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TRAF6 is a protein that plays a key role in cell signaling pathways. It functions as an E3 ubiquitin ligase, catalyzing the attachment of polyubiquitin chains to target proteins, which can lead to their activation or degradation. TRAF6 is involved in the regulation of various cellular processes, including immune response, inflammation, and cell survival.

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34 protocols using traf6

1

Signaling Pathway Protein Antibodies

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TRAF6, p-TAKThr184/187, p-IRAK4Thr345/Ser346, IRAK4, p-P38, P38, p-JNK, JNK, p-ERK, ERK, GR, and NF-κBp65 antibodies were purchased from Cell Signaling Technologies (Danvers, MA) with respective catalog numbers 8028S, 90C7, D6D7, 4363, 4511S, 8690S, 9251S,9252T, 4370S, 4695S, 12041T, D14E12. p-TAKSer439 was obtained from Abcam (Cat EPR2863). β-Actin and Lamin B antibodies were purchased from Santa Cruz Biotechnology (Santa Cruz, CA;, sc-47778, sc-6217). β-tubulin was purchased Sigma (St. Louis, MO cat# T8328). All antibodies were diluted in 5% BSA/TBS-T according to manufactures recommendation. JWH-015 was sourced from Tocris (Cat# 1341; ≥99% HPLC) and dissolved in DMSO at a stock concentration of 10 mM. For in vivo studies, JWH-015 was dissolved 3% DMSO/PBS.
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2

Antibody Procurement and Inhibitor Sources

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Antibodies against GP73, MAVS, GAPDH, AIF, MBP and GST were purchased from Proteintech (Wuhan, Hubei, China). Antibody against HCV NS5A (2F6) was purchased from BioFront (Anhui, Hefei, China). Antibodies against HCV Core and p-IRF3 were purchased from Abcam (Cambridge, MA, USA). Antibody against IRF3 was purchased from Santa Cruz Biotechnology (Dallas, Texas, USA). Antibodies against Flag, HA, c-Myc, TRAF6, Calnexin, Syntaxin 6, p-IκBα and IκBα were purchased from Cell Signaling Technology (Danvers, MA, USA). All inhibitors were purchased from Selleck Chemicals (Houston, TX, USA).
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3

Antibody-based NF-κB Signaling Pathway

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Antibodies against the following proteins were purchased from Santa Cruz Biotechology, Inc (Santa Cruz, CA, USA): TLR4 (1:800), total-P65 (T-P65) (1:800), inhibitor (I)κBα (1:500), phosphorylated-P65 (P-P65) (1:300) and GAPDH (1:4000). The antibodies against myeloid differentiation factor-88 (MyD88) (1:1000), tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6) (1:800) and transforming growth factor-β-activated kinase 1 (TAK1) (1:800) were purchased from Cell Signaling Technology, Inc. (Danvers, MA, USA).
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4

Investigating Inflammatory Liver Injury Mechanisms

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Human serum albumin (HSA) was obtained from Baxter (Deerfield, IL, United States). LPS, D-galactosamine, ALT kit, and AST kit were purchased from Sigma-Aldrich (St Louis, MO, United States). IL-6, IL-22, HMGB1 ELISA kits were purchased from BIKW Co., Ltd. (Beijing, China). Antibodies against Ubiquitin (Cat.3936), TRAF6 (Cat.8028), p38 (Cat.9212), p-p38 (Cat.9216), p65 (Cat.8242), p-p65 (Cat.3033), JNK (Cat.9252), p-JNK (Cat.4668), STAT1 (Cat.14995), and Actin (Cat.3700) were obtained from Cell Signaling Technology (United States). The magnetic RNA-Protein Pull-Down Kit was purchased from Thermo Fisher (United States). Real-time PCR kits were from Takara (Japan). NEAT1 lentivirus, sh-NEAT1 lentivirus, AAV8, and AAV8-NEAT1 were purchased from Genechem (China).
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5

Osteoclastogenesis Regulation by FAM19A5

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Human recombinant FAM19A5 was purchased from Biovendor (Brno, Czech Republic). Murine recombinant M-CSF and murine RANKL were purchased from Peprotech (Rocky Hill, NJ, USA). LPS was purchased from Sigma-Aldrich (St. Louis, MO, USA). WKYMVm and WRW4 were synthesized from Anygen (Gwangju, Korea). Polymyxin B, PTX, and PD98059 were purchased from Calbiochem (San Diego, CA, USA). LY294002 was obtained from BIOMOL Research Laboratories, Inc. (Plymouth Meeting, PA, USA). MK-2206 was purchased from Selleck Chemicals (Houston, TX, USA). Phospho-Akt (Ser473), Akt, phospho-ERK, ERK, RANK, TRAF6, and β-actin antibodies were purchased from Cell Signaling Technology (Beverly, MA, USA). c-fos and NFATc1 antibodies were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA).
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6

Immunofluorescence Analysis of Pellino1 and TRAF6 in THP-1 Cells

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After induction model, THP-1 cell was fixed with 4 % paraformaldehyde for 15 min and then incubated with using 0.25 % Triton X100 for 15 min at room temperature. THP-1 cell was incubated with Pellino1 (1:100, 31,474, Cell Signaling Technology) and TRAF6 (1:100, 8028, Cell Signaling Technology) at 4˚C overnight after blocking with 5 % BSA for 1 h. After washing with PBS for 15 min, THP-1 cell was incubated with goat anti-rabbit IgG-cFL 555 (1:100, sc-362,272, Santa Cruz Biotechnology) or anti-mouse IgG-cFL 488 antibody (1:100, sc-362,267, Santa Cruz Biotechnology) for 2 h at room temperature and stained with DAPI for 15 min and washed with PBS for 15 min. The images of THP-1 cell obtained using a Zeiss Axioplan 2 fluorescent microscope (carl Zeiss AG, Oberkochen, Germany).
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7

