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20 protocols using isg15

1

Antibody Immunoblotting for Cellular Signaling

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We used the following antibodies and dilutions for this study: ubiquitin (catalogue (cat.) no. 3936S, Cell Signaling Technology; 1:20:00), ISG15 (cat. no. HPA004627, Sigma Aldrich/Merck; 1:1,000), GAPDH (cat. no. 2118, Cell Signaling Technology; 1:2,000), GFP trap beads (cat no. gta-100, ChromoTek), GFP (cat. no. sc-9996, Santa Cruz Biotechnology; 1:2,000), IRF3 (cat. no. 4302, Cell Signaling Technology; 1:2,000), phospho-IRF3(Ser396) (cat. no. 4947, Cell Signaling Technology; 1:1,000), IκBα (cat. no. 4812, Cell Signaling Technology; 1:2,000), phospho-IκBα(Ser32/36) (cat. no. 9246, Cell Signaling Technology; 1:1,000), TBK1 (cat. no. 3013, Cell Signaling Technology; 1:2,000), pTBK1 (cat. no. 3300-1 Epitomics; 1:1,000), NF-κB p65 (cat. no. 8008, Santa Cruz Biotechnology; 1:2,000), lamin B1 (cat. no. sc-373918, Santa Cruz Biotechnology; 1:2,000).
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2

Interferon Signaling Pathway Protein Detection

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The antibodies used were IRF-1 (8478S, Cell Signaling), IFIT1 (14769S, Cell Signaling), IFIT3 (sc-393512, Santa Cruz Biotechnology), Mx1 (37849S, Cell Signaling), ISG15 (2758T, Cell Signaling), IFI44L (HK7931, Hushi Pharmaceutical Technology), Tri-Methyl-Histone H3 (Lys27) (C36B11) Rabbit mAb (9733, Cell Signaling), Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb (9751, Cell Signaling), anti-rabbit IgG, HRP-linked antibody (7074P2, Cell Signaling), anti-mouse IgG, HRP-linked antibody (7076P2, Cell Signaling). Anti-A/California/7/2009-like HA serum (sheep 606 and 610) (14/310) was purchased from National Institute for Biological Standards and Control (NIBSC). Anti-sheep IgG, HRP-linked antibody (F030231) was purchased from Beijing BioRab Technology. Mouse anti-hnRNP U monoclonal antibody (ab10297) was purchased from Abcam.
Polyinosinic-polycytidylic acid sodium salt (P9582) was purchased from Sigma-Aldrich. Human IFN-β (10704-H02H) was purchased from Sino Biological. MRT67307 HCl (T5162) and Pyrrolidinedithiocarbamate ammonium (T3147) were purchased from TargetMol.
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3

Antibody Immunoblotting for Cellular Signaling

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We used the following antibodies and dilutions for this study: ubiquitin (catalogue (cat.) no. 3936S, Cell Signaling Technology; 1:20:00), ISG15 (cat. no. HPA004627, Sigma Aldrich/Merck; 1:1,000), GAPDH (cat. no. 2118, Cell Signaling Technology; 1:2,000), GFP trap beads (cat no. gta-100, ChromoTek), GFP (cat. no. sc-9996, Santa Cruz Biotechnology; 1:2,000), IRF3 (cat. no. 4302, Cell Signaling Technology; 1:2,000), phospho-IRF3(Ser396) (cat. no. 4947, Cell Signaling Technology; 1:1,000), IκBα (cat. no. 4812, Cell Signaling Technology; 1:2,000), phospho-IκBα(Ser32/36) (cat. no. 9246, Cell Signaling Technology; 1:1,000), TBK1 (cat. no. 3013, Cell Signaling Technology; 1:2,000), pTBK1 (cat. no. 3300-1 Epitomics; 1:1,000), NF-κB p65 (cat. no. 8008, Santa Cruz Biotechnology; 1:2,000), lamin B1 (cat. no. sc-373918, Santa Cruz Biotechnology; 1:2,000).
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4

