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10 protocols using ripa protein extraction buffer

1

Protein Expression Analysis via Western Blot

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The total protein of the cells was extracted using RIPA protein extraction buffer (Beyotime, Shanghai, China) containing protease inhibitor. Proteins were separated using SDS-PAGE gels and transferred to a polyvinylidene fluoride (PVDF) membrane using a iBlot 2 Dry Blotting System (Life technologies, Thermo Fisher Scientific, Waltham, MA). The non-specific reactivity was blocked with nonfat milk at 4°C for one hour. The PVDF membranes were then incubated with primary antibodies including anti-decorin (1:1000), anti-E-cadherin (1:10000), anti-fibronectin (1:1000), anti-vimentin (1:1000), anti-Snail (1:1000), anti-Slug (1:1000), anti-Twist (1:1000), anti-LC3B (1:2000), anti-p62 (1:10000), anti-c-Met (1:1000), anti-p-c-Met (1:1000), anti-Akt (1:1000), anti-p-Akt (1:1000), anti-mTOR (1:10000), anti-p-mTOR, anti-ERK1/2 (1:10000), anti-p-ERK1/2, anti-β-actin (1:5000) and anti-GAPDH (1:5000) at 4°C overnight. These antibodies were from Abcam (Cambridge, MA). The membranes were then washed in TBST and incubated with Horseradish peroxidase-conjugated secondary antibodies (Beyotime, Shanghai, China) for 1 h. A Super ECL Plus Detection reagent (Applygen Technologies, Beijing, China) was used to develop the bands, which were captured by a Tanon-4200 Gel Imaging System (Tanon, Shanghai, China).
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2

Western Blot Analysis of Insulin Signaling

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Western blot was performed as previously described (Zhang et al., 2019a (link)). Briefly, HepG2 cells were seeded in 60 mm culture dishes (5 × 105 cells) for 24 h. After the treatments for 24 h followed by insulin (100 nM) incubation for 20 min, cells were washed with cold PBS, and then lysed with cold Radio Immunoprecipitation Assay (RIPA) protein extraction buffer containing 1% protease and phosphatase inhibitors (Beyotime biotechnology, Beijing, China) for 30 min on ice. An aliquot of 20 μg of the supernatant protein from each sample was heated with 4 × sodium dodecyl sulfate (SDS) sample buffer at 95 °C for 8 min, and separated electrophoretically on a 10% SDS–polyacrylamide gel. Subsequently, proteins were transferred onto PMSF membranes for 3 h and blocked for 1 h. PMSF membranes were then exposed to indicate primary antibodies in blocking buffer at 1:1,000 dilutions overnight at 4°C. The membranes were then incubated with the anti-rabbit IgG secondary antibody or and anti-mouse IgG HRP-linked antibody at 1:2,000 dilutions for 1 h. Visualization was performed using Tanon 5200 Multi chemiluminescent imaging system (Tanon Science & Technology Co., Ltd., Shanghai, China) with enhanced-chemiluminescence substrate, and the blots were analyzed using Image J software. Protein levels were corrected with values determined on β-actin blots. Three replicates were used.
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3

Western Blot Analysis of A549 and NCI-H23 Cells

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Western-blotting was implemented as the procedures reported by Fathi et al.24 (link). We extracted protein from each group of A549 and NCI-H23 cells by using a RIPA protein extraction buffer (Beyotime, Shanghai, China). By using the BCA protein test kit (Beyotime, Shanghai, China), we detected protein concentrations. And then, we separated and electrotransferred equal amounts of protein (40 μg) from each sample onto polyvinylidene difluoride (PVDF) membranes. After blocked and incubated with the primary antibodies, the membranes were then incubated with secondary antibodies. In the experiment, we used the antibodies as follows: anti-SLC7A11 antibody (1:1500, ab175186, Abcam), anti-GPX4 (1:2000, ab125066, Abcam), anti-β-actin antibody (1:1000, ab8227, Abcam). Finally, detection was done by chemiluminescence (Millipore Corporation, Temecula, CA, USA).
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4

