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18 protocols using ha tag

1

Western Blot Analysis of Viral Proteins

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Aliquots containing equal amounts of total proteins from cell lysates (10 μg of protein, DC protein assay, BioRad) and virion lysates (egfp levels normalized) were subjected to gel electrophoresis. After blotting to a PVDF membrane, proteins were detected using an antibody specific to HA-tag (Roche), hA3G (Abcam), HIV-1 p24 (Polymun), MMTV CA(p27) (a gift from A. Mason), actin (Sigma-Aldrich), HSP90 (Santa Cruz). Antibody-reactive proteins were detected with horseradish peroxidase-conjugated secondary antibody (DAKO) and ECL plus substrate (GE Healthcare).
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2

Western Blot Protein Detection Protocol

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Cells were lysed at 4°C in RIPA buffer (50 mM Tris, pH 8, 1% Triton, 150 mM NaCl, 0.5% SDS, 50 mM Triton, 1 mM EDTA) + Protease Inhibitor Cocktail (Roche, 11697498001), sonicated for 15 s, clarified via centrifugation, and stored in –80°C. Lysates were solubilized by mixing 1:1 in loading buffer (10% SDS, 40% glycerol, 3% Bromophenyl Blue, and 10% Beta-Mercaptoethanol). Proteins in lysates with loading buffer were first denatured by boiling for 5 min and cooled on ice for 2 min before being loaded into 10% polyacrylamide gels and run for ∼90 min at 125V. Resolved proteins were transferred onto nitrocellulose membranes for 1 h at 100V. Membranes were then blocked with 5% bovine serum albumin (BSA) for an hour before incubation with primary antibody, washed three times in PBST (2.0% Triton in phosphate-buffered saline [PBS]), and then finally incubated with secondary antibodies (Licor, IRDye 680RD Series, CW800 Series). Bands were visualized using a LI-COR Odyssey FC system. Primary antibodies used were Dsg1 (BD Bioscience, 610273), Desmoplakin (Millipore Sigma, MABT1492), E-cadherin (Invitrogen, 13-1900), GST (Bethyl Laboratories, A190-122P), HA tag (Roche, 11867423001), Occludin (Thermo Fisher, 71-1500), Plakoglobin (Santa Cruz, sc-7900), and Streptavidin-HRP (Thermo Fisher, 43-4323).
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3

Western Blot Analysis of Membrane Proteins

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Standard western blotting was carried out using 6%–20% gradient gels. The primary antibodies used were as follows: zDHHC5 (1:1,000, Sigma, HPA014670), NCX1 (1:1,000, Swant, R3F1), PLM (FXYD1, 1:1,000, Abcam, ab76597), Flotillin-2 (1:1,000, BD Biosciences, 610383), Caveolin-3 (1:4,000, BD Biosciences, 610420), HA-tag (1:5,000, Roche, 11867423001). The secondary antibodies used were as follows: Rabbit anti-mouse HRP (1:2,000, Jackson ImmunoResearch 111-035-144), Goat anti-rabbit HRP (1:2,000, Jackson ImmunoResearch 315-035-003), Goat anti-rat HRP (1:2,000, Jackson ImmunoResearch, 313-035-003), Donkey anti-guinea pig (1:2,000, Jackson ImmunoResearch, 106-035-003).
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4

Cell Lysis and Protein Analysis

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Cells were lysed in the buffer containing 50 mM Hepes, 150 mM NaCl, 10 mM EDTA, 100 mM NaF, 10 mM Na4P2O7, 1% Triton X-100, 0.1% SDS and protease inhibitor cocktail (Roche, West Sussex, UK) for 30 min on ice before centrifugation for 15 min at 20 000g. Thirty micrograms of protein was separated by SDS–PAGE and transferred to nitrocellulose membranes using standard techniques. Membranes were probed using standard immuno-blotting techniques with the following antibodies: CrmA (556472, Becton Dickinson, Oxford, UK), Mcl-1 (559027, Becton Dickinson); cleaved caspase-3 (9664, Cell Signalling, Beverly, MA, USA); cleaved caspase-7 (9491, Cell Signalling, Beverly, MA, USA); cleaved caspase-8 (9496, Cell Signalling); cleaved caspase-9 (9501, Cell Signalling); HA-tag (12013819001, Roche); Bcl-XL (AC-0098RUO, Epitomics, Cambridge, UK); Puma (IMG-458-2, Imgenex, Novus Biologicals, Cambridge, UK); Bak (06-536, Millipore, Watford, UK); Noxa (2437, ProSci Inc., Poway, CA, USA); Bax (sc-493, Santa Cruz, Dallas, TX, USA), Bcl-2 (sc-509, Santa Cruz), p21 (sc-397, Santa Cruz); and β-actin (ab8227, Abcam, Cambridge, UK).
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5

Immunoblotting Procedure for Protein Analysis

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Cell lysates and immunoprecipitated samples were separated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis and transferred onto polyvinylidene fluoride membranes. Membranes were blocked with 3% skim milk or 5% bovine serum albumin in Tris-buffered saline containing Tween 20. The resulting membranes were then incubated with primary antibodies against β-catenin/catenin beta-1 (E-5, Santa Cruz Biotechnology), PTGS2/COX-2 (D5H5, Cell Signaling Technology), FLAG tag (M2, Sigma-Aldrich), GAPDH (1E6D9, Proteintech), HA tag (3F10, Roche), IQGAP1 (H109, Santa Cruz Biotechnology), JNK (#9252, Cell Signaling Technology), phospho-SAPK/JNK (81E11, Cell Signaling Technology), Lamin B1 (3C10G12, Proteintech), Myc tag (9B11, Cell Signaling Technology), ROBO4 (AF2366, R&D Systems), TRAF7 (H-300, Santa Cruz Biotechnology), mono- and poly-ubiquitinylated conjugates (FK2, Enzo Life Sciences), and RAC1 (PA1-091, Thermo Fisher Scientific) and secondary antibodies conjugated with horseradish peroxidase. Immunoreactive bands were detected using an ImageQuant LAS4010 system (GE Healthcare). The primary antibodies used are listed in Table S3.
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6

