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448 protocols using radioimmunoprecipitation assay lysis buffer

1

Western Blot Analysis of Proteins in Cells

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Total proteins were extracted from cells using radioimmunoprecipitation assay lysis buffer (Beyotime Institute of Biotechnology, Haimen, China). Proteins were quantified using a Pierce bicinchoninic acid protein assay kit (Thermo Fisher Scientific, Inc.), followed by western blot analysis. 40 µg proteins from cell lysates were subjected to 12% SDS-PAGE. Once proteins were transferred to nitrocellulose membranes, they were incubated with antibodies targeting β-actin (cat. no. 58169, 1:1,000; Cell Signaling Technology, Inc., Danvers, MA, USA), CCR8 (cat. no. ab32131, 1:500; Abcam, Cambridge, UK), E-cadherin (cat. no. 3195, 1:1,000; Cell Signaling Technology, Inc., Danvers, MA, USA), matrix metalloproteinase (MMP)-2 (cat. no. 40994, 1:1,000; Cell Signaling Technology, Inc.) and vascular endothelial growth factor (VEGF)-C (cat. no. 2445, 1:1,000; Cell Signaling Technology, Inc.), followed by incubation with a horseradish peroxidase-labeled goat anti-rabbit secondary antibody (cat. no. ab6721, 1:3,000; Abcam) for 1.5 h at room temperature. Protein bands were visualized by Millipore enhanced chemiluminescence (cat. no. WBKLS0500; EMD Millipore, Billerica, MA, USA). ImageJ 1.45 software (NIH) was used to perform densitometric analysis of each band.
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2

Hippocampal Protein Extraction and Analysis

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Proteins were extracted from the hippocampal CA1 region using radioimmunoprecipitation assay lysis buffer (Beyotime, Shanghai, China). After determining the protein concentration using a bicinchoninic acid protein assay kit (Beyotime, Shanghai, China), proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and transferred onto polyvinylidene fluoride membranes (Millipore, Billerica, MA, USA). The membranes were then blocked with 5% skim milk and incubated with primary antibodies against PSD95 (1:500; Wanleibio, Shenyang, China; WL05046), MAP2 (1:1000; Wanleibio; WL04217), F-actin (1:1000; Abcam; ab205), and glyceraldehyde 3-phosphate dehydrogenase (1:1000; Wanleibio; WL01114) at 4°C overnight. The membranes were then washed with Tris-buffered saline with Tween and incubated with horseradish peroxidase-conjugated secondary antibodies (Beyotime, Shanghai, China) at 37°C for 45 minutes. Sensitive X-ray film was used to visualize the target bands.
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3

Western Blot Analysis of EMT Markers

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Briefly, protein was extracted from cells using radio immunoprecipitation assay lysis buffer (Beyotime, Shanghai, China). Samples were separated using 10% sodium dodecyl sulphate-polyacrylamide gel electrophoresis and then transferred onto polyvinylidene fluoride membranes. The membranes were blocked using 5% bovine serum albumin for 2 hours and then incubated with primary anti-human antibodies for detection of N-cadherin (#4061 at 1:1,000 dilution; Cell Signaling Technology, Inc., Danvers, MA, USA), E-cadherin (#14472 at 1:2,000 dilution; Cell Signaling Technology, Inc.), ZEB1 (ab203829, at 1:2,000 dilution; Abcam, San Francisco, CA, USA), ZEB2 (ab138222, at 1:4,000 dilution; Abcam) and GAPDH (ab181602, at 1:3,000 dilution; Abcam) overnight at 4°C. The membranes were incubated with the corresponding horseradish peroxidase-labeled goat anti-rabbit or anti-mouse immunoglobulin G antibody for 1 hour. After washing, the WB signal was detected using an enhanced chemiluminescence system (Bio-Rad, Hercules, CA, USA).
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4