Quantitative Analysis of Neurochemical Markers

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Brain tissue was micropunched for CeA. The tissue was transferred to an RIPA protein extraction buffer (Beyotime Biotechnology, China) containing protease and phosphatase inhibitors (MedChemExpress, China), homogenized, and centrifuged at 12,000 g at 4°C for 15 min. The supernatant was separated, and protein concentration was measured using the BCA assay (Beyotime Biotechnology, China). Western blot was carried with the previously described methodology. Briefly, samples were separated using SDS-polyacrylamide gel electrophoresis and transferred to PVDF membranes (Millipore), which were then blocked with 5% non-fat milk in TBST for 1 h. The membranes were then incubated with primary antibodies against Nat8l/ASPA/GCP II/GCP III/NAAGSI and β-actin overnight at 4°C. After washing for three times in TBST, the membranes were incubated with horseradish peroxidase-conjugated anti-rabbit/mouse secondary antibodies in TBST for 1 h at room temperature and then visualized with an ECL luminometer. Quantitative analysis was performed with ImageJ software. All experiments were performed at least three times.
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5

Protein Expression Profiling Techniques

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Cell lysates were prepared in RIPA protein extraction buffer (Beyotime Institute of Biotechnology, China) with protease inhibitors and phosphatase inhibitor cocktail (Roche, Germany). Proteins in lysates were separated by SDS-polyacrylamide gel electrophoresis and then transferred onto a polyvinylidene fluoride membrane (EMD Millipore Billerica, USA). Membrane was blocked with 5% nonfat milk and incubated with specific primary antibodies overnight at 4 °C. It was then incubated with horseradish peroxidase-conjugated secondary antibody for 1 h at 37 °C. Finally, the protein signals were visualized and quantified using Electrochemiluminescence (Thermo Fisher Scientific, USA) and ChemiDocTM MP Imaging System (Bio-Rad Laboratories, USA). Primary antibodies and corresponding manufacturers were showed as follows: TRIM26 (ab89290, 1:1000) and USP39 (ab131244, 1:1000) (Abcam, USA); N-cadherin (Rabbit mAb#13116, 1:1000), Ki-67 (mAb #9449) and snail (Rabbit mAb #3879, 1:1000) (Cell Signaling, USA); ZEB1 (22018-1-AP) (Proteintech, USA); mouse monoclonal antibodies against Flag and HA (OriGene, USA); and β-actin (1:40,000) (Sigma-Aldrich, USA).
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6

Quantitative Western Blot Analysis

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Total protein was extracted using RIPA protein extraction buffer (Beyotime Institute of Biotechnology) and quantified using the BCA Protein assay kit (Beyotime Institute of Biotechnology). Equal amounts of proteins (7–10 µg) were separated by 10% SDS-PAGE and transferred to a PVDF membrane (EMD Millipore). After blocking with 5% skimmed milk for 1 h at room temperature, the membrane was incubated at 4°C overnight with the following primary antibodies: Anti-HIF1α (cat. no. ab51608; 1:1,000; Abcam), anti-NF-κB (p65; cat. no. ab16502; 1:1,000; Abcam), anti-phosphorylated (p)-NF-κB (p-p65; cat. no. ab86299; 1:1,000; Abcam) and anti-β-actin (cat. no. 66009-1-IG; 1:20,000; ProteinTech Group, Inc.). Subsequently, the membrane was incubated with horseradish peroxidase-conjugated goat anti-rabbit IgG (1:5,000; cat. no. 5210-0174) and goat anti-mouse IgG (1:5,000; cat. no. 5210-0185; KPL, Inc.) secondary antibodies. Protein bands were visualized by Immobilon Enhanced Chemiluminescence (EMD Millipore). β-actin was used as the loading control. Optical density values of the protein bands were semi-quantified and analyzed using a gel image processing system Image Lab software (version 3.0; Bio-Rad Laboratories, Inc.).
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7