Antibody Immunofluorescence and Western Blot

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Antibodies used for immunofluorescence experiments in this study were: HA tag (3F10/11 Roche, 867 423 001), giantin (Santa Cruz, N-18/sc-46993), COXIV (3E11, New England Biolabs Ltd, 4850S), CI-MPR (Abcam ab124767), golgin-84 (Sigma HPA000992), TOM20 (BD Transduction Labs, 612278) and ZFPL1 (Sigma, HPA014909). Endosomes were labeled with Alexa Fluor 555 transferrin (ThermoFisher Scientific, T35352). Antibodies for Western blotting were the same as those used for immunofluorescence plus: STAMBPL1 (Sigma, SAB4200146), TBCK (Cambridge Bioscience, HPA039951), RELCH/KIAA1468 (Cambridge Bioscience, HPA040038), OSBPL9 (Abcam, ab151691), PIK3R4 (Abcam, ab128903), FLAG (M2) (Sigma, F1804), EEA1 (Abcam, ab109110), ARFGEF3 (ThermoFisher Scientific, PA5-57623), ALS2 (Abcam, ab170896) and α-tubulin (YL1/2; Kilmartin et al., 1982 (link)). Biotin was detected with Neutravidin-FITC (Invitrogen, 31006) and Streptavidin-HRP (Cell Signaling Technology, 3999S).
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7

Western Blot Analysis of Protein Expression

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Whole-cell extracts were prepared by lysing cells in Laemmli sample buffer. Equal amounts of total protein were fractionated on SDS-PAGE, and standard protocols were applied for western blotting. Proteins were revealed with primary antibodies against HA-tag (Roche; 12CA5), FLAG (Sigma; F3165), SRSF10 (Abcam; ab77209), hnRNP F or hnRNP H (kindly provided by Doug Black), hnRNP K (kindly provided by G. Dreyfuss), actin (Sigma; A5316), tubulin (ab4074; Abcam), using peroxidase-conjugated secondary antibodies and ECL detection reagent (Amersham). Secondary antibodies were either polyclonal anti-rabbit (Cell Signaling; 7074) or anti-mouse (Bio-Can; 115-035-003).
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8

Multicolor immunofluorescence protocol

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Cells were transfected in 8-well glass chambers (Millipore) and fixed with 4% paraformaldehyde 24 hours later. Cells were permeabilized with 0.1% Triton-X100 and blocked with 10% donkey serum. GFP and mCherry fluoresce was detected directly. The primary antibodies used were: SC-35 (1:300; Abcam, ab11826), PML (1:50; Santa Cruz, sc-966), coilin (1:500; Santa Cruz Biotechnology, sc-32860), B23 (1:200, Santa Cruz Biotechnology, sc-56622) Myc-tag (1:500 Cell Signaling Technologies, 71D10), HA-tag (1:250; Clone 3F10, Roche, 11867423001), FK2 (1:50; Enzo Life Sciences, BML-PW8810), V5-tag (1:300, Novus Biological, NB600–379). The secondary antibodies used were Alexa 555, 647 (1:5,000; Thermo-Fisher), and CF405S (1:1000; Biotium). Samples were mounted on ProLong Gold antifade with or without DAPI and cured before imaging on a Zeiss LSM 780 NLO microscope. Images were prepared with the Fiji software.
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9

Western Blot Analysis of Cellular Proteins

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Cells were lysed using IP buffer (20 mM Tris HCl [pH 7.5], 200 mM NaCl, 1 mM EDTA, 0.5% NP-40) supplemented with Complete Protease Inhibitor mixture (Roche). Samples were resolved by SDS–PAGE and transferred to polyvinylidene difluoride membranes (Perkin Elmer). Membranes were blocked in 5% non-fat milk and incubated overnight at 4°C with the appropriate primary antibody. Membranes were probed with the following primary antibodies: β-actin (clone C4; MP Biomedicals), GAPDH (6C5) (sc-32233; Santa Cruz), p53 (DO-1) (sc-126; Santa Cruz Biotechnology), DNMT1 (clone 60B1220.1; MAB0079; Abnova), PKR (3072; Cell Signaling Technology), phosphorylated PKR Thr 446 (PA5-37704; Thermo Fischer Scientific), EGFR (4267; Cell Signaling Technology), CCND1 (2978; Cell Signaling Technology), HA-tag (3F10; Roche), and ITGA1 (106267; Abcam).
Images were produced using the ChemiDoc XRS imaging system (Bio-Rad).
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10

Immunoblotting Analysis of Bacterial Proteins

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For analysis of proteins by immunoblotting, bacteria were cultured as described above (at time 0, ATc was added to a concentration of 0.25 µg/ml unless otherwise indicated, when appropriate). Aliquots of the cultures were removed and centrifuged at 5,000 × g for 10 min at 4°C, and bacterial pellets were washed once with PBS and incubated for 30 min on ice with lysozyme (50 µg/ml). Cells were then sonicated using 3 30-s pulses, and lysates were centrifuged at 10,000 × g for 10 min at 4°C. Protein concentrations were measured by the Bradford assay (Bio-Rad), and equal concentrations of lysates were mixed with reducing sample buffer, separated by SDS-PAGE, transferred to nitrocellulose, and analyzed by immunoblotting with antibodies to the HA tag (Roche), Pla (65 (link)), or RpoA.
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