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4 protocols using anti traf3

1

Comprehensive Cell Lysis and Immunoblotting

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Cells were washed twice with ice-cold phosphate-buffered saline (PBS; Wisent), harvested and lysed in 10mM Tris-HCl, 100mM NaCl, 0.5% Triton X-100, pH7.6 with EDTA-free Protease Inhibitor Cocktail (Roche). Cell lysates were clarified by centrifugation at 13,000 g for 20 min at 4°C and subjected to sodium dodecyl sulfate-polyacrylamide gel (SDS-PAGE). Western blot analysis was performed using mouse anti-PHF5A (Abnova), anti-IRF3 (Santa Cruz), anti-TRAF3 (Santa Cruz), anti-RIG-I (Alexis Biochemicals), anti-ACTIN (Chemicon International), anti-TBK1 (Imgenex and Santa Cruz), anti-IKBKE (Santa Cruz), anti-TUBULIN (ICN), anti-GAPDH (RDI) and rabbit anti-SNRNP200 (Sigma-Aldrich), anti-SF3A1 (Santa Cruz), anti-RELA (Santa Cruz), anti-NHP2L1 (Abcam), anti-DDX3X (Bethyl), anti-DDX60 (Abcam), TRIF (Cell Signaling), anti-ISG56 (Novus Biologicals), anti-MDA5 (Alexis Biochemicals), anti-MAVS (Alexis Biochemicals), anti-IKBKE (eBioscience), STAT1 (ABCAM), STAT1 tyr701 (ABCAM), IFNAR1 (Santa Cruz) and anti-IRF3-P-ser386 (Abcam). HRP-conjugated secondary antibodies were from Bio-Rad. The chemiluminescence reaction was performed using the Western Lighting Chemiluminescence Reagent Plus (PerkinElmer).
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2

Antibody Immunoblotting for Cellular Signaling

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Antibodies against phosphorylated and total IRF3, IKKε, TBK1, NF-κB p65, ERK, JNK, and p38 were purchased from Cell Signaling Technology (Danvers, MA, USA). Anti-TRAF3, anti-β-actin, and HRP-conjugated secondary antibodies were from Santa Cruz. Anti-Myc, anti-Flag, anti-HA, and anti-GFP were from Origene. Anti-PINK1, anti-Parkin, and anti-YAP1 were from Abcam Biotechnology (Cambridge, UK). Anti-K48-ubiquitin and anti-K63-ubiquitin were from Millipore (Kenilworth, USA).
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3

Western Blot Analysis of Proteins

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Proteins were extracted from the ultracentrifugation pellets and separated on a denatured SDS-polyacrylamide gel before transfer to a polyvinylidene difluoride membrane (0.45 um; Millipore, Bedford, MA, USA). Afterwards, the membranes were blocked with 5% non-fat dry milk in Tris-buffered saline with Tween 20 (TBST) for 1 hour. The membranes were probed with primary anti-TRAF3 (1:200, Santa Cruz, sc-949), anti-PTEN (1:1000, Cell Signaling, #9559), anti-p65 (1:200, Santa Cruz, sc-372), anti-NIK (1:200, Santa Cruz, sc-7211) or anti-NFATc1 (1:1000, Cell Signaling, #8032), respectively. To check the amount of proteins transferred to nitrocellulose membrane, GAPDH was used as control and detected by an anti-GAPDH (1:500; Santa Cruz, sc-25778) antibody. The membranes were then washed three times with TBST and incubated for 1 hour with HRP-conjugated secondary antibodies (1:2000; Santa Cruz, sc-2004). The antigen-antibody complexes were visualized using SuperSignal® West Dura Extended Duration Substrate (Thermo Scientific, Prod # 34075). Supplementary Fig. 7 depicts uncropped western blots.
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4

Immunoblotting and Immunofluorescence Antibody Dilutions

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Antibodies used for immunoblotting and their corresponding dilutions were anti-MAVS (Santa Cruz Biotech sc-365334; 1:500), anti-TOM20 (Santa Cruz Biotech sc-11415; 1:300), anti-alpha Sr-1 (Abcam ab28052; 1:1,500), anti-β-actin (Santa Cruz Biotech sc-1615-hrp, 1:2,000), anti-MFN2 (Cell Signaling #9482; 1:800), anti-TBK1 (Cell Signaling #3504; 1:1,000), anti-phospho-TBK1 (Ser172) (Cell Signaling #5483; 1:700), goat anti-rabbit IgG-HRP (Millipore #12-348; 1:2000), and goat anti-mouse IgG-HRP (Millipore #12-349; 1:2,000). Primary antibodies used for immunofluorescence were anti-MAVS (Santa Cruz Biotech sc-365334; 1:100 dilution), anti-TOM20 (Abcam ab56783; 1:100 dilution), anti-FACL4 (Thermo PA5-27137; 1:50), anti-PMP70 (Abcam ab3424; 1:650), anti-MFN2 (Cell Signaling #9482; 1:50), anti-TRAF3 (Santa Cruz Biotech sc-1828or Thermo Fisher Scientific PA1-41107; 1:50), anti-alpha Sr-1 (Abcam ab28052; 1:50), anti-vimentin (Thermo Fisher Scientific PA1-16759; 1:2,000), anti-GM130 (BD Biosciences #610822; 1:250), anti-reovirus σ1 5C6 and G5 ((95 (link)); mix of 1:2,500 each; Fig. 6B), and rabbit anti-reovirus T3D antisera (B. Sherry, unpublished; 1:2,000; Fig S5). Secondary antibodies were Alexa® 488-, Alexa® 594- or Alexa® 647-conjugated goat anti-mouse, anti-rabbit or anti-chicken IgG (Thermo Fisher Scientific; 1:750 - 1:1,000).
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