Evaluating Cartilage Protein Expression

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Total proteins were isolated from treated human T/C-28a2 cells using the lysis buffer and were quantified using the bicinchoninic acid (BCA) kit (Vazyme, Nanjing, China), followed by being loaded onto the sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). After separation for 1 h, proteins were transferred to the polyvinylidene fluoride (PVDF) membrane (Bio-Rad, California, USA) and the membrane was incubated with the primary antibody against type 2 collagen (1:500, #ab34712, Abcam, USA), Aggrecan (1:500; #216965, Abcam, USA), TRAF-6 (1:2000; #8028, Cell Signaling Technologies, USA), IκBα (1:3000; #4814, Cell Signaling Technologies, USA), p-IκBα (1:1000, #5209, Cell Signaling Technologies, USA), NF-κB p65 (1:2000; #3036, Cell Signaling Technologies, USA), lamin B1 (1:5000, #13435, Cell Signaling Technologies, USA), and β-actin (1:10,000, #3700, Cell Signaling Technologies, USA). Then, the membrane was incubated with the Horseradish Peroxidase (HRP)- linked goat anti-mouse (1:3000, #7076, Cell Signaling Technologies, USA) or goat anti-rabbit (1: 2000, #7074, Cell Signaling Technologies, USA) secondary antibodies, followed by 3 washes and exposure to ECL solution (Vazyme, Nanjing, China). Lastly, the quantification was conducted on the bands using the Image J software and normalized to the internal control β-actin or lamin B1.
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8

Prostate CAFs Protein Expression Analysis

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Prostate CAFs were seeded in 6-well plates at a density of 3 × 105 cells/well and were treated with MPSSS at different concentrations (0, 0.1, 0.2, 0.3, 0.4, and 0.5 mg/ml) for 24 h. Then the cells were lysed with RIPA buffer supplemented with 100 mΜ phenylmethylsulfonyl fluoride (PMSF), 25 μg/ml aprotinin, 1 mM sodium orthovanadate, and 50 nM NaF to obtain the total protein content. The total protein concentrations were determined by the BCA protein assay. Equal amounts of protein samples (30 μg/sample) were separated on 10% SDS polyacrylamide gels under denaturing conditions and were then electrotransferred onto nitrocellulose membranes (GE Healthcare, Milwaukee, WI, U.S.A.) for 70 min at 100 V. Then, the membranes were blocked with 3% BSA in PBS-T (0.1% Tween-20) for 1 h and were incubated overnight at 4°C with the primary antibodies. The primary antibodies used were against α-SMA, phospho-NF-ĸB p65, NF-ĸB p65, phospho-TAK, TAK, phospho-IKKα/β, TRAF6, and MyD88 (all from Cell Signaling Technology, U.S.A.) and were diluted at 1:1000; the primary antibody against GAPDH (Tianjin Sungene Biotech Co., Ltd.) was diluted at 1:2000 and was used as an internal standard.
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9

Subcellular Fractionation and Western Blot

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Subcellular fractions were generated using a Cell Fractionation kit (Cell Signaling). A total of 5–10 μg of sample was separated by 4–12% Bis-Tris Nupage gels (Invitrogen), transferred to polyvinylidenedifluoride membranes (Millipore) and developed with antibodies against GAPDH (no. 14C10, Cell Signaling), histone H3 (EMD Millipore), NF-κB p65 (no. D14E12, Cell Signaling), TRAF6 (no. 8028, Cell Signaling) or AHR (no. BML-SA210, Enzo Life Sciences). Blots were developed using a SuperSignal West Femto Maximum sensitivity kit (Thermo Scientific/Life Technologies). Quantification was done using Image J software v.1.48 (NIH).
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10

Signaling Pathway Analysis with Torilin

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Primary antibodies for iNOS, COX-2, β-actin, PARP, phospho-PI3K p85, PI3K, Akt, phospho-Akt, NF-κB, phospho-NF-κB, IκB-α, phospho-IκB-α, IKKβ, phospho-IKKα/β, phospho-p38, p38MAPK, phospho-JNK, JNK, phospho-ERK1/2, ERK1/2, MKK4, MKK6, MyD88, IRAK1, TRAF6, phosphor-TAK1, TAK1, phospho-c-fos, phosphor-c-jun, phosphor-ATF2, IL-1β, TNFα, and horseradish peroxidase-conjugated secondary antibody were from Cell Signaling Technology (Danvers, MA, USA). SB203580, SP600125, and PD98059 were from Sigma-Aldrich (St. Louis, MO). Consensus oligonucleotides for NF-κB and AP-1 were obtained from Santa Cruz Biotechnology (Santa Cruz, CA). γ−32 P-Labeled ATP was purchased from ICN (Costa Mesa, CA). A prostaglandin E2 EIA kit was from Enzo life Sciences (Ann Arbor, MI, USA). Easy Blue™ RNA extraction kit was from iNtRON, Korea. Millipore MILLIPLEX™ Mouse Cytokine/Chemokine enzyme-linked immunosorbent assay kit was from Millipore Corp. (St. Charles, MO). All materials, equipment, and biotinylated marker proteins for gel electrophoresis were from Bio-Rad. All other chemicals were purchased from Sigma-Aldrich (St. Louis, MO) unless otherwise stated. Torilin (98%) was prepared as previously indicated in [26 (link)] and dissolved in dimethyl sulfoxide and freshly diluted in culture media for all experiments.
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