Quantification of Lin28B Protein Expression

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The total proteins were extracted from cells using radioimmunoprecipitation assay lysis buffer (Beyotime Institute of Biotechnology, Shanghai, China), and subsequently quantified using the Bradford method (Bio-Rad Laboratories, Inc., Hercules, CA, USA). In total, 20 µg protein/well was loaded and separated by SDS-PAGE (10% gel) and then transferred to polyvinylidene difluoride membrane (Bio-Rad Laboratories, Inc.). Subsequent to blocking by 5% bovine serum albumin (Sigma-Aldrich; Merck KGaA), membranes were incubated with the following primary antibodies at 4°C overnight: Rabbit monoclonal Lin28B antibody diluted at 1:1,000 (Abcam) and polyclonal rabbit anti-GAPDH antibody diluted at 1:5,000 (ab115698; Abcam). The polyvinylidene fluoride membranes were then incubated with peroxidase-conjugated goat anti-rabbit secondary antibody (1:4,000; ab6721; Abcam) for 1 h after washing with PBST (Phosphate Buffered Saline containing 1% Tween-20). Finally, proteins were visualized using an enhanced chemiluminescence detection system (Thermo Fisher Scientific, Inc.).
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5

Western Blot Analysis of FOXP1 Expression

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Cells or homogenized tissues were lysed using radioimmunoprecipitation assay lysis buffer (Beyotime Institute of Biotechnology, Shanghai, China) containing a protease inhibitor cocktail (Sigma-Aldrich, St. Louis, MO, USA). The concentration of total protein was quantified using a BCA Protein Assay Reagent kit (Pierce, Thermo Fisher Scientific, Inc., Waltham, MA, USA) according to the manufacturer’s protocol. Equal amounts of total protein were separated using a 10% SDS-PAGE gel and then transferred onto PVDF membranes (EMD Millipore, Billerica, MA, USA).
Subsequent to blocking at room temperature with 5% fat-free dried milk diluted in Tris-buffered saline with 0.1% Tween-20 (TBST) for 2 h, the membranes were incubated with the primary antibodies overnight at 4 °C. The primary antibodies used in this study were as follows: rabbit anti-human FOXP1 antibody (1:1,000, cat. no. ab196978) and rabbit anti-human GAPDH antibody (1:1,000, cat. no. ab181603, both from Abcam, Cambridge, UK). Horseradish peroxidase-conjugated goat anti-rabbit secondary antibody (cat. no. ab205718, Abcam, Cambridge, UK) was used at a dilution of 1:5,000 for 2 h at room temperature and the protein signals were detected using a Pierce ECL Western Blotting Substrate (Pierce, Thermo Fisher Scientific, Inc., Waltham, MA, USA).
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6

Western Blot Analysis of Cell Signaling Proteins

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Cells were lyzed in ice-cold radioimmunoprecipitation assay lysis buffer (Beyotime Institute of Biotechnology) to extract the total protein. The nuclear protein was extracted using a Thermo Scientific NE-PER kit (Thermo Fisher Scientific) according to the standard instructions. Western blotting was performed as previously described40 . The following antibodies were purchased from Cell Signaling Technology (Danvers, MA): Survivin (dilution at 1:1000), P21 (1:1000), CDC2 (1:1000), P53 (1:1000), P-P53 (1:1000), CyclinA2 (1:1000), CyclinB1 (1:1000), Bax (1:1000), Bim (1:1000), Bcl2 (1:1000), Cleaved caspase3 (1:1000), Cleaved caspase 9 (1:1000), Cleaved PARP (1:1000), PI3K (1:1000), AKT (1:1000), P-AKT (1:1000), PRAS40 (1:1000), Rag C (1:1000), mTOR (1:1000), P-mTOR (1:1000), ERK1/2 (1:1000), P-ERK1/2 (1:1000). Ac-H3K9 (1:1000), Ac-H4K8 (1:1000), LaminA70 (1:5000), and β-action (1:5000) antibodies were purchased from Abcam (Cambridge, MA).
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7

Quantification and Analysis of Methyltransferase Complex

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The cell lysates were prepared using the radioimmunoprecipitation assay lysis buffer (Beyotime, Shanghai, China). The quantitation of protein in the samples was performed using the bicinchoninic acid (BCA) Protein Assay Kit (Beyotime). For SDS-PAGE, 20 μg of protein sample was loaded to each well followed by the transmembrane onto polyvinylidene fluoride membranes (Millipore, Billerica, MA, United States). The blocking of the membrane was conducted by incubating with 5% fat-free milk and then primary antibodies against METTL3 (ab195352; Abcam), METTL14 (ab223090; Abcam), WTAP (ab195380; Abcam), SIRT1 (ab110304; Abcam), and GAPDH (#5174, Cell Signaling Technology) overnight at 4°C. The blots were then washed in Tris-buffered Saline Tween-20 (TBST) three times and then incubated with secondary antibodies (A0208, A0216; Beyotime, Shanghai, China). The blots were examined by chemiluminescence using the Enhanced Chemiluminescence Detection kit (Pierce Biotechnology, Rockford, IL, United States). After exposure, the intensity of bands was analyzed by Image-Pro Plus 6.0 software.
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8

