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43 protocols using p erk

1

RIPA Lysis Protein Extraction Immunoblotting

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Using Radioimmunoprecipitation assay buffer (RIPA) lysate, mouse tissues were lysed for 30 min on ice, and protein supernatants were collected by centrifuging at 4 °C and 12,000 rpm for 15 min. The concentration of protein was determined using the BCA assay. The proteins were denatured by adding a loading buffer and heating the mixture for 10 min. The total amount of protein was limited to about 40 μg. After 30 min of electrophoresis at 80 V, the voltage was increased to 120 V for an additional 90 min, and then electroconversion was performed. BSA blocked the PVDF membrane for 2 hours at room temperature. The required antibodies (ERK, proteintech, Cat No. 11257-1-AP, 1:1000; p-ERK, proteintech, Cat No. 28733-1-AP, 1:2000; JNK, proteintech, Cat No. 24164-1-AP, 1:1000, p-JNK, proteintech, Cat No. 80024-1-RR, 1:1000; P38, proteintech, Cat No. 14064-1-AP, 1:1000; p-P38, proteintech, Cat No. 28796-1-AP, 1:1000 and GAPDH, Elabscience, Cat No. E-AB-20059, 1:5000) were diluted in the primary antibody’s dilution solution and incubated overnight at 4°C.After three TBST treatments, the secondary antibody was added and incubated for 2 h at room temperature. The ECL luminescence developer was configured according to specifications, exposed using a chemiluminescence instrument, and the results were analyzed.
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2

Immunofluorescence Staining and Pyroptosis Assay

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Immunofluorescence staining was performed as previously described [22 (link)]. Briefly, the cells and tissue sections were washed with PBS-0.25% Tween-20 (PBS-T) three times, blocked with 5% goat serum, and incubated with the primary antibodies rabbit anti-NLRP3 (1:200, CST, USA), caspase-1 (1:200, Abcam, USA), IL-1β (1:200, CST, USA), and PERK (1:200, Proteintech, China) overnight at 4 °C. Then, the cells and tissue sections were incubated with the fluorescent secondary antibody (goat anti-rat antibody or goat anti-rabbit antibody, Proteintech, China, diluted 1:100) for 1 h. Finally, the cells and tissue sections were counterstained with 4′-6-diamidino-2-phenylindole (DAPI) and observed with a fluorescence microscope. (Beyotime, China).
Pyroptosis was detected by propidium iodide (PI) staining following the manufacturer’s recommendations [23 (link)]. The quantification of fluorescence intensity was performed using ImageJ software.
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3

Western Blot Analysis of Apoptosis Markers

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SDS-Page electrophoresis and transfer of proteins to nitrocellulose membranes were performed according to standard procedures. Ponceau S (0.1%) staining of membranes verified transfer of proteins and equal loading. Membranes were incubated with antibodies to CD133 (Miltenyi Biotec, Auburn, CA, USA), cleaved and intact PARP, BAD, p-BAD, BCL-XL, MCL-1 (BioLegend, San Diego, CA, USA) cleaved active caspase-3, cleaved active caspase-9, BCL-2, active BAX (Novus Biologicals, Centennial, CO), AKT and p-AKT (Santa Cruz Biotech, Dallas, TX, USA), ERK, p-ERK, or to β-Actin (ProteinTech, Rosemont, IL, USA) as a loading control. Immunoblots were sequentially reprobed with other antibodies after stripping them of antibodies. Immune complexes were detected by incubation with horseradish peroxidase-conjugated antibodies to mouse or rabbit IgG (1:3000), followed by enhanced chemiluminescence (ECL; Pierce, Rockford, IL, USA) and imaging in a GE Healthcare Amersham Imager 600.
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4

Western Blot and Immunohistochemistry Protocol

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Western blotting was performed as described previously [20 (link)]. Samples of equivalent total protein (20 μg) were loaded. Primary antibodies against CD63, CD9 (Santa Cruz Biotechnology, Santa Cruz, CA, USA), c-MYC, p-EGFR, p-MEK, p-ERK(Cell Signaling Technology, Danvers, MA, USA), GAPDH, DNAJB11, HSPA5, ATF6, IRE1, XBP1, PERK, ATF4, EGFR, Raf-1, MEK, and ERK1/2 (ProteinTech Group, Rosemont, IL, USA) were used. Immunohistochemical (IHC) assay was performed following a previously described procedure [21 (link)].
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5