Bowman-Birk Inhibitor Characterization and Antibody Usage

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Bowman-Birk inhibitor (BBI) was purchased from Sigma-Aldrich (St. Louis, MO, USA). The product is isolated from Glycine max (soybean) and purified from crude trypsin inhibitor (Sigma Cat #T9128). It consists of 90% protein as assayed by Biuret, with the remainder a phosphate buffer salt. The stock solution was prepared in sterile culture grade water at 1 mg/ml. Rabbit antibodies against ISGs (ISG56, ISG15, OAS-1, viperin), RIG-I/MDA-5, p-IRF3 and p-STAT1/3 were purchased from Cell Signaling Technology (Danvers, MA). Rabbit antibodies against Mx2 was purchased from Novus Biologicals (Littleton, CO). Anti-human interferon alpha/beta receptor chain 2 (anti-IFNAR), clone MMHAR-2 (MAb) (Cat #:21385-1), was purchased from PBL Assay Science (Piscataway, NJ).
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5

Western Blot Analysis of Immune Proteins

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Cells were collected in RIPA lysis buffer (Thermo Scientific, cat#89900) containing protease inhibitor mixture (Sigma, cat#P-8340). Protein concentration was quantified using a BCA Protein concentration Kit (Beyotime, cat#P0009). Total cell lysates were subjected to SDS-polyacrylamide gel electrophoresis (PAGE) and transferred to polyvinylidene difluoride membrane. The membrane was incubated with primary antibodies (overnight at 4°C) and sequentially horseradish peroxidase (HRP)-conjugated secondary antibody at room temperature for 1 hour. Membranes were probed with HRP-conjugated secondary mouse antibody (Santa Cruz, cat#sc-516102) at room temperature for 1h. Enhanced chemiluminescence substrates (ECL) (Tanon, cat#180501) were used to visualize the protein abundances. Primary antibodies used were EZH2 (D2C9) (Cell Signaling Technology, cat#5246), TLR3 (TLR3.7) (Santacruz, cat#sc-32232), MDA-5 (D74E4) (Cell Signaling Technology, cat#5321), ISG15 (Cell Signaling Technology, cat#2743), Actin (Santacruz, cat#sc-8432).
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6

Western Blot Analysis of Influenza-Induced Proteins

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Cells were washed once by ice-cold PBS, and then were lysed using RIPA buffer (R0010, Solarbio) containing Phenylmethanesulfonyl fluoride (PMSF) (P0100, Solarbio). Proteins were separated by SDS-PAGE, and then transferred onto PVDF membrane (Roche Diagnostics). PVDF membranes were incubated with the following diluted primary antibodies: Anti-A/California/7/2009-like HA serum (sheep 606 and 610) (14/310, NIBSC), IRF-1 (8478S, Cell Signaling), IFIT1 (14769S, Cell Signaling), IFIT3 (sc-393512, Santa Cruz Biotechnology), Mx1 (37849S, Cell Signaling), ISG15 (2758T, Cell Signaling), IFI44L (HK7931, Hushi Pharmaceutical Technology). Membranes were washed three times in Tris-buffered saline containing 1% Triton X-100 and then were incubated with horseradish peroxidase (HRP)-conjugated secondary antibodies (7074P2, Cell Signaling, F030231, Beijing BioRab Technology). Immunoreactive bands were visualized by enhanced chemiluminescence using Super ECL Plus Detection Reagent (P1050, Applygen) using Tanon-5200 (Tanon).
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7

