Bak−/− MEFs (sex: ND) Grant Dewson Laboratory Chin et al., 2018
Vdac1−/−/Bax−/− MEFs (sex: ND) Grant Dewson Laboratory Chin et al., 2018
PKR−/− MEFs (sex: ND) Anthony Sadler Laboratory Irving et al., 2012
Mcl1−/− Cas9/Blasticidin MEFs This paper N/A
Mcl1−/− pSLIK-neo MEFs This paper N/A
Mcl1−/− pSLIK-hTDP-43 WT MEFs This paper N/A
Mcl1−/− pSLIK-hTDP-43 Q331K MEFs This paper N/A
PpidCRISPR−/− pSLIK-neo MEFs This paper N/A
PpidCRISPR−/− pSLIK-hTDP-43 WT MEFs This paper N/A
PpidCRISPR−/− pSLIK-hTDP-43 Q331K MEFs This paper N/A
Mouse motor neuron-like hybrid cells NSC-34 (sex: ND) Cellutions Biosystems CLU140
pSLIK-neo NSC-34 This paper N/A
pSLIK-hTDP-43 WT NSC-34 This paper N/A
pSLIK-hTDP-43 Q331K NSC-34 This paper N/A
Human iPSC healthy control HC1 (NCRM-1) (male, cord blood) National Institute of Neurological Disorders and Stroke Efthymiou et al., 2015
Human iPSC healthy control HC2 (NCRM-5) (male, cord blood) National Institute of Neurological Disorders and Stroke Efthymiou et al., 2015
Human iPSC healthy control HC3 (WT1) (sex: ND, age: 8) Alessandro Rosa Laboratory Lenzi et al., 2015
Human iPSC healthy control HC4 (female, age: 62) This paper N/A
Human iPSC healthy control HC5 (male, age: 74) This paper N/A
Human iPSC healthy control HC6 (female, age: 88) This paper N/A
Human iPSC ALS-TARDBP G298S (TALSTDP-47.10) (male, age: 43) Target ALS Foundation RRID: CVCL_FA03
Human iPSC ALS-TARDBP M337V (CiRA00026) (female, age: 62) Cell Bank Riken BioResource Research Center RRID: CVCL_T783 (Egawa et al., 2012)
Human iPSC ALS-TARDBP A382T (male, age: 50) Alessandro Rosa Laboratory Lenzi et al., 2015
Human iPSC ALS-C9ORF72 HRE 1 (female, age: 56) This paper N/A
Human iPSC ALS-C9ORF72 HRE 2 (male, age: 59) This paper N/A
Human iPSC ALS-C9ORF72 HRE 3 (male, age: 52) This paper N/A
Human iPSC ALS-SOD1 1 (G93A) (male, age: 47) This paper N/A
Human iPSC ALS-SOD1 2 (I114T) (sex: male, age: 62) This paper N/A
Human iPSC ALS-SOD1 3 (G85S) (sex: female, age: 29) This paper N/A
Mouse primary bone marrow-derived macrophages (WT) (sex: male, age d150) This paper N/A
Mouse primary bone marrow-derived macrophages (Prp-TDP-43Tg/+) (sex: male, age d150) This paper N/A

Experimental Models: Organisms/Strains

Mouse: C57BL/6J (WT) Jackson Laboratory Cat# 000664
Mouse: B6.Cg-Tg(Prnp-TARDBPA315T)95Balo/J (Prp-TDP-43Tg/+) Jackson Laboratory Cat# 010700
Mouse: Prp-TDP-43Tg/+ x Sting+/− This paper N/A
Mouse: Prp-TDP-43Tg/+ x Sting−/− This paper N/A

