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5 protocols using anti ppm1a

1

Inhibition of TGF-β Signaling Pathway

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Human recombinant TGF-β1 was obtained from R&D Systems (Minneapolis, MN). The TGF-β RI (TβRI) kinase inhibitor SB431542 was obtained from Millipore (Billerica, MA), and SD-208 was purchased from Sigma (St Louis, MO). The following antibodies were used in this study: anti-PPM1A, anti-MMP2, anti-MMP9, anti-Smad2, anti-Smad3, anti-phosphorylated Smad2 and anti-phosphorylated Smad3 (Cell Signaling Technology, Beverly, MA) as well as anti-E-cadherin, anti-GAPDH, anti-CK19, anti-phosphorylated Smad2/3 and anti-Vim (Santa Cruz, CA, USA). SB431542 was applied during the TGF-β1 perfusion.
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2

Immunoprecipitation and Immunoblotting Analysis

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The cells were incubated with an appropriate volume of immunoprecipitation lysis buffer (Pierce, Thermo Scientific) and a protease inhibitor mixture for 4 hours at 4°C. The supernatant lysates were collected and were then incubated with 2 μg of primary antibodies overnight at 4°C: anti-Flag (1:100; Proteintech, 66008-3), anti-HA (1:100; Proteintech, 51064-2), anti-NDRG2 (1:100; Abcam, ab174850), and anti-PPM1A (1:100; Cell Signaling Technology, 3549). After incubation for 4 hours at 4°C, the protein A/G magnetic beads (MedChemExpress, HY-K0202) were washed three times with the lysis buffer. The proteins were eluted in loading buffer and analyzed by immunoblotting analysis.
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3

Signaling Pathways of Host Immune Response

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Expression plasmids encoding Flag-, Myc-, or HA-tagged human TBK1, IKKε, IRF3, caRIG-I, MAVS, STING, PPM1A or its D239N and R174G mutations, and the IRF3/7-responsive reporters IFNβ_Luc and 5xISRE_Luc have been described by Lin et al. (28 (link)) and Xu et al. (56 (link)). Site-directed mutagenesis was used to generate expression plasmids encoding TBK1/IKKε with amino acids Ser172 replaced by Ala or Glu. TBK1 truncations, including TBK1 amino acids 1 to 299, 1 to 382, and 299 to 729 were generated by PCR-based cloning, which was performed using a kit from Stratagene. Detailed information will be provided upon request. All coding sequences were verified by DNA sequencing.
Poly(I:C) was from Invivogen. GFP- and luciferase-tagged herpes simplex virus–1 (HSV-1) was a gift from J. Han (Xiamen University, Xiamen). gVSV was a gift from Z. J. Chen (University of Texas Southwestern Medical Center, Dallas). SeV (Cantell strain) was from Charles River Laboratories. λPPase was from BioLabs. The monoclonal anti-IRF3, anti-pIRF3, anti-TBK1, anti-pTBK1 (S172), anti-IKKε, anti-IKKε (S172), anti-MAVS, anti-Myc, anti-PPM1A, and anti-HA antibodies were from Cell Signaling Technology. Anti–α-tubulin and anti-Flag antibodies were from Sigma. Ppm1a−/− C57BL/6 mice were generated by Feng Laboratories.
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Immunoprecipitation and Immunoblotting of Cellular Proteins

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Liver lysates upon hepatectomy surgery and HEK293 cells with indicated treatments were lysed using a modified Myc lysis buffer (MLB) (20 mM Tris-Cl, 200 mM NaCl, 10 mM NaF, 1 mM NaV2O4, 1% NP-40, 20 mM β-glycerophosphate, and protease inhibitor (pH 7.5)) [77 (link)]. Cell lysates were then subjected to immunoprecipitation using antibodies of anti-Flag (Sigma-Aldrich, F3165-5MG, 1:200 dilution), anti-Myc (2276S, Cell Signaling Technology, 1:200 dilution), or anti-HA (3724S, Cell Signaling Technology, 1:200 dilution) for transfected proteins, or using anti-PPM1A (3549, Cell Signaling Technology, 1:100 dilution) antibody for endogenous proteins. After 3 to 4 washes with MLB, adsorbed proteins were resolved by SDS-PAGE (Bio-Rad) and immunoblotting with the indicated antibodies. Cell lysates were also analyzed using SDS-PAGE and immunoblotting to control the protein abundance.
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5

Antibody Sources for Protein Analysis

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Specific antibodies were purchased from the following commercial sources: Anti-AFP, anti-ALB, anti-CD44, anti-Evi1, anti-flag (mouse), anti-HA, anti-HNF4α, anti-H3, anti-H3K36me3, anti-Myc, anti-OCT4A, anti-P300, anti-PPM1A (rabbit), anti-pSmad2 (S465/467), anti-pSmad2 (S245/250/255), anti-pSmad3 (s423/425), anti-Smad2, anti-Smad3 (rabbit), anti-SnoN, anti-Sox2, anti-TAT, and normal rabbit IgG from Cell Signaling Technology (Danvers, MA); anti-PPM1A (mouse), anti-SC35, and anti-SETD2 were from Abcam (Cambridge, MA); Anti-Smad4 and normal mouse IgG were from Santa Cruz Biotechnology (Santa Cruz, CA); Anti-β-actin, and anti-flag (rabbit) from Sigma-Aldrich (St. Louis, MO); Alexa594 goat anti-mouse IgG from Life Technology (Carlsbad, CA); Dylight488 goat anti-rabbit IgG from Vector Labs (Burlingame, CA).
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