Western Blot Analysis of Signaling Pathways

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The tissues and cells were collected in RIPA buffer containing protease and phosphatase inhibitors. Total protein concentration was quantified with BCA Protein Assay Reagent Kit (Beyotime, Shanghai, China). The proteins were separated by SDS–PAGE and transferred onto polyvinylidene difluoride (PVDF) membranes (Millipore, Burlington, MA, USA) via electroblotting. The membranes were blocked in 5% skimmed milk in TBST (TBS, 0.1% Tween 20) for 2 h and incubated overnight at 4 °C with primary antibodies against p- JNK (Santa Cruz Biotechnology, Dallas, TX, USA, Cat# sc-6254), JNK (Santa, Cat# sc-7345), p-ERK (Santa, Cat# sc-7383), ERK (Santa, Cat# sc-135900), p-p38 (Santa, Cat# sc-7975-R), p38 (Santa, Cat# sc-7149), BAX (Santa, Cat# sc-20067), Bcl-2 (Santa, Cat# sc-7382), caspase-3 (Proteintech, Wuhan, China, Cat# 11648-2-AP), caspase-9 (Cell Signaling Technology, Danvers, MA, USA, Cat# 9508S) and GAPDH (Santa, Cat# sc-32233). The PVDF membranes containing proteins were incubated with horseradish peroxidase-conjugated secondary antibodies. Subsequently, target proteins were stained with ECL chemiluminescence detection kit (FDbio Science Biotech Co., Ltd., Hangzhou, China). Densitometric analysis was performed using an imaging station.
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6

Protein Expression Analysis in Mechanically Stressed Cells

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The collected NP tissues was ground to powder in liquid nitrogen. The cells at 24 h after treated with mechanical stress or above tissues powder were placed in RIPA lysis buffer (Beyotime, China) supplemented with 1 mM PMSF (Beyotime, China) on ice for 30 min. The collected liquid was centrifuged at 12,000 rpm for 15 min at 4 ℃. The protein concentration was detected with a BCA protein assay kit (PC0020, Solarbio). The protein samples from each group were separated in 8%, 10%, or 12% SDS–polyacrylamide gels (SDS-PAGE) and then transferred to a polyvinylidene difluoride (PVDF) membrane (Millipore, USA). After blocking with QuickBlockTM Blocking Buffer (Beyotime, China) for 20 min at room temperature, the membranes were incubated with rabbit primary antibodies against ACSL4 (1:2000, Proteintech), Bip (1:2000, Proteintech), Piezo1 (1:1000, Proteintech), Calnexin (1:5000, Proteintech), GPX4 (1:1000, Proteintech), ATF6 (1:2000, Proteintech), PERK (1:1000, Proteintech), Aggrecan (1:1000, Proteintech), Col-2 (1:1000, Novus), ADAMTS-5 (1:1000, Abcam), MMP-13 (1:1000, Proteintech), SelK (1:500, Proteintech), GAPDH (1:5000, Proteintech) overnight at 4 ℃. Then, the membranes were incubated for 90 min at room temperature with secondary antibody. The bands were visualized using an Amersham Imager 600, and the density was quantified using ImageJ software.
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7

