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11 protocols using protein phosphatase inhibitor

1

Western Blot Analysis of Spinal Cord Injury

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Spinal cord tissue samples were collected after the scarification of rats. The spinal cord segments at the contusion epicenter and lumbar spinal cord were dissected and frozen at −80°C (Zhang et al., 2017 (link)). Tissues were lysed in RIPA buffer (Beyotime, China) with 1% phenylmethylsulfonyl fluoride (Beyotime) and 1% protein phosphatase inhibitor (Beyotime) on ice for 30 min. The samples were centrifuged at 14,000 rpm and 4°C for 20 min. The supernatant was removed and used for Western blotting. Total protein (40–60 μg) was load onto SDS-PAGE, and then transferred to PVDF membranes and blocked in 5% non-fat milk/Tris-buffered saline/Tween-20 (TBST) at room temperature for 2 h. Membranes were probed overnight at 4°C with P2X4R, IL-1β (1:1000, Abcam), IL-18 (1:1000, Abcam), MMP-9 (1:1000, Invitrogen) antibodies. After incubation with horseradish peroxidase-conjugated anti-rabbit secondary antibody (1:2000, Sigma) for 1 h at room temperature, the bands were visualized with enhanced chemiluminescence reagents (Sigma). Densitometric quantification of the membranes was performed using Image J.
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2

Western Blot Analysis of Protein Signaling

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Cells were lysed in RIPA buffer with 1% phenylmethylsulfonyl fluoride and 1% protein phosphatase inhibitor (Beyotime, China) on ice for 20 min. Proteins in the mouse tissue homogenate were extracted with RIPA buffer (Beyotime, China). Lysates were centrifuged at 12,000 rpm for 30 min at 4°C to obtain supernatants. Equal amounts of protein lysates in RIPA were separated on 8%, 10% or 12% SDS-PAGE gels before being transferred to polyvinylidene fluoride membranes (Merck Millipore, USA). The membranes were blocked with 5% milk and then incubated with primary antibodies in primary antibody dilution buffer (Beyotime, China) at 4°C overnight. The blots were probed with the following antibodies: Tau 1:1,000, P-Tau Thr181 1:1,000, Akt 1:1,000, P-Akt Ser 473 1:2,000, P-ERK1/2 Thr202/Tyr204 1:2,000, ERK1/2 1:1,000, Caspase 3 1:1,000, P-PKCζ/λ Thr410/403 1:1,000 (Cell Signal Technology, USA); KIBRA 1:500, PKCζ 1:1,000 (Santa Cruz, USA); PARP-1 1:1,000 (Abcam, UK); β-actin 1:2,000 (Proteintech, China). The membranes were subsequently incubated with peroxidase-conjugated secondary antibodies and developed using the enhanced chemiluminescence (Merck Millipore) method. Band densities were quantified by densitometry using Fluor ChemQ software.
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3

Protein Expression Analysis Protocol

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Whole-cell protein was extracted with the RIPA lysis buffer containing protease inhibitor (Beyotime) and protein phosphatase inhibitor (Beyotime) on ice. Equal amounts of protein (30 μg) were loaded into 10% (w/v) SDS-PAGE and transferred to a polyvinylidene difluoride membrane (Millipore, St. Louis, MO, USA), with the membrane then incubated with primary antibodies at 4 °C overnight, followed by three series of TBST washing and 2 h of HRP-conjugated secondary antibodies incubation at room temperature. The proteins were visualized through chemiluminescence and imaged on a Gelview 6000 Pro (BLT Co., Ltd, Guangzhou, China). The protein bands were quantified by densitometry analysis using Image J software.
The primary antibodies used in this study included antibodies against GAPDH (1:1000; Affinity Biosciences), Vim (1:1000; Abcam), E-cad (1:1000; Affinity Biosciences), N-cad (1:1000; Santa Cruz, Cincinnati, OH, USA), PI3K (1:1000; Santa Cruz), AKT (1:1000; Santa Cruz), p-PI3K (1:1000; Affinity Biosciences), p-AKT (1:1000; Affinity Biosciences), and PTHR1 (1:1000; Affinity Biosciences).
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4

