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12 protocols using anti nf κb p50

1

Proximity Ligation Assay for NF-κB Interactions

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HEY cells were cultured on 12-mm glass cell culture coverslips (Thermo Fisher Scientific). Cells were washed three times with phosphate-buffered saline (PBS) and then fixed for 15 min in PBS with 4% paraformaldehyde. After washing with gentle shaking, cells were permeabilized for 5 min with methanol and washed. The proximal-ligation assay to detect the interaction of p50 with p65, anti- NF-κB p50 (Santa Cruz Biotech, Dallas, TX; Cat: sc-8414) and anti-NF-κB p65 (Santa Cruz; Cat: sc-372) and for p65- SIRT1 interaction, anti-NF-κB p65 (Santa Cruz Biotech; Cat: sc-8008) and anti-SIRT1 (Santa Cruz; Cat: sc-15404) were used with a Duolink PLA assay kit (Sigma Aldrich). Images were acquired Zeiss LSM 700 (Zeiss).
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2

Metastatic Potential of HCC Cell Lines

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Three human HCC cell lines with unique metastatic characteristics were investigated. Hep3B cell line with the lowest metastasis potential [19 (link)] was purchased from Cell Bank of the Chinese Academy of Sciences (Shanghai, China); MHCC97L cell line with the moderate metastasis potential and HCCLM3 cell line with the highest metastasis potential were kindly obtained from the Liver Cancer Institute of Fudan University (Shanghai, China) [20 (link), 21 (link)]. All cell lines were maintained in DMEM medium (Gibico), supplemented with 10 % fetal bovine serum (FBS, Gibico), penicillin (100 U/ml), and streptomycin (100 μg/ml). Cells were incubated at 37 °C with 5 % CO2, and were harvested with 0.25 % trypsin/EDTA (Gibico) in their logarithmic growth phase, washed with PBS, and resuspended in new media. The reagents used were as follows: Recombinant human HMGB1 (rhHMGB1) and recombinant human RAGE/Fc chimera, homologs to soluble form of RAGE (sRAGE), utilized as ex-RAGE were purchased from R&D systems (Inc., Minneapolis, MN, USA). The antibodies used were as follows: anti-HMGB1 neutralizing antibody, anti-RAGE neutralizing antibody (Abcam), anti-GAPDH (Cell Signal Technology), anti-NF-κB P50, anti-NF-κB P65, and goat IgG (Santa Cruz).
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3

Transcription Factor Binding Assay

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EMSA was performed with 32P-labeld probes and 2 μg of nuclear extracts in 20 μl of EMSA reaction buffer [2 μg of poly(dI-dC)poly(dI-dC), 20 mM HEPES (pH7.9), 1 mM MgCl2, 40 mM KCl, 0.1 mM EDTA, 1 mM DTT and 12% glycerol]. Nuclear extracts were prepared from non-activated, CD3-activated (for 1.5 h and 24 h) EL4 cells as described previously (20 (link)). To perform competition assays, 100-fold excess of unlabeled competitor oligonucleotides was added to EMSA reaction mixture. To perform supershift assay, nuclear extracts in EMSA reaction buffer were incubated for 15 min with anti-Sp1 (Santa Cruz, PEP2), anti-Sp3 (Santa Cruz, D-20), anti-NF-κB p50 (Santa Cruz, D-17), and anti-NF-κB p65 (Santa Cruz, C-20), and probes were added into the reaction mixture.
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4

Toxoplasma gondii Infection Immunostaining

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For immunostaining study, AHNP (S-NSC) cells were grown on glass cover slip before infected with Toxoplasma gondii. 24 hours after infection, cells were fixed with paraformaldehyde and standard immunefluroescent staining protocol was adopted for studying the localization of targets of interest, including NFκB, STAT3, tyrosine hydroxylase, and dopamine. Antibodies utilized include: anti-NFκB p50 (Santa Cruz Biotech, SC-7178); P-STAT3 (Y705), cell signaling (#91315); anti-tyrosin hydroxylase (Sigma, T1299); and dopamine antibody (Novus Biologicals, NB120-1001).
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5

Western Blot Analysis of Cellular Proteins

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Western blot was performed and total protein extracts were prepared from tissues and cell lines according to a standard method as described previously.22 (link) Cellular nuclear protein subfractions were extracted using a commercial extraction kit (Active Motif, Tokyo, Japan), according to the protocol provided by the manufacturer. The following primary antibodies were used: anti-IKBKE (1:500; Sigma-Aldrich, St Louis, Missouri), anti-α-tubulin (1:1000; Sigma-Aldrich), anti-Elongation Factor 1 Alpha (EF-1a) antibody (1:1000; Upstate, Temecula, California), anti-NF-κB p50 (1:500; Santa Cruz Biotechnology, Santa Cruz, California), and anti-Bcl-2 and anti-caspase-3 (1:1000; Cell Signaling Technology, Danvers, Massachusetts). The secondary antibodies included goat anti-rabbit IgG-HRP and rabbit anti-mouse IgG-horse radish peroxidase (HRP).
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6

