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19 protocols using ab76493

1

Western Blot Analysis of Signaling Proteins

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The total protein was extracted from tissues and cells, and the protein concentration was measured using a BCA kit (Thermo Fisher Scientific, USA). A total of 30 μg of total protein was subjected to polyacrylamide gel electrophoresis and transferred onto a PVDF membrane (Amersham, USA). The membrane was blocked with 5% skim milk powder at room temperature for 1 h and incubated at 4 °C overnight with rabbit antibodies against TLR4 (2 ug/mL, ab13556, Abcam, UK), IRF3 (1 ug/mL, ab68481, Abcam, UK), phosphorylation of IRF3 (1 mg/mL, ab76493, Abcam, UK), YAP (10 mg/mL, ab76252, Abcam, UK), CDX2 (10 mg/mL, ab76541, Abcam, UK), E-cadherin (10 mg/mL, ab40772, Abcam, UK), N-cadherin (1 mg/mL, ab18203, Abcam, UK), Bax (1: 1000, ab32503, Abcam, UK) and Bcl-2 (1: 1000, ab32124, Abcam, UK). The membrane was washed 3 times with PBST (PBS buffer containing 0.1% Tween-20), 10 min each times. Subsequently, horseradish peroxidase-labeled secondary goat anti-rabbit IgG (10 mg/mL, ab6721, Abcam, UK) was added to the membrane for incubation at room temperature for 1 h. The membrane was washed 3 times with PBST buffer for 10 min each. After scanning and development with an optical luminometer (GE Healthcare, USA), the protein band intensities were performed using Image Pro Plus 6.0 software (Media Cybernetics, USA), followed by analysis of the relative protein expression.
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2

Western Blot Analysis of Immune Signaling

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The total proteins were extracted and separated by 10% or 15% SDS-PAGE and were transferred to polyvinylidene difluoride membranes (Millipore, Bedford, Massachusetts, USA) using a semi-dry Gel Transfer Device (Bio-Rad, Hercules, California, USA). The membranes were blocked using 5% non-fat milk and probed with primary antibodies and HRP-conjugated secondary antibodies. Antigen-antibody complexes were visualised using a chemiluminescent ECL detection system and analysed using a ChemDoc XRS+image analyser. GAPDH or β-actin was used as an internal control. The antibodies used included anti-β5i (1:5000, ab180606, Abcam), anti-RIG-I (1:2000,3743, Cell Signaling Technology), anti-Phospho-NF-κB p65 (1:1000, 3033, Cell Signaling Technology), anti-Phospho-IRF3 (1:500, ab76493, Abcam), anti- IFNβ (1:500, ab275880, Abcam), anti- MxA (1:500, sc-166412, Santa Cruz), anti-MuRF1 (1:2000, ab172479, Abcam), anti-β-actin (1:5000, YM3028, Immunoway) and anti-GAPDH (1:10000, YM3029, Immunoway). The selective β5i inhibitor PR-957 was purchased from Selleck Chemicals (Houston, Texas, USA).
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3

Deciphering Innate Immune Signaling

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Rabbit antibodies against human p-TBK1 Ser172 (catalog no. 5483), TBK1 (catalog no. 3504), IRF3 (catalog no. 11904), p-STING Ser366 (catalog no. 85735), and STING (catalog no. 13647) were obtained from Cell Signaling Technology. Rabbit antibodies against human p-IRF3 Ser386 (ab76493), MAVS (ab31334), and green fluorescent protein (GFP) (ab290) were purchased from Abcam. Rabbit antibody against HA was purchased from HUAXINGBIO (HX1820). Mouse antibodies against laminB1 (sc-365962) were purchased from Santa Cruz Biotechnology. Mouse anti-FLAG antibody (M2) (F1804), M2-conjugated agarose (A2220), mouse anti-HA antibody (H3663), and anti-HA–conjugated agarose (A2095) were purchased from Sigma-Aldrich. Rabbit anti-PPM1G antibody (A300-881A) was purchased from Bethyl Laboratories. Poly(I:C) and poly(dA:dT) were purchased from InvivoGen (tlrl-pic, tlrl-patn-1). Mouse anti-ORF33 antibody was provided by F. Zhu (Florida State University, USA). Mouse anti-K8/KbZIP and anti-ORF45 antibodies were provided by Y. Yuan (University of Pennsylvania, USA). Human IFNβ ELISA Kit was purchased from R&D Systems (DIFNB0). Duolink In Situ–Fluorescence kit for PLA was purchased from Sigma-Aldrich (DUO92008, DUO92002, and DUO92004).
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4

