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5 protocols using sc 33641

1

Western Blot Analysis of Protein Lysates

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Protein lysates were obtained using Pierce IP lysis buffer (#87787; ThermoFisher) freshly supplemented with Halt Protease and Phosphatase Inhibitor Cocktail (#78440; ThermoFisher). Protein concentration was determined using Pierce BCA Protein Assay Kit (#23225; ThermoFisher). Equal protein amounts were run on Tris-HCl Criterion Precast gels (Bio-Rad) and transferred onto Immobilon-P membranes (Millipore). Blots were blocked in 5% nonfat dry milk (Santa Cruz Biotechnology) or 5% BSA in TBS-T 0.1% for 1 h. The antibodies used were anti-Dnmt3a (ab188470, 1:1,000; Abcam), anti-actin HRP (ab20272, 1:2,000; Abcam), anti-Irf3 (sc-33641, 1:1,000; Santa Cruz Biotechnology), and anti-Rela (S8242S, 1:1,000; Cell Signaling). Secondary stains include goat anti-rabbit HRP (1:5,000; Prometheus Labs) and rabbit anti-mouse HRP (1:5,000; Abcam).
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2

Innate Immune Response Signaling Pathway

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Anti-CPSF5 (1:5000; 10322-1-AP, Proteintech), anti-CPSF6 (1:5000; ab175237, Abcam), anti-CPSF7 (1:2000; 55195-1-AP, Proteintech), anti-RIG-I (1:1000; D14G6, Cell Signaling), anti-MDA5 (1:1000; D74E4, Cell Signaling), anti-IFIT3 (1:2000; 15201-1-AP, Proteintech), anti-ISG15 (1:2000; 15981-1-AP, Proteintech), anti-DDX21 (1:2000; 10528-1-AP, Proteintech), anti-DHX15 (1:2000; 12265-1-AP, Proteintech), anti-CCL2 (1:2000; 66272-1-Ig, Proteintech), anti-IRF3 (1:1,000; sc-33641, Santa Cruz), anti-phosphorylated IRF3 (1:1000; 4D4G, Cell Signaling), anti-TBK1 (1:1000; D1B4, Cell Signaling), anti-phosphorylated TBK1 (1:1000; D52C2, Cell Signaling), anti-VSVG (1:1000; V5507, Sigma), anti-ICP27 (1:1000; ab31631, Abcam), anti-GAPDH (1:20000; 60004-1-Ig, Proteintech), anti-HA (1:5000; clone HA-7, H6533, Sigma), anti-Flag (1:5000; clone M2, F1804, Sigma), Anti-rabbit IgG (H+L), (Alexa Fluor 555 Conjugate) (1:1000, 4413, Cell Signaling), goat anti-mouse IgG-HRP (1:10000; HA1006, HuaBio), goat anti-rabbit IgG-HRP (1:10000; HA1001, HuaBio). The poly(I:C) (LMW) and poly(dA:dT) were purchased from InvivoGen. Lipofectamine 3000 and Lipofectamine RNAiMAX were purchased from Invitrogen. Act D (actinomycin D) was purchased from Sigma.
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3

ChIP Assay for M2 Macrophage Transcription Factors

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Involvement of NF-κB, IRF3, and STAT-3 in M2-associated gene expressions was validated by ChIP assays. The protocol used was based on the manufacturer’s instruction of EZ-ChIP kit (EMD Millipore). Briefly, macrophages were treated with 1% formaldehyde before cell lysis and DNA fragmentation. After being precleared with protein G-conjugated agarose, a 10 μL aliquot of cell lysate was saved as “input” fraction and the remaining lysate was incubated with control IgG or the antibody against NF-κB (1:100, cat. #1546-1, Epitomics), IRF3 (1:100, cat. #sc-33641, Santa Cruz Biotechnology), or STAT-3 (1:200, cat. #12640, Cell Signaling) for immunoprecipitation. DNA was extracted from the immunoprecipitate for further PCR amplification. The primers and PCR conditions are listed in Table S2.
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4

Quantitative Western Blot Analysis

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At least 500,000 J-Lat 11.1 cells or 2 × 106 CD4+ T cells were lysed per condition. Cells were washed with dPBS and lysed in ice-cold lysis buffer (100 mM NaCl, 10 mM Tris, pH 7.5, 1 mM EDTA, 0.5% Nonidet P-40, protease and phosphatase inhibitor cocktail [Roche]). Cell lysates were denatured in Laemmli sample buffer and incubated for 5 min at 95 °C. The proteins were separated by SDS-PAGE and transferred onto nitrocellulose membranes (Bio-Rad). Membranes were blocked with 5% nonfat milk in Tris-buffered saline pH 7.4 and 0.5% Tween 20 (TBST) and then incubated with primary antibodies. After three washes with TBST, the membranes were incubated with horseradish peroxidase-conjugated secondary antibodies (Rockland Immunochemicals; 1:10,000) and detected using Western Lightning Plus-ECL reagent (Perkin Elmer). Signal intensity and densitometry analyses were conducted using ImageJ (NIH). The following antibodies were used: anti-Puromycin (12D10 Sigma-Aldrich; 1:1000), anti-GAPDH (ab8245, Abcam; 1:5000) and anti-DDX3 (ab128206, Abcam; 1:2000), anti-Phospho-IRF3 (Ser386) (37829, Cell Signalling Tech; 1:1000), anti-HSP70 (4872, Cell Signalling Tech; 1:1000), anti-IRF3 (sc33641, Santa Cruz; 1:1000), anti BIRC5 (sc17779, Santa Cruz; 1:1000) and anti-tubulin (B7, Santa Cruz; 1:3000).
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5

Analyzing Innate Immune Signaling Pathways

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The antibodies used and the sources are as follows: Antibodies against TBK1 (1:1,000, 3013), p-TBK1 (1:1,000, 5483), IKKε (1:1,000, 3416), p-IKKε (1:1,000, 8766), p-IRF3 (1:500, 4947) were purchased from Cell Signaling Technology. Antibodies against cGAS (1:2,000, 26416-1-AP), STING (1:2,000, 19851-1-AP), HA tag (1:2,000, 51064-1-AP), His tag (1:2,000, 66005-1-lg), and β-actin (1:20,000, 66009-1-lg) were purchased from Proteintech Group Inc. IRF3 antibody (1:1,000, sc-33641), RNF5 antibody (1:1,000, sc-81716), and c-Myc antibody (1,1,000, sc-40) were obtained from Santa Cruz Biotechnology. Monoclonal anti-Flag (1,1,000, F1804) antibody was purchased from Sigma-Aldrich, Inc. Anti-Calreticulin antibody (1,100, ab2907) was purchased from Abcam. Poly(dA:dT) (tlrl-patn) and cGAMP (tlrl-nacga 23–02) were purchased from Invivogen. Lipofectamine 2000 transfection reagent and Opti-MEM were from Thermos Fisher Scientific. Protease inhibitors were purchased from Roche. PMSF was purchased from Solarbio Life Sciences, Beijing, China.
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