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10 protocols using anti phospho p65

1

Protein extraction and western blot

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Total protein was extracted using 2% SDS lysis buffer including protein phosphatase inhibitor (Applygen, Beijing) and heated for 10 min. Protein samples were separated by 8% (v/v) SDS-PAGE gels and transferred onto nitrocellulose membranes (Millipore, Ireland). After blocking in 5% (w/v) Albumin Bovine-V (BSA-V, Solarbio, China) for 1 h at room temperature, the protein bands were incubated with primary antibodies at a dilution ratio of 1:1000 overnight at 4 °C. The primary antibodies contain anti-GAPDH (FL-335; Santa Cruz Bio technology), anti-TGM2 (Proteintech), anti-PD-L1 (Proteintech), anti-STAT3 (CST) and anti-Phospho-STAT3 (Ser705, CST), anti-Akt (CST), and anti-Phospho-Akt (Ser473, CST), anti-P65 (Abcam) and anti-Phospho-P65 (Ser536, Abcam). The protein bands were incubated in HRP-conjugated secondary antibodies (Zsbio, China, 1:5000) at room temperature for 1 h.
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2

Pepsin-Induced NF-κB Activation Assay

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FaDu cells grown in 6-well plates were treated with pepsin (0.2 mg/mL) in pH7.0 for 30 min. Levels of phosphorylated of IκB and p65 were evaluated by Western analysis. Rabbit polyclonal anti- p65, anti-phospho-p65, anti-IκB, and anti-phospho- IκB antibodies were purchased from Abcam (Cambridge, UK). The secondary antibodies were Goat anti-rabbit antibodies conjugated with horseradish peroxidase purchased from Abcam (Cambridge, UK). Signals were visualized by ChemiDoc XRS+ using the Image LabTM Software (Bio-Rad Laboratories, Munich, Germany). Protein levels were quantified by scanning densitometry.
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3

Protein Expression Analysis Protocol

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Protein samples were extracted with RIPA-buffer (Heart, China) from LTP-treated cells after 24 h in culture, then heated at 95 °C °C for 5 min with sample buffer (250 mM Tris-HCl, pH 6.8, 10% glycerol, 4% sodium dodecyl sulfate, 2% β-mercaptoethanol, and 0.003% bromophenol blue). Proteins were separated on 12% SDS-PAGE, and electrophoretically transferred onto polyvinylidene difluoride (PVDF) membrane (Millipore, USA), and then blocked with 5% dried skim milk in Tris buffer saline with 0.1% Tween-20 (TBST) for 2 h at room temperature. The blocked membranes are rinsed three times in TBST for 10 min, and then incubated in the primary antibodies (anti-phospho p65, 1:5000, Abcam; anti-NF-κB P65 and anti-NF-κBIα Polyclonal Antibody, 1:2000, ABclonal; anti-cyclinD1, 1:200, Santa Cruz; anti-β-actin, 1:2000, CWbio) overnight at 4 °C. After being washed three times with TBST, the secondary antibody horseradish peroxidase (CWbio) was incubated on the membrane for 2 h at room temperature. Then the PVDF membranes were washed three times with TBST and incubated with ECL Plus Reagent (Millipore, USA) and scanned using the chemiluminescence (BioRad, USA). Immunoreactive products were quantified by image-Pro plus 6.0 software to determine the optical density of protein bands.
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4

Western Blot Analysis of Extracellular Vesicle Markers

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The Western blot was conducted following routine procedures, as described previously (20 (link)). Briefly, proteins were extracted using radioimmunoprecipitation buffer containing protease inhibitor cocktail (Abcam). Protein concentration was measured by BCA assay kit (Abcam). The 20 µg of protein were loaded on SDS-PAGE gel and then subjected to transfer. The primary antibodies used in the study included: anti-CD63 (1:1,000; Abcam), anti-β actin (1:2,000; Abcam), anti-CD9 (1:1,000; Abcam), anti-Alix (1:1,000; Abcam), anti-TLR4 (1:1,000; Abcam), anti-phospho-p65 (1:1,000; Abcam), anti-p65 (1:1,000; Abcam).
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5

Multifaceted Immunofluorescence Assay for Cellular Stress Response

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PC-3 cells were cultured in the cell culture chamber. The cells were fixed in 4% paraformaldehyde for 15 min, permeabilized using 0.2% triton X-100 for 10 min, followed by staining with rabbit anti-human γH2AX, rabbit anti-human 53BP1, mouse anti-human phospho-histone H3, rabbit anti-human phospho-p65 (Cell signal technology) and mouse anti-human PD-L1 antibody (Abcam) or normal control IgG 6–8 hours at 4°C. Then, Alexa Flour 488-conjugated goat anti-rabbit IgG and Alexa Flour 594-conjugated goat anti-mouse IgG were added and incubated for 1 hour at 37°C. The nucleus was stained with 4'6-diamidino-2-phenylindole and mounted with ProLong Gold Antifade Reagent (Life Technologies). The images were analyzed using a Zeiss LSM 880 Confocal Imaging System (Zeiss, Jena, Germany).31 (link)
Paraffin-embedded tissues were sectioned and subjected to immunostaining using primary antibodies such as anti-PD-L1, anti-CD45, anti-phospho-ATM, anti-phospho-p65, anti-CD3 and anti-interferon-γ (IFNγ) (Abcam). The isotype-matched primary antibodies served as the controls. Antibody binding was visualized using fluorescence-labeled secondary antibodies under a Zeiss LSM 880 Confocal Imaging System.
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6