Protein Extraction and Western Blot Analysis

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Total proteins were extracted using a RIPA protein extraction buffer (Beyotime, Shanghai, China), and the concentration was detected using the BCA Protein Assay Kit (Beyotime, Shanghai, China). Equal amounts (7–10 μg) of proteins were separated by 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and then transferred to a polyvinylidene fluoride (PVDF) membrane (Millipore Corporation, Billerica, MA, USA). After blocking in 5% skimmed milk (in PBS) for 1 h at room temperature, the membrane was incubated with primary antibodies at 4 ºC overnight. Detection was done by peroxidase-conjugated secondary antibodies (KPL, Gaithersburg, MD, USA) and chemiluminescence (Millipore Corporation, Temecula, CA, USA). Anti-PRIM2 antibody (1:2000, ab241990), anti-SLC7A11 antibody (1:1000, ab175186), anti-β-catenin antibody (1:5000, ab32572) and anti-β-actin antibody (1:1000, ab8226) were purchased from Abcam, Inc.
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8

Western Blot Protein Quantification

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Proteins were extracted from cells using RIPA protein extraction buffer (Beyotime Institute of Biotechnology), and were quantified by the Bradford assay as previously described30 (link). The same amount up to 30ug of protein was subjected to 10% SDS-PAGE and transferred to PVDF membranes. After being blocked in 10% skimmed milk, the membranes were incubated with Rab10 polyclonal antibody (1:1000 dilution; cat. no. ab104859, Abcam) at 4 °C overnight, washed 3 times for 5 min and then incubated with the corresponding horseradish peroxidase (HRP)-conjugated anti-rabbit IgG (1:5000 dilution; cat. no. sc-2004 Santa Cruz Biotechnology, Inc.) at room temperature for 60 min. The protein bands were visualized with ECL Super Signal reagent (Pierce; Thermo Fisher Scientific, Inc.). The relative intensity of the bands was determined using Image J software (version 1.41o, Java 1.6.0_10, https://imagej.nih.gov/ij/, Wayen Rasband, National Institutes of Health). Where gels/blots are used in figures were compliance with the digital image and integrity policies (www.nature.com/srep/policies/index.html#digital-image).
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9

HepG2 Triglyceride Content Assay

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HepG2 cells were seeded in 6-well plates at a density of 1.5 × 105 cells for 24 h. After 24 h of treatment, cells were washed with PBS, and then lysed on ice for 30 min with cold radio immunoprecipitation assay (RIPA) protein extraction buffer (Beyotime Biotechnology, Beijing, China) containing 1% protease and phosphatase inhibitors. The triglyceride content assay was performed according to the instruction of the TG test kit (Nanjing Jian Cheng Bioengineering Research Institute, Nanjing, China). TG concentrations were standardized to the total protein content measured from the whole cell lysates.
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10

Western Blot Analysis of Epithelial-Mesenchymal Transition and Stem Cell Markers

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Cell lysates were collected by RIPA protein extraction buffer (Beyotime Institute of Biotechnology, Beijing, China) with protease inhibitor cocktail (Roche, Basel, Switzerland). Cell lysates were separated on 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels and transferred onto a polyvinylidene fluoride membrane (EMD Millipore Billerica, MA, USA). The membrane was then incubated with specific primary antibodies at 4 °C overnight (Table 3). Horseradish peroxidase-conjugated anti-mouse or anti-rabbit secondary antibody was added separately. The bands were captured using the ChemiDocTM MP Imaging System (Bio-Rad Laboratories, Inc., Hercules, CA, USA).

Primary antibodies used for western blot analysis

AntibodiesSpeciesManufactureCatalog#Dilution
E-cadherinRabbitProteintech20874-1-AP1:500
VimentinRabbitProteintech20874-1-AP1:1000
N-cadherinRabbitProteintech22018-1-AP1:500
SnailRabbitProteintech22018-1-AP1:500
ZEB1RabbitProteintech22018-1-AP1:1000
Bcl-2RabbitProteintech12789-AP1:1000
BaxRabbitProteintech50599-2-lg1:500
CD133RabbitProteintech18470-1-AP1:50
Bmi1RabbitProteintech10832-1-AP1:50
OCT4RabbitProteintech11263-1-AP1:50
SOX2RabbitProteintech11064-1-AP1:50
NanogRabbitProteintech14295-1-AP1:50
GFAPRabbitProteintech16825-1-AP1:20
NestinRabbitProteintech19483-1-AP1:20
β-actinMouseProteintech60008-1-lg1:1000
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