Inhibiting Cancer Cell Proliferation with OSW-1

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OSW-1 (C47H68O15, purity ≥95%) was purchased from Cayman Chemical Company (Ann Arbor, Michigan, United States), dissolved in dimethyl-sulfoxide DMSO (Sigma-Aldrich, St. Louis, MO, United States) then stored in the dark at − 20°C. OSW-1 was diluted with cell culture medium to the required concentrations, with DMSO concentration <0.1%, to avoid side effects. Dulbecco’s modified Eagle medium (DMEM) and fetal bovine serum (FBS) were purchased from Thermo Fisher Scientific (Gibco, United States). Cell counting Kit-8 (CCK-8), RNase, penicillin/streptomycin, propidium iodide, Annexin V-FITC Apoptosis Detection Kit, RIPA lysate, protease inhibitor, protein phosphatase inhibitor, BCA protein assay kit, and electrochemiluminescence (ECL) kit were purchased from Beyotime Biotechnology Company (Shanghai, China). 740Y-P was purchased from TargetMol (Shanghai, China). Primary antibodies against P21 (ab109520), cyclin B1 (ab32053), CDK1 (ab133327), PARP-1 (ab191217), cleaved-PARP-1 (ab32064), cleaved caspase-3 (ab214430), beta Actin (ab8226), PI3K(ab191606), p-PI3K (ab278545), AKT1 (ab183556), and p-AKT1 (ab81283) were purchased from Abcam (Cambridge, MA, United Kingdom). Primary antibodies against cleaved caspase-9 (#9502) and secondary antibodies (goat anti-mouse IgG and goat anti-rabbit IgG, #98164 and #91196) were purchased from Cell Signaling Technology (Beverly, MA, United States).
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5

Protein Expression Analysis of BMMs

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BMMs were cultured with PDA, ALN, and PDA-ALN. After 7 days of incubation, cells were treated with Cytoplasmic Protein Extraction Kit supplemented with protease inhibitor cocktail and protein phosphatase inhibitor (Beyotime Biotechnology). The solution was separated by SDS-PAGE electrophoresis and transferred to PVDF membranes (Millipore, USA), which were incubated with 5% nonfat milk (CST, USA) in PBS for 1 h room temperature at first, then the primary antibody at 4 °C overnight. On the second day, the membranes were incubated with secondary antibodies before washing with PBS-T. The primary antibodies, including anti-NFATc1 and anti-TRAF3, were purchased from Abcam (Cambridge, UK). Finally, the membranes were detected by Odyssey Infrared Imaging System.
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6

Protein Extraction and Western Blot Analysis

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The throat tissues were mechanically grinded in a glass homogenizer, the RIPA lysis buffer (Beyotime, Jiangsu, China) and protein phosphatase inhibitor (Beyotime, Jiangsu, China) were added to lysed the samples for 1 h on ice. In order to acquire supernatant, homogenates were centrifuged for 10 min at 12,000 rpm and 4 °C [29 (link)]. BCA protein test kit (Beyotime, Jiangsu, China) was used for the protein quantification. Then boiling the soluble extracts with Loading buffer (Beyotime, Jiangsu, China) for 10 min. The equal amount of protein exact of samples were electrophoresed on a 10% SDS-PAGE, then the electrophoretic proteins are transferred onto a PVDF. After blocking, membrane was probed with goat polyclonal antibodies against NF-κB p65 (1:2000; Proteintech, USA), COX-2 (1:1000; Proteintech, USA), GAPDH (1:5000; Proteintech, USA). The second day, rinsing the membrane with tris-buffered saline Tween (TBST) 3 times for 10 min, and incubating with goat anti-rabbit IgG (1:5000; Proteintech, USA), which can conjugate with appropriate secondary antibody HRP. Afterwards, cleaning the membrane again with TBST and treated with a chemiluminescence analysis kits (Beyotime, Jiangsu, China) for visualization. The bands were analyzed (relative to GAPDH expression) by using Gel-pro analyzer [30 (link)].
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7