Quantification of Signaling Pathway Proteins in Sciatic Nerve

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Sciatic nerves were dissected (n = 5) and frozen immediately in liquid nitrogen. Total protein was extracted, quantified using a bicinchoninic acid (BCA) protein assay reagent kit (ASPEN), and heated for 10 min at 95°C. Equal amounts of proteins were separated by 4%–12% Bis–Tris sodium dodecyl sulfate‒polyacrylamide gel electrophoresis (Baiqiandu) and transferred to polyvinylidene fluoride membranes (Millipore). Nonspecific binding sites were blocked by incubation in 5% nonfat dry milk in TBST (Tris‐buffered saline, 0.1% Tween 20) for 1 h. Membranes were then incubated at 4°C for 12 h with primary anti‐Akt antibodies (1:2000; Cell Signaling Technology), anti‐phospho‐Akt (pAkt; 1:2000; Cell Signaling Technology), anti‐s6k (1:1000; Cell Signaling Technology), anti‐phospho‐s6k (ps6k; 1:1000; Cell Signaling Technology), anti‐p65 (1:1000; Abcam), anti‐phospho‐p65 (1:1000; Abcam), or control GAPDH (1:6000, Abcam). After three washes in TBST, bound antibodies were detected by incubation with the corresponding secondary antibodies (1:50,000) for 1 h. Data were analyzed using Image‐Pro Plus software, version 6.3 (Media Cybernetics, Inc., Rockville, MD, USA).
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7

Immunohistochemistry in MPTP Mouse Model

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GTB was purchased from Spectrum (New Brunswick, NJ). MPTP was procured from Sigma-Aldrich (St. Louis, MO). Mouse anti–TH antibody (ImmunoStar, Hudson, WI), goat anti-Iba1 antibody (Abcam, Cambridge, MA), rabbit anti-GFAP antibody (Agilent Technologies, Santa Clara, CA), mouse anti-iNOS Ab (BD Biosciences, San Jose, CA), anti GTP-p21Ras (New East Biosciences) and anti-phospho-p65 (Abcam) antibodies were purchased from different vendors. Cy2-and Cy5-conjugated secondary antibodies were obtained from Jackson Immuno-Research Laboratories (West Grove, PA).
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8

Quantification and Immunoblotting of Signaling Proteins

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Cell proteins were extracted using RIPA buffer containing a mixture of protease and phosphatase inhibitors. The protein content of each sample was quantified using the bicinchoninic acid assay method with bovine serum albumin (Biosharp, China). Subsequently, an equal amount of protein was subjected to electrophoresis on a polyacrylamide gel and transferred to the PVDF membrane. The following antibodies were applied: anti-JNK (1:1000, Abcam, USA), anti-phospho-JNK (1:1000, Abcam, USA), anti-p65 (1:1000, Abcam, USA), anti-phospho-p65 (1:1000, Abcam, USA), and anti-GAPDH (1:1000, Abcam, USA). Finally, the chemiluminescence detection system (Immobilon Western, USA) was used to visualize the immunolabeled bands.
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9

Protein Expression Analysis in Chondrocytes

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Proteins were extracted from chondrocytes using RIPA buffer containing protease inhibitor cocktail (Sigma-Aldrich). The total protein concentration was determined using the Protein Assay Kit (Bio-Rad). Next, 20-μg of total proteins diluted in sodium dodecyl sulfate sample buffer were resolved on 4–20% Mini-PROTEAN-TGX Precast Protein gels (Bio-Rad). Subsequently, proteins were electrophoretically transferred to Polyvinylidene fluoride membrane (Invitrogen). Membranes were blocked with Odyssey® Blocking Buffer (Li-Cor Biosciences) for 1h. Blots were incubated overnight at 4°C with the following primary antibodies: anti-POSTN (1:1000, Abcam), anti-phospho-p65 (1:1000, Abcam), anti-MMP-13 (1:4000, Abcam), or anti-total-p65 (1:1000, Abcam). The next day, membranes were washed and subsequently incubated with fluorescently labeled secondary antibody IRDye 680RD goat anti-rabbit IgG (1:20,000, Li-Cor). For cell lysates, the housekeeping anti-β-actin (1:4000, Sigma-Aldrich) was used as the primary antibody for cell lysates, and the fluorescently labeled IRDye 800CW goat anti-mouse IgG (1:20,000, Li-Cor) was used as the secondary antibody. Blots were imaged using an Odyssey Infrared Imager and the signal intensity was quantified using ImageJ software.
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10

Immunofluorescence Staining of Paraffin-Embedded Tissue

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Paraffin-embedded sections were deparaffinized with xylene and rehydrated using a graded series of ethanol (70%→50%→30%). Proteinase K (10-μg/mL, Abcam) was applied to the sections for antigen retrieval for 20-min at 37°C. The slides were washed with PBS and blocked with 10% normal goat serum (NGS). Subsequently, slides were incubated overnight at 4°C with the following primary antibodies diluted in 2% NGS: anti-Postn (1:100, Abcam), anti-phospho-p65 (1:100, Abcam), anti-MMP-13 (1:200, Abcam), and in-house anti-type-II collagen (Col-2, 1:200). The slides were washed with PBS and incubated with the corresponding Alexa 488-, or Alexa 594-conjugated secondary antibodies in 2% NGS for 1h at room-temperature, and counterstained with Fluoro-Gel II with 4′,6-diamidino-2-phenylindole (DAPI, Electron-Microscopy-Sciences). All images were visualized using a Confocal Laser-Scanning-Microscope (Leica-Biosystems). Signal intensity was quantified in 20–30 cells/section using LAS-X software (Leica-Biosystems).
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