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5 protocols using c4606

1

Immunofluorescence Imaging of Flavivirus

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Cells grown on the cover-slip were fixed for 20 min in 4% paraformaldehyde solution (Sigma) in phosphate-buffered saline (PBS, Euroclone). Cells were permeabilized for 30 min in blocking solution, containing 0.2% Triton X-100 (Sigma) and 10% donkey serum (Sigma) and incubated overnight at 4 °C with the primary mAb in blocking solution. The following mAbs specific for Flavivirus E protein (1:200, Millipore, MAB10216), double-stranded RNA (1:300, English and Scientific Consulting Kft, Hungary), vimentin (1:300, Bioss, BS-0756R) and calreticulin (1:300, Sigma, C4606) were used. Cells were then washed with PBS and incubated for 1 h with Hoechst and either anti-mouse Alexa Fluor-488 or anti-rabbit Alexa Fluor-594 secondary Abs (1:1,000 in blocking solution, ThermoFisher Scientific). High resolution wide field fluorescence images were acquired on a Nikon Eclipse Ni-U microscope equipped with a Nikon 60x plan apo 1.40 oil or a 20x plan apo 0.75 objective and a Nikon DS-Qi2 camera.
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2

Comprehensive Western Blotting Antibody Assay

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Western blotting experiments were performed using the following primary antibodies: vinculin (V9131, clone hVIN-1 Sigma-Aldrich, 1:10,000), GAPDH (ab9485, Abcam, 1:1,000 or AM4300, clone 6C5, Ambion, 1:20,000), β-actin (sc-69879, clone AC-15, Santa Cruz Biotechnology, 1:2,000), p32 (A302-863A, Bethyl Laboratories, 1:5,000 or sc-10258, clone D-19, Santa Cruz Biotechnology, 1:1,000), XRN2 (A301-103A, Bethyl Laboratories, 1:2,000), CARF (A303-861A, Bethyl Laboratories, 1:2,000), NDUFS3 (Abcam 14711, 1:1,000), VDAC1 (ab3434-100, Abcam, 1:2,000), Hsp60 (BD611562, BD Biosciences, 1:5,000), Tom20 (FL-145, sc-11415, Santa Cruz Biotechnology, 1:1,000), calreticulin (C4606, Sigma-Aldrich, 1:10,000), calnexin (ab22595, Abcam, 1:5,000), SRSF1 (32-4600, Thermo Fisher Scientific, 1:250), puromycin (MABE343, clone 12D10, Merck-Millipore, 1:25,000), HA-tag (3724, clone C29F4, Cell Signaling Technologies, 1:1,000). The following HRP-linked secondary antibodies were used: anti-goat IgG (A5420, Sigma-Aldrich, 1:10,000), anti-mouse IgG (7076S, Cell Signaling Technologies, 1:5,000), anti-rabbit IgG (NA934-1ML, Sigma-Aldrich, 1:10,000).
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3

Antibody Characterization and Validation

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The following antibodies were used for immunohistochemical, immunofluorescence and Western blot analyses: sheep polyclonal antibody against uromodulin (ab9029, Abcam, Cambridge, UK) (1:200 for IF and for IHC); rat monoclonal antibody against HA (#11 867 423 001, Roche) (1:500 for IF and 1:1,000 for WB); rabbit polyclonal antibody against calreticulin (C4606, Sigma-Aldrich) (1:500 for IF); rat antibody against mouse F4/80 (MCA497GA, Serotec, BioRad)(1:50 for IF and IHC); rabbit polyclonal antibody against Atf3 (sc-188, Santa Cruz Biotechnology, Dallas, TX) (1:50 for IF and 1:500 for WB); goat polyclonal against Lipocalin 2/NGAL (AF1857, R & D Systems, Bio-Techne, Minneapolis, MN) (1:500 for WB); rabbit polyclonal against Kim1 (TIM-1) (NBP1-76701, Novus Biologicals, Bio-Techne) (1:500 for WB); mouse monoclonal antibody against β-Actin (A2228, Sigma-Aldrich) (1:20,000 for WB); mouse monoclonal antibody against Gapdh (sc-32233, Santa Cruz Biotechnology) (1:20,000 for WB).
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4

Comprehensive Western Blotting Antibody Assay

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Western blotting experiments were performed using the following primary antibodies: vinculin (V9131, clone hVIN-1 Sigma-Aldrich, 1:10,000), GAPDH (ab9485, Abcam, 1:1,000 or AM4300, clone 6C5, Ambion, 1:20,000), β-actin (sc-69879, clone AC-15, Santa Cruz Biotechnology, 1:2,000), p32 (A302-863A, Bethyl Laboratories, 1:5,000 or sc-10258, clone D-19, Santa Cruz Biotechnology, 1:1,000), XRN2 (A301-103A, Bethyl Laboratories, 1:2,000), CARF (A303-861A, Bethyl Laboratories, 1:2,000), NDUFS3 (Abcam 14711, 1:1,000), VDAC1 (ab3434-100, Abcam, 1:2,000), Hsp60 (BD611562, BD Biosciences, 1:5,000), Tom20 (FL-145, sc-11415, Santa Cruz Biotechnology, 1:1,000), calreticulin (C4606, Sigma-Aldrich, 1:10,000), calnexin (ab22595, Abcam, 1:5,000), SRSF1 (32-4600, Thermo Fisher Scientific, 1:250), puromycin (MABE343, clone 12D10, Merck-Millipore, 1:25,000), HA-tag (3724, clone C29F4, Cell Signaling Technologies, 1:1,000). The following HRP-linked secondary antibodies were used: anti-goat IgG (A5420, Sigma-Aldrich, 1:10,000), anti-mouse IgG (7076S, Cell Signaling Technologies, 1:5,000), anti-rabbit IgG (NA934-1ML, Sigma-Aldrich, 1:10,000).
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5

Immunofluorescence Labeling of Cellular Organelles

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Cells grown on coverslip in 12-wells plate were fixed in 4% paraformaldehyde (PFA) for 20 min, permeabilised 10 min with 0.5% triton and blocked 30 min with 10% donkey serum. Cells were labelled for 1 h 30 min at room temperature with the indicated antibodies (goat polyclonal anti-uromodulin (0855140, MP Biomedicals, Santa Ana, CA, dilution 1:500); rabbit polyclonal anti-calreticulin (C4606, Sigma, dilution 1:500); mouse monoclonal anti KDEL (ADI-SPA-827, Enzo Life Sciences, Farmingdale, NY, dilution 1:500) followed by 1h incubation with the appropriate Alexa-Fluor conjugated secondary antibodies (1:500; Thermofisher). Cells were stained with 4,6-diamidino-2-phenylindole (DAPI) and mounted using FluorSave Reagent (Calbiochem, San Diego, CA). All pictures were taken with an UltraVIEW ERS spinning disk confocal microscope (UltraVIEW ERS-Imaging Suite Software, Zeiss 63X/1.4; PerkinElmer Life and Analytical Sciences Boston, MA). All images were imported in Photoshop CS (Adobe Systems, Mountain View, CA) and adjusted for brightness and contrast.
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