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10 protocols using anti myc a 14

1

Antibody Inventory for Cell Biology

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Anti-FLAG rabbit polyclonal antibodies and the anti-FLAG (M2) and anti-β-tubulin (TUB 2.1) mouse monoclonal antibodies were purchased from Sigma-Aldrich; the anti-FLAG mouse monoclonal antibody (1E6) from FUJIFILM Wako Pure Chemical Corporation; the anti-HA mouse monoclonal antibody (16B12) from Covance; the anti-ZO-1 rat monoclonal antibody (R40.76), anti-β-catenin (H-102), anti-HA (Y-11), and anti-Myc (A14) rabbit polyclonal antibodies from Santa Cruz Biotechnology; the anti-Myc (9E10) mouse monoclonal and anti-HA (3F10) rat monoclonal antibodies from Roche Applied Science; anti-MBP rabbit polyclonal antibodies from New England Biolabs; anti-Par3 rabbit polyclonal antibodies from EMD Millipore; the anti-occludin mouse monoclonal antibody (OC-3F10), anti-ZO-1, anti-claudin-1, and anti-claudin-2 rabbit polyclonal antibodies, and Alexa Fluor 647-conjugated anti-ZO-1 mouse monoclonal antibody (ZO-1A12) from Thermo Fisher Scientific; the anti-E-cadherin rabbit monoclonal antibody (24E10) and anti-phospho-myosin light chain 2 (MLC2) (Thr18/Ser19) rabbit polyclonal antibodies from Cell Signaling Technology; anti-TMEM25 rabbit polyclonal antibodies (A13805) from Boster; and the anti-GFP rat monoclonal (GF090R) or mouse monoclonal (GF200) antibodies from Nacalai Tesque.
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2

Immunofluorescence Assay for MERS-CoV N Protein

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Huh-7 cells were transfected with the corresponding expression construct and infected as mentioned 24 h posttransfection. Cells were washed once with PBS and fixed with 4% paraformaldehyde in PBS, followed by permeabilization with 0.1% Triton X-100 in PBS. Cells were further washed with PBS for three times before blocking with 3% BSA in PBS for 1 h. Primary Abs anti-FLAG (M2; Invitrogen) and anti-myc (A14; Santa Cruz Biotechnology) as well as the guinea pig antiserum against N protein of MERS-CoV were diluted at 1:1000, 1:100, and 1:200, respectively, in 3% BSA in PBS for incubation at 4°C overnight. Cells were washed three times with PBS the next day before incubation with secondary Abs AP307R (myc; MilliporeSigma), AP124F (FLAG; MilliporeSigma), and Alexa Fluor 647–conjugated goat anti-guinea pig IgG (H chain + L chain) Ab (A-21450, 1:500; Invitrogen) plus DAPI at 1:200 in 3% BSA in PBS for 1 h at room temperature. Cells were washed with PBS for three times and visualized by confocal microscope.
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3

Protein Quantification by Western Blot

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All antibodies used in this study are listed in Supplementary Table S4. Antibodies against GFP (GF28R, mouse) were used in a dilution of 1:5,000 (Thermo Fisher Scientific), anti-GFP PABG1 (rabbit) 1:4,000 (Chromotek). Anti-myc 9E10 (mouse) or anti-myc A-14 (rabbit) antibodies were used in a dilution of 1:1,000 (Santa Cruz). Antibodies against Hem15 (rabbit) and Dre2 (rabbit) (courtesy of U. Mühlenhoff, Marburg, Germany), Mex67 (rabbit) (courtesy of C. Dargemont, Paris, France), Nop1 28F2 (mouse) (Santa Cruz), Npl3 (rabbit) (custom-made, H. Krebber), Zwf1 (rabbit) (Santa Cruz), Gbp2, Hrb1 (custom-made, H. Krebber) were used in dilutions of 1:10,000, 1:20,000, 1:20,000, 1:4,000, 1:5,000, 1:4,000, 1:50,000, 1:20,000, respectively. Secondary anti-mouse IgG-HRP and anti-rabbit IgG-HRP were diluted 1:20,000 (Dianova) and detected with WesternBright Chemilumineszenz Substrat Quantum (Biozym) and detected with a FUSION-SL or FUSION FX chemiluminescence detection system (Peqlab). Western Blot signals were quantified with the Bio1D software (Peqlab) or the Fiji-software. The signal intensity of the co-precipitated protein bands was related to the intensity of the pulled-down protein bands. The ratio between mutant strains was compared to wild type.
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4

Antibody Characterization for Research

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Antibodies for experiments were as follows: rabbit polyclonal anti-Cse4 (Strunnikov laboratory), anti-Tub2 antibodies (Basrai laboratory), anti-HA (12CA5; Roche, Indianapolis, IN), anti-HA (ab9110; Abcam, Cambridge, MA), anti-myc (A-14; Santa Cruz Biotechnology, Dallas, TX), anti-GST (ab6613; Abcam), anti-Smt3 (y-84; Santa Cruz Biotechnology), and anti-H3 (ab1791; Abcam). Anti-Cse4 was used at a dilution of 1:1000, anti-HA was used at a dilution from 1:1000 to 1:10,000, anti-Tub2 and anti-Smt3 were used at 1:3000, and anti-GST and anti-H3 were used at 1:5000.
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5