Protein Expression Analysis in Cells

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The total protein was extracted in ice-cold radioimmunoprecipitation assay lysis buffer (Beyotime, Shanghai, China), and the concentration of protein was quantified using a bicinchoninic acid protein assay kit (Beyotime). Equal amounts (20 µg/lane) of protein were fractionated using SDS-PAGE and transferred to polyvinylidene difluoride membranes. These membranes were then incubated with anti-Bax, anti-Caspase-3, anti-Cleaved Caspase-3, anti-Bcl-2, anti-cyclin B1, anti-cyclin D1, anti-P21, anti-CDC21, anti-PI3K, anti-p-mTOR, anti-mTOR, anti-p-EKR1/2, anti-EKR1/2, anti-pAKT, anti-AKT, and anti-GAPDH (Cell Signaling Technology, Danvers, MA, USA). Next the membranes were incubated with peroxidase-conjugated secondary antibodies. The Western blot bands were visualized using electrochemi-luminescence kits in accordance with the manufacturer’s instructions (Abcam, Cambridge, UK). GAPDH was used for normalization of protein loading.
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9

Western Blot Analysis of Heart Proteins

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Heart tissues were homogenized in radioimmunoprecipitation assay lysis buffer (Beyotime Institute of Biotechnology, Haimen, China). The homogenates were centrifuged at 1,600 × g for 10 min at 4°C. A bicinchoninic acid assay kit (Beyotime Institute of Biotechnology) was used for protein quantification. A total of 20 µg protein was electrophoresed on 10–15% SDS-PAGE gels and transferred onto polyvinylidene fluoride membranes (EMD Millipore, Billerica, MA, USA). Membranes were subsequently blocked with 5% (w/v) non-fat milk in TBS containing 0.1% (v/v) Tween-20 and incubated overnight at 4°C with anti-PPARα (cat no. WL00978; 1:1,000; Wanleibio, Co., Ltd., Shanghai, China), anti-Desmin (cat no. ab32362; 1:8,000; Abcam, Cambridge, UK), anti-GRP78 (cat no. WL00621; 1:1,000; Wanleibio, Co., Ltd.), and anti-GADPH (cat no. ab181602; 1:8,000; Abcam). Following washing, bound antibodies were detected following incubation for 1 h at room temperature with peroxidase-conjugated goat anti-rabbit IgG (cat no. ZB-2301; 1:10,000; OriGene Technologies, Inc., Beijing, China). Blots were developed using Western Lightning BeyoECL Plus reagent (Beyotime Institute of Biotechnology) and were quantified using ImageJ software (version 2.1.4.7; National Institutes of Health, Bethesda, MD, USA).
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10

Osteogenic Protein Expression Analysis

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To determine the protein expression of certain markers, protein extracts from BMSCs (day 3 or day 7 after the induction of osteogenesis) were prepared in radioimmunoprecipitation assay lysis buffer (Beyotime) supplemented with a proteasome inhibitor (Beyotime). Total proteins were separated by 10% sodium dodecyl sulfate-polyacrylamide gel electrophoresis and then transferred to a polyvinylidene difluoride membrane (Millipore, Shanghai, China). The membranes were then blocked in 5% BSA at room temperature for 1 h and then incubated overnight at 4 °C with antibodies specific to GAPDH (1:2000, CST), RUNX2 (1:1000; CST), COL1A1 (1:1000; Abcam), t-AKT (1:1000; CST), p-AKT (1:1000; CST), t-p38 (1:1000; CST), p-p38 (1:1000; CST), or β-catenin (1:1000; CST). After that, a secondary antibody (1:5000, Boster Biologic Technology, Wuhan, China) was applied for 2 h at room temperature. The immunoreactive bands were finally visualized and quantified using a Bio-Rad XRS chemiluminescence detection system (Bio-Rad, CA, USA).
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