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27 protocols using vimentin

1

Immunohistochemical Analysis of Tissue Samples

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After the embedded tissue was cut into 4 μm sections and deparaffinized, the sections were treated with 3% H2O2 for 10 min to block endogenous peroxidase activity. After antigen retrieval in a microwave oven, the sections were incubated with normal goat serum at 37 °C for 10 min. Afterwards, the sections were incubated with the following primary antibodies: SMA (Affinity, Changzhou, China), HIF-1α (Affinity, Changzhou, China), E-cadherin (Affinity, Changzhou, China) and Vimentin (Affinity, Changzhou, China). After 2 h, the sections were washed and incubated with a secondary antibody (Zhongshan Biotechnology Co., Ltd., Beijing, China) at 37 °C for 30 min. After staining with 3,3′-diaminobenzidine, the tissues sections were incubated with hematoxylin staining solution for 20 s, washed with tap water for 5 min, and observed for staining intensity under a microscope. Each experiment was performed in triplicate.
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2

Western Blot Analysis of Protein Expression

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The cells and tissue specimens were lysed with radioimmunoprecipitation assay buffer (Beyotime Institute of Biotechnology, Shanghai, China) containing phenylmethanesulfonyl fluoride (Beyotime) and a protease inhibitor (CoWin Biosciences). The protein concentration was determined using a bicinchoninic acid protein assay kit (Beijing Solarbio Science and Technology Co., Ltd. Beijing, China). Each sample with equal amounts of protein were separated using 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis. After running 1–2 h under 120V, the protein was transferred onto a polyvinylidene difluoride membrane. Next, the membranes were blocked with 5% not-fat milk for 1 h at room temperature and incubated with primary antibodies c-Myc, HIF-1α, CXCR4, SDF-1, vimentin, E-cadherin, and β-actin overnight at 4°C (Affinity Biosciences). Subsequently, the membranes were washed 3 times with tris-buffered saline and Tween-20 and incubated with a horseradish peroxidase-conjugated goat anti-rabbit or anti-mouse secondary antibody (Cell Signaling Technology, Beverly, MA, USA). Finally, the membranes were treated with a chemiluminescence reagent and exposed to X-ray. The band intensities were quantified using image J software (National Institutes of Health, Bethesda, MD, USA). Relative protein expression was quantified using control protein β-actin.
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Western Blot Analysis of EMT Markers

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For the extraction of total protein, cells were lysed in radio-immunoprecipitation assay (RIPA) buffer (Beyotime) containing PMSF (Sigma). The concentration of total protein was quantified using BCA protein assay kit (Beyotime). Equal amounts (60 μg) of proteins were separated by 10% SDSPAGE and transferred onto PVDF membranes (0.45 μm; Millipore). The membranes were blocked with 5% fat-free milk in Tris-buffered saline containing 0.1% Tween-20 (TBST) for 1 h. Subsequently, the blots were incubated overnight at 4°C with E-cadherin (1:1000; Abcam), Vimentin (1:1000; Affinity, USA), Zeb1 (1:250; Affinity), Zeb2 (1:250; Affinity) and GAPDH (1:4000; Proteintech, USA). After washing three times with TBST and incubating with secondary antibody (anti-rabbit antibody, 1:4000; Affinity) at room temperature for 1 h, the membranes were washed again and incubated with enhanced ECL detection reagent (Millipore). Finally, the intensities of protein bands were quantified using ImageJ, version 1.5 (NIH).
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4

Cinnamaldehyde Molecular Characteristics and Antibody Sources

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Cinnamaldehyde (Aladdin, Shanghai, China) has the chemical formula C9H8O, a relative molecular mass of 132.16, and a purity of >99.5%. EGF was purchased from MedChemExpress (MCE, Shanghai, China).
Antibodies against mTOR, p-mTOR (Ser2448), pan-AKT, p-AKT (Ser473), PI3K, p-PI3K(Tyr458), E-cadherin, N-cadherin, vimentin, and Snail were purchased from Affinity Biosciences (Affinity Biosciences, OH, United States). Antibodies against Ki67, MMP9, EGFR (Tyr1068), cleaved-PARP, PARP, cleaved-caspase-3, and caspase-3 were purchased from Cell Signaling Technology (Danvers, MA, United States). The antibody against β-actin was purchased from Proteintech (Proteintech, Chicago, United States).
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5

Molecular Mechanisms of Cellular Fibrosis

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PTL (> 99%) was provided by Shangdeyaoyuan Co. (Tianjin, China). DEX sodium phosphate (> 98.5%) was purchased from Meilun Biological Technology Co. (Dalian, China), and BLM sulfate (> 91%) was obtained from Meilun Biological Technology Co. (Dalian, China). The NF-κB, Snail, β-actin, GAPDH, E-cadherin, vimentin, MMP1, α-SMA and Col-1 antibodies were purchased from Affinity Biosciences Co. (Beijing, China). The mouse TNF-α, mouse IL-4, mouse TGF-β1, and mouse interferon gamma ELISA Kits were purchased from Meilian Biological Technology Co. (Shanghai, China). Chlorine ammonia T (> 97.08%) and p-dimethylaminobenzaldehyde (> 97.08%) were obtained from (> 99.71%). Reverse-4-hydroxy-l-proline (> 99.4%) was purchased from Bailingwei Technology Co. (Beijing, China). Perchloric acid (> 70%) was obtained from Jingchun Biological Technology Co. (Shanghai, China).
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6