Lipofectamine 2000 Transfection Protocol

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Lipofectamine 2000 and 4–12% NuPage gel were purchased from Invitrogen (Carlsbad, CA, USA). Protein phosphatase inhibitor was purchased from Beyotime Biotechnology (Beijing, China). Protein A-Agarose was from Santa Cruz Biotechnology (Dallas, TX, USA). Guinea pig anti-insulin (dilution: 1:2000) was from Merck Millipore (Billerica, MA, USA) and mouse anti-proinsulin antibody was from Novus Biologicals (Littleton, CO, USA). Rabbit anti-Hsp90 (dilution: 1:2000) antibody was from Assay designs (Ann Arbor, MI, USA). Rabbit anti-cleaved caspase 3 antibody was from Cell Signalling Technology (Danvers, MA, USA). Annexin V with Alexa Fluor™ 555 conjugation, Goat anti-guinea pig IgG Alexa Fluor 555 and goat anti-rabbit IgG Alexa Fluor 435 was bought from Invitrogen (Carlsbad, CA, USA). Rabbit anti-Myc antibody was from Immunology Consultants Labs. Horseradish peroxidase–conjugated antibodies were from Jackson ImmunoResearch Laboratories (West Grove, PA, USA). Enhanced chemiluminescence Western blotting substrate was from Millipore (Billerica, MA, USA). Trans35S label and pure 35S-methionine were from PerkinElmer (Waltham, MA, USA).
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8

Protein Extraction and Western Blotting

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Total protein was extracted in RIPA lysis buffer (Beyotime Biotechnology, Shanghai, China) supplemented with phenylmethylsulfonyl fluoride (PMSF, Beyotime) and protein phosphatase inhibitor (Beyotime). The protein concentrations were measured using the BCA Protein Assay (Beyotime). The samples were separated on a 10% SDS-polyacrylamide gel and then transferred to a nitrocellulose membrane, which was blocked in 5% skim milk for 1 h and then incubated with primary antibodies at 4 °C overnight. After the washing steps, the membranes were incubated with HRP-labeled secondary antibodies for 1 h at 37 °C. The bands were visualized using Immobilon Western HRP (Millipore, Germany). Relative band densities of proteins in western blottings were normalized against GAPDH.
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9

Berberine and Serdemetan Cytotoxicity Evaluation

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Berberine was purchased from Chroma Biotechnology Company (Chengdu, China) with a purity of up to 98%. Berberine was dissolved in dimethyl sulfoxide (DMSO) and subsequently diluted to the required concentrations with complete cell culture medium, with a final DMSO concentration of <0.1%. Dulbecco’s modified Eagle’s medium (DMEM), fetal bovine serum (FBS) were purchased from Thermo fisher (Gibco, USA). Serdemetan was purchased from Topscience (Shanghai, China). RIPA lysate, protease inhibitor, protein phosphatase inhibitor, cell counting Kit-8 (CCK-8), RNase, penicillin/streptomycin and propidium iodide were purchased from Beyotime Biotechnology Company (Shanghai, China). Anti-p53, anti-phospho-p53, anti-cyclin B1, and anti-p21 antibodies were purchased from Abcam (Cambridge, MA, USA). Anti-cyclin D1 antibody were purchased from Cell Signaling Technology (Danvers, MA, USA). Anti-phospho-p21 antibody and electro-chemi-luminescence (ECL) kit was purchased from Absin (Shanghai, China). Goat anti-mouse IgG and goat anti-rabbit IgG were purchased from Nachuan biotechnology co., LTD. (Harbin, China).
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10

Protein Abundance Quantification by Western Blot

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To examine the protein abundance, cells were lysed in RIPA buffer (Beyotime, Shanghai, China) containing 1% phenylmethylsulfonyl fluoride (Beyotime) and 1% protein phosphatase inhibitor (Beyotime) on ice for 30 min. The samples were centrifuged at 14,000 rpm and 4°C for 20 min. Loading buffer (Beyotime, Shanghai, China) was added to the protein lysate, which then were incubated at 95ºC for 5 min.
Total proteins (40-60 µg) were separated by electroporation on 10% SDS-PAGE. For immunoblotting proteins were electro-transferred onto PVDF membranes and blocked with 5% nonfat milk in triethanolaminebuffered saline (TBS) with 0.1% Tween 20 (TBS-T) at room temperature for 1 h. Then, the membrane was incubated with polyclonal rabbit anti-p-tauSer235(1:1000, cell signaling), Bax(1:1000, cell signaling) at 4°C overnight. All antibodies were diluted in TBS-T with 5% BSA. After washing with TBST the blots were incubated with secondary anti rabbit secondary antibody (1:2000, Sigma, United States) for 1 h at room temperature. After washing antibody binding was visualized with enhanced chemiluminescence reagents(Beyotime, Shanghai, China). Membranes were also probed with Actin antibody as loading control. Densitometric analysis was performed using quantity One software (Abbiotec, United States).
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