Protein Expression Analysis in Mechanically Stressed Cells

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The collected NP tissues was ground to powder in liquid nitrogen. The cells at 24 h after treated with mechanical stress or above tissues powder were placed in RIPA lysis buffer (Beyotime, China) supplemented with 1 mM PMSF (Beyotime, China) on ice for 30 min. The collected liquid was centrifuged at 12,000 rpm for 15 min at 4 ℃. The protein concentration was detected with a BCA protein assay kit (PC0020, Solarbio). The protein samples from each group were separated in 8%, 10%, or 12% SDS–polyacrylamide gels (SDS-PAGE) and then transferred to a polyvinylidene difluoride (PVDF) membrane (Millipore, USA). After blocking with QuickBlockTM Blocking Buffer (Beyotime, China) for 20 min at room temperature, the membranes were incubated with rabbit primary antibodies against ACSL4 (1:2000, Proteintech), Bip (1:2000, Proteintech), Piezo1 (1:1000, Proteintech), Calnexin (1:5000, Proteintech), GPX4 (1:1000, Proteintech), ATF6 (1:2000, Proteintech), PERK (1:1000, Proteintech), Aggrecan (1:1000, Proteintech), Col-2 (1:1000, Novus), ADAMTS-5 (1:1000, Abcam), MMP-13 (1:1000, Proteintech), SelK (1:500, Proteintech), GAPDH (1:5000, Proteintech) overnight at 4 ℃. Then, the membranes were incubated for 90 min at room temperature with secondary antibody. The bands were visualized using an Amersham Imager 600, and the density was quantified using ImageJ software.
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8

Investigating Oxidative Stress and Inflammatory Markers in DSS-Induced Colitis

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Dextran sodium sulfate (DSS) was purchased from MP Biomedicals (Irvine, CA, USA). Assay kits for MDA, CAT, GSH-Px, and SOD were procured from Grace Biotechnology Co. (Suzhou, China). All of the primers were purchased from Sangon Biotech (Shanghai) Co., Ltd. (Shanghai, China). IL-1β, IL-6, TNF-α, IL-10, and IFN-γ ELISA kits were purchased from Shanghai Enzyme-linked Biotechnology Co., Ltd. (Shanghai, China). Polyclonal antibodies and secondary antibodies for occludin, JNK, P-JNK, ERK, P-ERK, and TLR-4 were from Proteintech Group, Inc. (Wuhan, China).
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9

Western Blot Analysis of Signaling Pathways

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For western blotting, cell lysis buffer for western and IP (Bestbio, Shanghai, China) was used to prepare J774A.1 cell proteins. The protein concentrations of J774A.1 were quantified using the bicinchoninic acid (BCA) assay (Thermo Fisher Scientific Inc, Waltham, MA, USA). The samples of J774A.1 proteins was adjusted to a concentration of 30~50 μg perwell. After electrophoresis, protein samples were transferred to a polyvinylidene difluoride membrane that was blocked with 5% milk in TBS-T (TBS containing 0.05% Tween 20) for 1 h at room temperature. After washing the membrane with TBS-T, it was incubated with the specific antibodies against p-ERK (proteintech, Chicago, IL, USA), ERK (proteintech, USA), p-p38 (CST, Danvers, MA, USA), p38 (proteintech, Chicago, IL, USA), p-JNK (proteintech, Chicago, IL, USA), JNK (proteintech, Chicago, IL, USA), p-NF-κB p65 (CST, USA), NF-κB p65 (proteintech, Chicago, IL, USA), β-actin (proteintech, Chicago, IL, USA), or VapA (ABclonal, Wuhan, China) in dilution 1:1000 at 4 °C overnight. The membrane was washed with TBS-T and incubated with horseradish peroxidase-conjugated secondary antibodies for 1 h. Membrane was then washed thoroughly with TBS-T before the addition of a chemiluminescent substrate and exposure.
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10

Astrocyte Proteome Analysis by Western Blot

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Total protein extracted from astrocytes was separated by 12% SDS-PAGE. The separated proteins were transferred to a nitrocellulose (NC) membrane and incubated with antibodies against GFAP (Proteintech, Rosemont, USA), Shh (Abcam), Ptch (Sigma-Aldrich), Smo (Sigma-Aldrich), Gli-1 (Sigma-Aldrich), GRP78 (Proteintech), PERK, eIF2 (Proteintech), phospho-eIF2 (EnoGene Biotech Co., New York, USA), IRE1 (Signalway Antibody, Baltimore, USA), phospho-IRE1 (Boster, Pleasanton, USA), CHOP (Proteintech), and β-actin (Proteintech). The NC membrane was washed with TBS/T three times and then incubated with a 1:10,000 dilution of anti-rabbit or mouse horseradish peroxidase antibody (Sigma-Aldrich). The bands were detected by ECL reagents (EMD Millipore, Burlington, USA) and captured by a ChemiDoc Imaging System (Bio-Rad). ImageJ software analysis was employed to detect the optical density of the target proteins.
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