DHTS Bioactivities and Molecular Mechanisms

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DHTS (PubChem CID: 11425923) was purchased from Xi’an Honson Biotechnology (Xi’an, China), and the purity was >90% according to a high-performance liquid chromatographic analysis. A stock solution of DHTS was prepared in dimethyl sulfoxide (DMSO) and stored at −20 °C. Anti-Bad, anti-Bcl-2, anti-Bcl-xL, anti-caspase-3, anti-caspase-8, anti-caspase-9, anti-PARP, anti-phospho-JNK, and anti-phospho-p38 antibodies were purchased from Cell Signaling Technology (Danvers, MA, USA); anti-NF-κB p50, anti-NF-κB p65, anti-p-I-κB, and anti-Bim antibodies were purchased Santa Cruz Biotechnology (Santa Cruz, CA, USA); anti-phospho-ERK and anti-FasL antibodies were purchased from BD Biosciences Taiwan (Taipei, Taiwan); anti-Bax and anti-GAPDH antibodies were purchased from GeneTex International (Hsinchu City, Taiwan); anti-Fas blocking antibody was purchased from MBL International (Woburn, MA, USA); the anti-α-tubulin antibody was purchased from Zymed Laboratories (South San Francisco, CA, USA).
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7

Inducible Expression of HA-MCPIP1 in HEK293 Cells

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Human embryonic kidney T-REx-293/hemagglutinin (HA)-MCPIP1 and T-REx-293/HA-MCPIP1-D141N cell lines were kindly provided by Dr. Yi-Ling Lin (Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan). The cells can be induced by tetracycline (Tet) to express HA-MCPIP1 or HA-MCPIP1-D141N and were cultured in Dulbecco’s modified Eagle medium (DMEM) containing 10% fetal bovine serum (FBS). Anti-cleaved caspases-3, -7, -8, and -9 as well as anti-phospho-extracellular signal-regulated kinase (ERK), anti-phospho-JNK, anti-phospho-p38, anti-phospho-IκBα, anti-phospho-IKKα/β, anti-IκBα, anti-cFLIP, anti-cIAP1, anti-HA, and anti-poly(ADP ribose) polymerase (PARP) antibodies were purchased from Cell Signaling Technology (Beverly, MA, USA); the anti-GAPDH, anti-KPNA3, anti-KPNA4, and anti-MCPIP1 antibodies were obtained from GeneTex International (Hsinchu City, Taiwan); the anti-IKKα/β, anti-NF-κB p50, and anti-NF-κB p65 antibodies, and Protein A/G PLUS-Agarose were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA); and the anti-α-tubulin antibody was obtained from Sigma-Aldrich (St. Louis, MO, USA).
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8

NF-κB Binding Assay in T Cells

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Single-stranded oligonucleotides were synthesized by Eurofins MWG Operon and annealed.
Overnight resting and anti-CD3/anti-CD28 stimulated CD4+ T cells from wt or Cbl-b- deficient mice were lysed and nuclear extracts were prepared. The following oligonucleotides were used, and the core binding motifs are underlined:
Binding reactions and supershifts were performed for 30 min at 4–8°C using the Binding Buffer B-1 (Active Motif 37480) together with Stabilizing Solution D (Active Motif 37488) containing 4 μg mouse T cell nuclear extracts (Active Motif 36042) and 2 μg of anti NF-κB (p50) (Santa Cruz-1190) antibody.
Binding reactions with the 3 × 105 cpm labeled probe were performed for 20 min at 4°-8°C using Binding Buffer C-1 (Active Motif 37484) together with Stabilizing Solution D (Active Motif 37488). Samples were run on a 4% native polyacrylamide gel in 0.5 × TBE for 3 h at 250 V. For competition assays, 10-fold unlabeled oligonucleotides identical to the radioactive-labeled probes were added to the binding reaction.
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9

Evaluation of Cell Line Characteristics

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The HeLa, C33A, and Caski cell lines were obtained from American Type Culture Collection (ATCC) and were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum at 37°C, 5% CO2. Anti-MMP2, MMP9, TIMP-1, TIMP-2, β-actin,p38 and p-p38 were obtained from Cell Signaling Technology (Beverly, MA). Anti-NF-κB-p50, p65/Rel A and Histone H1 antibodies were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). 3-(4, 5-Dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide (MTT) and all other chemicals were obtained from Sigma (St Louis, MO), unless otherwise indicated.
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10

Molecular Profiling of Prostate Cancer

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Dorsolateral prostate tissue from treated and control groups were subjected to preparation of total tissue lysate and isolation of cytosolic and nuclear fractions as described previously [38 (link)]. For Western blotting, 25 μg of protein was resolved over 4–20% Tris-glycine polyacrylamide gel and then transferred onto the nitrocellulose membrane. The blots were blocked using 5% non-fat dry milk and probed using appropriate primary antibodies overnight at 4°C. The antibodies used were anti-IKKα (sc-7218), anti-IKKβ (sc-34673), anti-NF-κB/p65 (sc-8008), anti-NF-κB/p50 (sc-8414), anti-IκBα (sc-1643) anti-p-IκBα (sc-8404), anti-Bax (sc-493), anti-Bcl2 (sc-7382), anti-COX-2 (sc-795), anti-cyclin D1 (sc-533), anti-PCNA (sc-56), and anti-VEGF (sc-152) procured from Santa Cruz Biotechnology, Santa Cruz, CA. Antibodies including anti-cleaved caspase-3 (#9661), anti-Bcl-xL (#2762), anti-p-IKKα/β (#2078) were purchased from Cell Signaling Technology, Danvers, MA. Anti-β-actin (#A1978) was obtained from Sigma-Aldrich, St. Louis, MO. The membrane was then incubated with appropriate secondary mouse (sc-2005) and rabbit (sc-2004) antibody horseradish peroxidase conjugate (Santa Cruz Biotechnology) followed by detection using chemiluminescence ECL kit (GE Healthcare Biosciences). For equal loading of proteins, the membrane was probed with appropriate loading controls.
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