Western Blot Analysis of Signaling Proteins

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Total proteins obtained from cells and tissues were subjected to SDS–PAGE (Biosharp, China) and then transferred to PVDF (Millipore, USA) membranes and blocked in 5% skimmed milk for 1 ​h. The membranes were incubated overnight at 4 ​°C with primary antibodies against ADCY7 (Thermo Fisher, USA), IL-1β (Affinity, China), MMP-13 (Affinity, China), N-cadherin (Affinity, China), E-cadherin (Affinity, China), vimentin (Affinity, China), α-SMA (CST, USA), p-PKA substrate (CST, USA), p-PLIN1(Abcam, USA), PLIN1 (Abcam, USA), p-HSL (CST, USA) and GAPDH. The following day, the membranes were incubated with fluorophore-conjugated secondary antibody (LI-COR Corp., NE). Protein bands were imaged with an enhanced LI-COR Odyssey infrared imaging system (LI-COR Corp., NE). The protein levels were normalized to the GAPDH levels.
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7

Nuclear and Cytoplasmic Protein Extraction

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The Nuclear and Cytoplasmic Protein Extraction Kit (Beyotime Biotechnology Co., Ltd. P0027) was used to extract nuclear and plasma proteins from the tissues and cells. All lysates contained protease inhibitors. The quantified proteins were separated by 10% SDS-PAGE. After transferring the protein to the PVDF membrane and blocking with 5% BSA, the PVDF membrane was blocked at room temperature with the following primary antibodies: HIF-1α (Affinity, Changzhou, China), TGFΒ1 (Affinity, Changzhou, China), SAMD3 (Affinity, Changzhou, China), p-SMAD3 (Affinity, Changzhou, China) E-cadherin (Affinity, Changzhou, China), Vimentin (Affinity, Changzhou, China), Lamin B (Affinity, Changzhou, China) and GAPDH (Affinity, Changzhou, China). GAPDH and Lamin B were used as loading controls. After 4 h, the excess primary antibody was removed, and the PVDF membrane was incubated with HRP-labelled secondary antibody at room temperature for 2 h. Protein intensity was detected with an Image Lab instrument (Bio-Rad, USA). Each experiment was performed in triplicate.
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8

Western Blot Analysis of Protein Markers

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Proteins were extracted from cells and tissues using RIPA buffer, and the concentration of total protein was determined using a BCA Assay Kit (Yeasen Biotech). The protein samples underwent separation using SDS-PAGE and were subsequently transferred to PVDF membranes, followed by blocking in 5% non-fat milk for 2 h. Next, the membranes were incubated with specific primary antibodies overnight at 4°C, followed by secondary antibodies for 1 h. The detection of the band signals was accomplished using an electrochemiluminescence (ECL) system. The following primary antibodies were used in this study TSG101 (Affinity), CD63 (Affinity), N-cadherin (Affinity), E-cadherin (Affinity), vimentin (Affinity), GAPDH (ABclonal), RAS (ABclonal), p-RAF1 (ABclonal), RAF1 (ABclonal), p-MEK1/2 (ABclonal), MEK1/2 (ABclonal), p-ERK1/2 (ABclonal), ERK1/2 (ABclonal), and TPR (Abcam).
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9

Neoprzewaquinone A Cytotoxicity Evaluation

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Neoprzewaquinone A (purity ≥98%) was obtained from Herbpurify (Chengdu, China). SGI-1776 and Netarsudil (purity ≥98%) were purchased from Selleck (Chengdu, China). RPMI 1640, DMEM, DMEM/F12 media and Fetal Bovine Serum (FBS) were acquired from Gibco (NewYork, NY, USA). Paraformaldehyde (PFA; 4%) was purchased from Biosharp (Hefei, China). The BCA protein assay kit, cell cycle analysis kit, annexin V-FITC/PI apoptosis detection kit and Hoechst 33258 were obtained from Beyotime (Shanghai, China). The trypsin, crystal violet (1%), and Mondansylcadaverine (MDC) assay kit were purchased from Solarbio (Beijing, China). The primary antibodies against ROCK1, ROCK2, mTOR/p-mTOR, MYPT1/p-MYPT1, PIM1, BAD/p-BAD, STAT3/p-STAT3, E-cadherin, Vimentin, cyclin B1, cyclin D1, Beclin1, ATG5, LC3B, GAPDH, β-actin, and HRP-conjugated secondary antibodies were purchased from Affinity (Jiangsu, China). The electrochemiluminescence (ECL) western blot detection kit was purchased from Abbkine (Redlands, CA, USA).
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10

Trop2 and β-Catenin Interaction Analysis

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Cellular proteins were lysed using standard methods. Cellular proteins were separated by 10% SDS‐PAGE and transferred onto nitrocellulose membranes. The membranes were blocked with TBS containing 0.1% Triton X‐100 and 5% nonfat milk for 2 hours at RT and then were incubated with Trop2 (R&D SYSTEMS), E‐cadherin (Invitrogen), fibronectin (Affinity), vimentin (Affinity), β‐catenin (Santa Cruz Biotechnology), and β‐actin antibody (Abcam) at 4°C overnight. After being washed, the membranes were incubated with HRP‐conjugated anti‐IgG at RT for 1 hour. Signal detection was carried out with an ECL system (Tanon, shanghai, China). BGC823 and MGC803 were transfected with different plasmids and then lysed in cellular lysis buffer (Sangon Biotech, Shanghai, China) for 15 minutes on ice. Extracts were clarified by centrifugation at 13 000 g for 25 minutes at 4°C for co‐immunoprecipitation. After centrifugation, the supernatant was collected, and then incubated with protein G PLUS‐agarose immunoprecipitation beads (Santa Cruz Biotechnology) at 4°C for 1 hour. Then, they were incubated with special antibodies against Trop2, β‐catenin at 4°C on a rocker platform. The antibody‐coated beads were then incubated with the lysates at 4°C overnight. Immunoprecipitates were collected, washed, lysed, and boiled. The boiled samples were analyzed by Western blot analysis as describe above.
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