Protein Extraction from Embryos

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Embryos were lysed in a buffer consisting of 20 mM Tris–HCl, pH 7.5, 150 mM NaCl, 1.5 mM MgCl2, 2 mM EGTA, 25 mM β-glycerophosphate, 10 mM sodium pyrophosphate, 1 % Nonidet P-40, 10 mM NaF, 1 mM vanadate, 1 mM DTT, and 1× Protein Inhibitor Cocktail (Sigma). Extracts were then centrifuged, and supernatants were collected. Anti-Myc (A14, Santa Cruz), anti-GFP (JL8, Clontech), anti-Rac1 (23A8, Millipore) or anti-α-tubulin (DM1A, Sigma) antibodies were used as primary antibodies, and anti-mouse IgG HRP-conjugated (1:10,000; GE healthcare) and anti-rabbit IgG HRP-conjugated (1:10,000; GE healthcare) were used as secondary antibodies.
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6

Immunofluorescence analysis of tagged proteins in S2 cells

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To coat transfected S2 cells onto cover slides, cover slides are treated with 1% poly-lysine for 30 min, washed with distilled water, 70% EtOH and then air-dried. Cells are loaded onto the treated slides for 30 min incubation, then fixed for 15 min with 4% paraformaldehyde and washed four times for 5 min with PBS. Cells are permeabilized with three 10 min incubations with 0.1% Triton in PBS (PBST) and followed by incubation with blocking buffer (1% Goat serum in PBST) for 1 h. Primary antibody (1:200 of anti-Myc [A14] from Santa Cruz and 1:50 of anti-HA [F7] from Santa Cruz) are added to the blocking buffer and incubated with cells at 4°C overnight. Cells are washed with four 15 min PBST incubation, treated with the secondary antibody (488 anti-mouse, and 568 anti-rabbit) for 1 h, and then washed again with four 15 min PBST incubations. Cells are finally mounted with Vectorshield mounting buffer with DAPI.
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7

Coimmunoprecipitation Protocol for Protein Interactions

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Coimmunoprecipitation experiments were carried out as described previously (Zhang et al. 2008 (link); Gerace and Moazed 2015 (link)). All strains were grown simultaneously in 150 mL cultures to an equal OD595 ≈ 1.5. Pelleted cells were washed with 1× PBS and 0.5 g pellets were saved. Whole-cell lysate (WCE) was obtained through bead beating (425–600 µm Glass Beads, Sigma-Aldrich) and tandem spinning followed by incubation with 2 μL Benzonase (25 unit/µL, EMD Millipore) for 2 h at 16°C. Protein A/G Agarose (Roche) coupled with the appropriate antibody were used to immunoprecipitate Myc-, HA-, and GFP-tagged proteins. FTP-tagged proteins were pulled down directly with IgG Sepharose (GE Healthcare). IP samples were incubated on an end-over-end rotator for 2 h at 4°C before being washed and eluted with 1× SDS Sample Buffer. Immunoprecipitated fractions and the equivalent of 2%–5% of the input extracts were analyzed by Western blot using anti-Flag (M2, Sigma), anti-Myc (A14, Santa Cruz), PAP (Sigma), anti-HA (Y11, Roche), or anti-GFP (Roche) antibodies.
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8

Immunoblot Analysis of NRF3 and Related Proteins

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The antibodies utilized in the current immunoblot analysis were anti-NRF3 (#9408), anti-FLAG (M2; Sigma), anti-α-Tubulin (DM1A; Sigma), anti-Lamin B (Invitrogen), anti-Nrf1 (D5B10; Cell Signaling Technology), anti-HRD1 (D302A; Cell Signaling Technology), anti-VCP (H-120; Santa Cruz), anti-HA (Y-11; Santa Cruz, 3F-10; Roche), anti-Myc (A-14; Santa Cruz), anti-DDI2 (A304-629; Betyl Laboratories) and anti-KIS1 (UHMK1) (a kind gift from Alexandre Maucuer, Universite Pierre et Marie Curie).
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9

Immunoblot Analysis of RLTPR Interactions

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Total proteins were solubilized in extraction buffer (25 mM Tris-HCl, pH 7.6, 150 mM NaCl2, 1% NP-40, 1 mM EDTA, 1× proteinase inhibitor cocktail mix, 1 mM PMSF, and 1 mM Na3VO4). Immunoblot analysis was performed using SDS-PAGE. Immunoblotting was performed using Ab against an N-terminal RLTPR peptide (E-15; Santa Cruz Biotechnology, Inc.), the C-terminal RLTPR peptide 1,186–1,310 (EM-53; Roncagalli et al., 2016 (link)), vinculin (EPR8185; Abcam), and GAPDH (FL335; Santa Cruz Biotechnology, Inc.). For coimmunoprecipitation experiments, V5-tagged and Myc/DDK-tagged RLTPR were cotransfected by X-tremeGENE 9 DNA transfection reagent (Roche) in HEK293T cells. Protein extracts were immunoprecipitated using anti-Myc (A-14; Santa Cruz Biotechnology, Inc.) and agarose A/G beads (Santa Cruz Biotechnology, Inc.) after a background-clearing step with an isotype control and agarose A/G beads (Santa Cruz Biotechnology, Inc.). Immunoprecipitated proteins were subsequently resolved on SDS-PAGE. Blots were probed with anti-DDK (TA50011-1; OriGene) and anti–V5-HRP (R962-25; Invitrogen) Abs.
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10

Polyclonal Antibody Production and Inhibitor Assays

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Purified rabbit polyclonal anti-73uORF antibody was raised using as antigen the whole 73 predicted ammino-acid sequence (GenScript, Piscataway, NJ, USA). Rabbit polyclonal antibody anti-myc (A-14) and mouse monoclonal antibody anti-GCH1 (G-8) were purchased from Santa Cruz Biotechnology, INC, while mouse monoclonal antibody anti-lamin A/C (4C11) was purchased from Cell Signaling Technology, INC. Proteosome inhibitor MG132 (Cat number M7449) and autophagy inhibitor 3-MA (Cat Number: 189490) were purchased from Sigma-Aldrich and used as described in the results section.
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