Immunoblotting Using Diverse Antibodies

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The following antibodies were used for immunoblotting: mouse monoclonal antibodies raised against BRCA2 (1:1000, OP95, Calbiochem), GAPDH (1:30000, NB600-502, Novus Biologicals), α-Tubulin (1:30,000, TAT-1, Cancer Research UK Monoclonal Antibody Service); rabbit monoclonal antibody raised against ERK1/2 (1:5000, 4695, Cell Signaling), STING (1:1000, 13647, Cell Signaling), IRF3 (1:1000, AB76409, Abcam), phospho-IRF3 (1:1000, AB76493, Abcam), STAT1 (1:1000, 9175, Cell Signaling), phospho-STAT1 (1:1000, 9167, Cell Signaling); rabbit polyclonal antibodies raised against phospho-KAP1 (1:1000, A300-767A, Bethyl Laboratories), KAP1 (1:5000, A300-274A, Bethyl Laboratories), SMC1 (1:5000, A300-055A, Bethyl Laboratories).
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5

Antibody Validation for Protein Interactions

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Antibodies against HSPD1 (mouse original, ab3080), IRF3 (rabbit original, ab76367), and phospho S386-IRF3 (rabbit original, ab76493) were purchased from Abcam, HK. Anti-myc McAb (rabbit original, 9402S), anti-flag McAb (rabbit original, 2368S) were from Cell Signaling Technology. Anti-Flag antibody (M2, mouse) and the ANTI-FLAG M2 Affinity Gel were from Sigma. Anti-GAPDH was from Cali-Bio (mouse original, CB100127). The secondary antibodies goat anti-rabbit Fc-HRP 4041-05 and goat anti-mouse Fc-HRP 1033-05 were from SouthernBiotech. The secondary fluorescence-labeled antibodies goat anti-rabbit IgG H&L (FITC, ab6717) and goat anti-mouse IgG H&L (Cy3, ab97035) were from Abcam. The 4–6-diamidino-2-phenylindole-dihydrochloride (DAPI) was from Invitrogen.
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6

Immunoblotting of SARS-CoV-2 Induced Signaling

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Cells were lysed, and an equal amount of each lysate was subsequently analyzed by SDS–PAGE following standard procedures. The antibodies used for immunoblotting were: rabbit-anti-cGAS (D1D3G, #15102 S, Cell Signaling Technology, 1:500), rabbit-anti-STING (D2P2F, #13647 S, Cell Signaling Technology, 1:500), rabbit-anti-phospho-STING (Ser366) (D7C3S, #19781 S, Cell Signaling Technology, 1:500), rabbit-anti-IRF3 (ab76409, Abcam, 1:1000), rabbi-anti-phospho-IRF3 (ab76493, Abcam, 1:1000), rabbit-anti-GAPDH (BE0024, EASYBIO, 1:2000), mouse-anti-β-Tubulin (CW0098, CWBIO, 1:2000), rabbit-anti-SARS-CoV-2 spike protein (40589-T62, Sino Biological, 1:1000), rabbit-anti-SARS-CoV-2 nucleocapsid protein (NP) (40143-R019, Sino Biological, 1:1000), rabbit-anti-Sendai virus (PD029C1, MBL, 1:1000), rabbit-anti-ACE2 (10108-T60, Sino Biological, 1:1000), mouse-anti-MAVS (sc166583, Santa Cruz, 1:500), goat-anti-mouse IgG-HRP secondary antibody (115035003, Jackson ImmunoResearch), mouse-anti-Lamin A/C (MABT538, Sigma-Aldrich, 1:500), rabbit-anti-Lamin B1 (ab16048, Abcam, 1:500), goat-anti-rabbit IgG-HRP secondary antibody (111035003, Jackson ImmunoResearch). For STING dimer detection, reducing reagents were not added to the lysates, and samples were not heated before loading.
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7

Comprehensive Immunoblotting Antibody Panel

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The following antibodies were used for immunoblotting: rabbit polyclonal antibody raised against 53BP1 (1:5,000, NB100‐304, Novus Biologicals), DNA‐PKcs (1:1,000, A300‐519A, Bethyl Laboratories), phosphorylated KAP1 (Ser824) (1:1,000, A300‐767A, Bethyl Laboratories), KAP1 (1:5,000, A300‐274A, Bethyl Laboratories), phosphorylated RPA (Ser4/Ser8) (1:4,000, A300‐245A, Bethyl Laboratories), phosphorylated IRF3 (Ser386) (1:1,000, ab76493, Abcam), IRF3 (1:1,000, ab76409, Abcam), phosphorylated STAT1 (Tyr701) (1:1,000, 9167, Cell Signalling), STAT1 (1:1,000, 9175, Cell Signalling), SMC1 (1:5,000, BL308, Bethyl Laboratories); mouse monoclonal antibodies raised against XRCC4 (1:1,000, 611506, BD biosciences), BRCA2 (1:1,000, OP95, Calbiochem), RPA (1:1,000, ab2175, Abcam), GAPDH (1:30,000, 6C5, Novus Biologicals), α‐Tubulin (1:30,000, TAT‐1, Cancer Research UK Monoclonal Antibody Service) and POLQ (1:10,000, (Fernandez‐Vidal et al, 2014 (link))).
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8