Western Blot Analysis of Viral Proteins

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Cells were harvested and lysed in a cell lysis buffer (Beyotime, China). Whole-cell lysates in each sample were quantified, and the same amounts of proteins were subjected to 12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and electro-transferred to polyvinyl difluoride (PVDF) membrane (Merck Millipore, United States). Membranes were blocked with 3% bovine serum albumin (BSA) (Sangon Biotech, China) in TBST (20 mM Tris-HCl PH8.0, 150 mM NaCl, 0.05% Tween 20) at room temperature for 1 h. The membranes were then incubated with indicated primary antibodies (anti-PRRSV N) (MEDIAN, Republic of Korea), -GAPDH, -p65, -PKR, -p-eIF2α, -CHOP, -p-IRF3, -ISG15, -myc, -histone 3 (Cell Signaling Technology, United States), and -mCherry (Abcam, England) at 1:1,000 at 4°C overnight. Membranes were washed with TBST buffer four times, followed by incubation of indicated secondary antibodies at a dilution of 1:5,000. GAPDH served as an internal control. Protein signals were visualized using a chemiluminescence (ECL) reagent (NCM Biotech, China). Three replicates were included for each treatment.
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8

Western Blot Analysis of Cellular Proteins

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Cell lysates were placed in RIPA buffer with the Halt Protease and Phosphatase Inhibitor Cocktail (Thermo Fisher Scientific). Lysates were size-fractionated by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to nitrocellulose membranes. Membranes were independently probed with indicated antibodies and visualized using Clarity Western ECL 10 Substrate (Bio-Rad). Primary antibodies were: ATGL (#2138; Cell Signaling Technology), USP18 (#4813; Cell Signaling Technology), β-actin (#3700; Cell Signaling Technology), HA tag (#3724S, Cell Signaling Technology), UBE1L (#61266, Cell Signaling Technology), Tubulin, UCP1 (#PA1–24894, ThermoFisher Scientific), Myc-tag (#2276S, Cell Signaling Technology), and ISG15 (#2743, Cell Signaling Technology). Secondary antibodies were Goat anti-rabbit IgG (#170–6515; Bio-Rad) or Goat anti-mouse IgG (#170–6516; Bio-Rad).
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9

IFN-α Induced Stat1 Activation Assay

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Cells plated at 2 × 105cells/well/2 mL media were plated in a 6-well plate the night before IFN-α treatment as described. After 30 min, media were removed, and cells were lysed and collected using 150 μL 1X NuPAGE LDS Sample Buffer (Invitrogen, Thermo Fisher). Lysates were stored at −80°C. Lysate samples were directly sonicated with a microtip at 20% amplitude 3X for 5 s before being incubated at 95°C for 5 min. Lysate samples (10 μL) were electrophoresed on a Nu-PAGE 4%–12% Bis-Tris gel with MOPS buffer at 150 V for 70 min and transferred to a membrane using an iBlot2 gel transfer system. The membrane was blocked with 5% milk in PBS-T, incubated with primary antibodies overnight at 1:1,000 dilution at 4°C, followed by secondary antibody incubations at 1:10,000 dilution for 60 min at 25°C. Antibody binding was detected using Immobilon Western Chemiluminescent HRP Substrate and imaged using Protein Simple Fluor Chem R. The following antibodies were used for western blot analysis: Stat1 (#14994), Phospho-Stat1 Tyr701 (#9167), ISG15 (#2758) from Cell Signaling Technologies (Danvers, MA, USA), and beta actin HRP (#ab20272) from Abcam (Cambridge, MA, USA).
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10

Western Blot Quantification of Immune Proteins

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Samples were prepared and run as described (27 (link)). Briefly, protein concentration was determined by Bradford reaction (Bio-Rad) according to manufacturer instructions. 35 ug/well were prepared in lysis buffer and 6X reducing SDS sample buffer (Bio-Rad) and boiled for 5-10 minutes prior to loading. Samples were run on 4-15% gradient SDS-PAGE gels (Bio-Rad), transferred to polyvinylidene difluoride membrane (Bio-Rad) and blocked for at least one hour at room temperature in 5% milk in tris-buffered saline containing Tween20 (TBS-T, 0.1% Tween20). Rabbit polyclonal antibodies for ISG15, RIG-I, and actin (Cell Signaling) and goat anti-rabbit secondary detection antibody conjugated to horseradish peroxidase (Millipore) were described (27 (link)). Western blots were developed with Immobilon Crescendo Western HRP substrate (Millipore).
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