Oligonucleotides

Genotyping: Human TARDBP (A315T) forward https://www.jax.org/Protocol?stockNumber=010700&protocolID=26362 GGATGAGCTGCGGGAGTTCT
Genotyping: Human TARDBP (A315T) reverse https://www.jax.org/Protocol?stockNumber=010700&protocolID=26362 TGCCCATCATACCCCAACTG
Genotyping: Mouse Sting forward This paper GCTGGGAATTGAACGTAGGA
Genotyping: Mouse Sting reverse This paper GAGGAGACAAAGGCAAGCAC
Genotyping: Mouse Sting KO forward This paper GTGCCCAGTCATAGCCGAAT
Human TARDBP A315T mutagenesis forward This paper GGATTAATGCTGAA
CGTACCAAAGTTCATCCCACCA
Human TARDBP A315T mutagenesis reverse This paper TGGTGGGATGAACT
TTGGTACGTTCAGCATTAATCC
Human TARDBP Q331K mutagenesis forward This paper CCCCAACTGCTCTT
TAGTGCTGCCTGGGC
Human TARDBP Q331K mutagenesis reverse This paper GCCCAGGCAGCACT
AAAGAGCAGTTGGGG
Human STING sgRNA forward This paper AGAGCACACTCTCCGGTACC
Human STING sgRNA reverse This paper GGTACCGGAGAGTGTGCTCT
Mouse Ppid sgRNA forward This paper CGTGCCAAAGACTGCAGGTA
Mouse Ppid sgRNA reverse This paper TACCTGCAGTCTTTGGCACG
qPCR: Human IFNB1 forward Balka et al., 2020 TGTCGCCTACTACCTGTTGTGC
qPCR: Human IFNB1 reverse Balka et al., 2020 AACTGCAACCTTTCGAAGCC
qPCR: Human TNF forward Balka et al., 2020 TCTCTCAGCTCCACGCCATT
qPCR: Human TNF reverse Balka et al., 2020 CCCAGGCAGTCAGATCATCTTC
qPCR: Human MNX1 forward This paper GCACCAGTTCAAGCTCAAC
qPCR: Human MNX1 reverse This paper GCTGCGTTTCCATTTCATCC
qPCR: Human CHAT forward This paper AGCCTCATCTCTGGTGTACTC
qPCR: Human CHAT reverse This paper GCCCATAGTATTGCTTCATGC
qPCR: Human HPRT forward Balka et al., 2020 TCAGGCAGTATATCCAAAGATGGT
qPCR: Human HPRT reverse Balka et al., 2020 AGTCTGGCTTATATCCAACACTTCG
qPCR: Mouse Ifnb1 forward Balka et al., 2020 CCAGCTCCAAGAAAGGACGA
qPCR: Mouse Ifnb1 reverse Balka et al., 2020 TGGATGGCAAAGGCAGTGTA
qPCR: Mouse Ifna6 forward This paper GCTTTCCTGATGGTTTTGGTG
qPCR: Mouse Ifna6 reverse This paper AGGCTTTCTTGTTCCTGAGG
qPCR: Mouse Ifit1 forward This paper AGAGTCAAGGCAGGTTTCTG
qPCR: Mouse Ifit1 reverse This paper TGTGAAGTGACATCTCAGCTG
qPCR: Mouse Mx1 forward This paper GATCCGACTTCACTTCCAGATGG
qPCR: Mouse Mx1 reverse This paper CATCTCAGTGGTAGTCAACCC
qPCR: Mouse Irf7 forward This paper AAGCTGGAGCCATGGGTATG
qPCR: Mouse Irf7 reverse This paper CGATGTCTTCGTAGAGACTGTTGG
qPCR: Mouse Tnf forward Balka et al., 2020 CCAAATGGCCTCCCTCTCAT
qPCR: Mouse Tnf reverse Balka et al., 2020 TGGTGGTTTGCTACGACGTG
qPCR: Mouse Il1b forward Balka et al., 2020 TTGACGGACCCCAAAAGATG
qPCR: Mouse Il1b reverse Balka et al., 2020 CAGCTTCTCCACAGCCACAA
qPCR: Mouse Il6 forward Balka et al., 2020 CCAGAAACCGCTATGAAGTTCC
qPCR: Mouse Il6 reverse Balka et al., 2020 CGGACTTGTGAAGTAGGGAAGG
qPCR: Mouse Hprt forward Balka et al., 2020 TGAAGTACTCATTATAGTCAAGGGCA
qPCR: Mouse Hprt reverse Balka et al., 2020 CTGGTGAAAAGGACCTCTCG
DNA assay: Human MT-ND1 forward This paper CTCTTCGTCTGATCCGTCCT
DNA assay: Human MT-ND1 reverse This paper TGAGGTTGCGGTCTGTTAGT
DNA assay: Human MT-ND2 forward This paper GTAGACAGTCCCACCCTCAC
DNA assay: Human MT-ND2 reverse This paper TTGATCCCGTTTCGTGCAAG
DNA assay: Human POLG1 forward This paper CTGCCATAAGGTCTGCAGGT
DNA assay: Human POLG1 reverse This paper CTCCTTTCCGTCAACAGCTC
DNA assay: Human L1ORF1 gDNA forward Papasotiriou et al., 2017 AGAACGCCACAAAGATACTCCTCG
DNA assay: Human L1ORF1 gDNA reverse Papasotiriou et al., 2017 CTCTCTTCTGGCTTGTAGGGTTTCTG
DNA assay: Mouse Nd1 forward White et al., 2014 CAAACACTTATTACAACCCAAGAACA
DNA assay: Mouse Nd1 reverse White et al., 2014 TCATATTATGGCTATGGGTCAGG
DNA assay: Mouse Nd2 forward White et al., 2014 CCATCAACTCAATCTCACTTCTATG
DNA assay: Mouse Nd2 reverse White et al., 2014 GAATCCTGTTAGTGGTGGAAGG
DNA assay: Mouse L1 gDNA forward Newman et al., 2012 TAGGAAATTAGTTT
GAATAGGTGAGAGGGT
DNA assay: Mouse L1 gDNA reverse Newman et al., 2012 TCCAGAAGCTGTCAGGTTCTCTGGC
DNA assay: RNA18S gDNA forward Chang et al., 2013 GTAACCCGTTGAACCCCATT
DNA assay: RNA18S gDNA reverse Chang et al., 2013 CCATCCAATCGGTAGTAGCG

Recombinant DNA

pSLIK-Neo Aaron D. Gitler Laboratory Armakola et al., 2012
pSLIK-hTDP-43 Aaron D. Gitler Laboratory Armakola et al., 2012
pSLIK-hTDP-43 Q331K Aaron D. Gitler Laboratory Armakola et al., 2012
pGW1-hTDP-43-EGFP Steven Finkbeiner Laboratory Armakola et al., 2012
pGW1-hTDP-43 A315T-EGFP This paper N/A
pGW1-hTDP-43 Q331K-EGFP This paper N/A
pMIH-FLAG-mmcGAS Benjamin Kile Laboratory White et al., 2014

Software and Algorithms

Fiji https://fiji.sc/ RRID: SCR_002285
Image Lab https://www.bio-rad.com/en-us/sku/1709690-image-lab-software RRID: SCR_014210
Prism 8 https://www.graphpad.com/ RRID: SCR_002798
Imaris https://imaris.oxinst.com/packages RRID: SCR_007370
Adobe Illustrator https://www.adobe.com/products/illustrator.thml RRID: SCR_010279
CaseViewer https://www.3dhistech.com/solution/caseviewer/ RRID: SCR_017654
FlowJo v.10 https://www.flowjo.com/solutions/flowjo RRID: SCR_008520
MouseMove Samson et al., 2015 N/A