Western Blot Analysis of Cell Signaling

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Preparation of cell lysates was carried out using the lysis buffer, as described previously [13 (link)]. Approximately 50 µg of total protein from each treatment was resolved on an SDS-polyacrylamide gel and transferred onto the nitrocellulose membranes (Bio-Rad, Kidlington, UK) by electro-blotting. The following primary antibodies were used: anti-Ki67 (ab92742; dilution 1:1,000), anti-Bax (ab32503; dilution 1:1,000), anti-interleukin 6 (anti-IL-6, ab6672; dilution 1:500), anti-tumor necrosis factor-α (anti-TNFα, ab6671; dilution 1:1,000), anti-TANK binding kinase-1 (anti-TBK1, ab227182; dilution 1:2,000), anti-interferon regulatory factor 3 (anti-IRF3, ab25950; dilution 1:500), anti-phosphorylated TBK1 (anti-p-TBK1, ab186469; dilution 1:500), anti-p-IRF3 (ab76493; dilution 1:3,000), and anti-β-actin (ab8226, loading control; dilution 1:5,000) (all from Abcam, Cambridge, UK). The immuno-detected proteins were analyzed by chemiluminescence on a ChemiDoc System (Bio-Rad).
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9

Progesterone and Dasatinib Modulate IFN Signaling

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Progesterone (HY-N0437) and Dasatinib (HY-10181) (MedChemExpress); IFN-γ (300-02, Peptech); Anti-mouse IFNAR-1-in vivo (clone MAR1-5A3; Selleck A2121); ELISA kits for progesterone (582601, Cayman Chemical), GnRH (MM-0506M1) and LH (MM-44039M1) (MEIMAIN), murine IFN-β(42400, PBL), murine CXCL10 (EMC121, Neobioscience), murine TNFα (430904, BioLegend), murine IL-6 (431304, BioLegend); Mouse monoclonal antibodies against HA (TA180128, OriGene), Flag (F3165) and β-actin (A2228) (Sigma), IRF3 (sc-33641, Santa Cruz Biotechnology); Rabbit polyclonal antibodies against PGR (8757), SRC (2109), p-SRCY419 (2101) and p-Tyrosine (9411S) (Cell signaling technology), TBK1 (ab40676), p-TBK1S172 (ab109272) and p-IRF3S386 (ab76493) (Abcam) were purchased from the indicated companies. SeV, EMCV and HSV-1 were previously described.75 (link),76 (link) HEK293 cells were obtained from ATCC. The T-47D cells were provided by Dr. Jing Zhang (Wuhan University). The Calu-3 cells were provided by Dr. Ke Lan (Wuhan University).
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10

Western Blot Analysis of Interferon Signaling

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Cell monolayers were washed with PBS and lysed with Radio Immunoprecipitation Assay Lysis (RIAL) Buffer (Beyotime, P0013C). Lysates were harvested and further cleared by centrifugation at 12,000 g for 10 min at 4 °C. The concentration for the total protein content was determined with a BCA protein assay kit (Beyotime). Total of 30 μg protein lysate was resolved by 12% SDS-PAGE and transferred onto nitrocellulose membranes. The membranes were incubated with 5% skim milk for 2 h at room temperature, then incubated overnight at room temperature for 2 h with specific rabbit anti-IFN-β antibody (ab140211, Abcam), rabbit anti-flag antibody (ab1162, Abcam), rabbit anti-GADPH antibody (ab22555, Abcam), rabbit anti-IRF3 antibody (ab68481, Abcam), rabbit anti-IRF3 (phosphor S386) antibody (ab76493, Abcam), rabbit anti-NF-κB p65 antibody (ab32536, Abcam) and mouse anti-NP antibody (MAB3326, Abnova). After three rinses, membranes were incubated at room temperature for 1 h with IRDye 680DX conjugated anti-rabbit/mouse IgG (1:8000; Rockland Immunochemicals). The membranes were analyzed with an Odyssey infrared imaging system (LI-COR Biosciences).
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