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3 protocols using anti ddx6

1

Antibody Validation for mRNA Decay Factors

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Antibodies used in this study were as follows: rabbit polyclonal anti-DDX6 (Bethyl Laboratories), rabbit polyclonal anti-Pat1b (Bethyl Laboratories), rabbit polyclonal anti-DCP2 (Bethyl Laboratories), mouse monoclonal anti-EDC3 (Abcam), rabbit polyclonal anti-GW182 (Bethyl Laboratories), mouse monoclonal anti-eIF4E (BD Transduction Laboratories), rabbit polyclonal anti-PABP (Abcam), rabbit monoclonal anti-Ago2 (Cell Signaling), mouse monoclonal anti-myc (BioShop Canada Inc.), mouse monoclonal anti-β-actin (Sigma). Rabbit polyclonal antibodies against CNOT1 and CNOT7 were kindly provided by T. Yamamoto.
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2

SARS-CoV-2 Nucleocapsid Protein Interactome

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Cells were lysed in buffer containing 50 mM Tris-HCl (pH 8.0), 150 mM NaCl, 4 mM EDTA, 0.1% NP-40, 10 mM NaF, protease inhibitor cocktail (Nacalai Tesque, Kyoto, Japan). Lysates were precleared with 30 μL of protein-G-Sepharose (GE Healthcare Bio-Sciences). Precleared supernatants were incubated with 5 μg of anti-SARS-CoV-2 nucleocapsid antibody mixture (GTX135357 and GTX632269 [6H3]; GeneTex) or anti-DDX21 (A300-627A; Bethyl Lab), anti-DDX6 (A300-460A; Bethyl Lab), or anti-MOV10 (A301-571A; Bethyl Lab) antibody at 4°C for 1 h. Following absorption of the precipitates on 30 μL of protein G-Sepharose resin for 1 h, the resin was washed four times with 700 μL of lysis buffer. Proteins were eluted by boiling the resin for 5 min in 2× Laemmli sample buffer. The proteins were then subjected to SDS-PAGE, followed by immunoblot analysis using anti-SARS-CoV-2 nucleocapsid (GTX632269 [6H3]), anti-DDX21, anti-DDX6, or anti-MOV10 antibody.
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3

Antibody Generation and Characterization

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Rabbit polyclonal anti-pS316-TTP antibody was generated with the synthesized oligo-peptide PRRLPIFNRI(p)SVSE (Pocono Rabbit Farm & Laboratory, USA). The antiserum was purified by affinity chromatography by first collecting antibody binding to a PRRLPIFNRI(p)SVSE-peptide column, and, after elution, collecting the flow-through from a subsequent unphosphorylated PRRLPIFNRISVSE-peptide column. Immunoblots were probed with the following antibodies at the indicated concentrations: rabbit polyclonal anti-FLAG (Millipore Sigma, F7425; 1:1,000), mouse monoclonal anti-FLAG M2 (Millipore Sigma, F1804; 1:1,000), rabbit polyclonal anti-DDX6 (Bethyl, A300-461A; 1:1,000), rabbit polyclonal anti-GIGYF2 (Santa Cruz Biotechnology, sc-134708; 1:50), mouse monoclonal anti-14-3-3 (Santa Cruz Biotechnology, sc-1657; 1:1,000), rabbit polyclonal anti-TTP (Sigma-Aldrich, T5327; 1:500), rabbit polyclonal anti-CNOT1 (Proteintech, 14276-1-AP; 1:200), rabbit polyclonal anti-CNOT9 (Proteintech, 22503-1-AP, 1:500), mouse monoclonal anti-GAPDH (Cell Signaling Technology, 97166, 1:1,000), rabbit polyclonal anti-EDC4 ((42 (link)); 1:200) rabbit polyclonal anti-pSer178-TTP ((11) a generous gift from Dr. Georg Stoecklin, Heidelberg University; 1:500).
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