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14 protocols using ripa lysing buffer

1

Protein Extraction and Western Blot Analysis

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The extraction of cell cytoplasmic and mitochondrial fractions were performed using the Mitochondria/Cytosol Fractionation Kit (BioVision, CA, USA) according to the manufacturer’s protocol. Total cell proteins were extracted by RIPA lysing buffer (Beyotime Institute of Biotechnology, China) and protein concentration was determined by the BCA Bradford protein assay kit (Beyotime Institute of Biotechnology, China). The extracted proteins were then mixed with loading buffer and boiled for 10 min. Equal amounts of proteins (40 μg) were separated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to polyvinylidene difluoride (PVDF) membranes (Millipore, Germany). After being blocked with 5% non-fat dry milk for 2 h, membranes were incubated overnight at 4 °C with primary antibodies against GAPDH (1:1000, Abcam, USA), VDAC (1:2000, abcam, USA), cytochrome C (1:500, Abcam, USA), Bcl-2 (1:500, Abcam, USA), Bax (1:800, Abcam, USA), cleaved caspase 3 (1:500, Abcam, USA), caspase 8 (1:500, Abcam, USA), cleaved caspase 9 (1:500, Abcam, USA), and then incubated with horseradish peroxidase-conjugated secondary antibody (ZSGB-BIO, China) for 2 h at room temperature. Membranes were visualized by an enhanced chemiluminescence (ECL) kit (Thermo, USA) and quantified by densitometry using an image analyzer (BandScan, USA).
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2

Exosome Protein Characterization Protocol

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The protein in U-EXO was collected using RIPA lysing buffer (Beyotime, China). Protein concentration was determined using a BCA kit (Beyotime, China). The CD9 and TSG101 protein expression in U-EXO were determined by western blot. Rabbit anti-human CD9 antibody (PROTEINTECH, USA) and rabbit anti-human TSG101 antibody (PROTEINTECH, USA) were used. HRP-labeled Goat Anti-rabbit IgG (Beyotime, China) was used as the secondary antibody.
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3

Quantifying mTOR and TGF-β Signaling

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Fresh heart tissues from mice were harvested and lysed using RIPA lysing buffer (Beyotime, Shanghai, China) to extract total protein. The primary antibodies were listed as follows: anti-GAPDH, anti-mTOR, anti-phosphorylated-mTOR (Ser2448) (p-mTOR), anti-p70S6K, anti-p-p70S6K (Thr389), anti-4EBP1, anti-p-4EBP1(Ser65), anti-Smad2, anti-p-Smad2 (Ser465/467), anti-Smad3, and anti-p-Smad3 (Ser423/425) (Cell Signaling Technology, USA); anti-TGF-β1 (Santa Cruz Biotechnology, USA); and anti-collagen I (Abcam, UK). Signals were detected using the FluorChem E data system (Cell Biosciences, USA) and then quantified using Quantity One 4.52 (Bio-Rad, USA).
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4

Cellular Protein Isolation and Western Blot Analysis

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The total cellular protein was isolated with RIPA Lysing Buffer (Beyotime, Shanghai, China), and the protein concentration was measured using a BCA Protein Assay Kit (Beyotime). Membranes were probed with specific primary antibodies against AMPKγ (ab32508), OCT4 (ab200834), SOX2 (ab171380) (Abcam, Cambridge, MA, USA), AMPKα (#2603), p-AMPKα (#2535), FOXO3a (#12829), Caspase-3 (#9662) and β-actin (#4967) (Cell Signaling, Danvers, MA, USA). Protein bands were visualized as previously described42 (link).
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5

Western Blot Analysis of α-SMA

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Total proteins were extracted from cultured cells using RIPA lysing buffer (Beyotime, China), according to the manufacturer’s protocol. Proteins were separated by 10%–12% SDS/PAGE gels and transferred to PVDF membrane (Millipore), which was then blocked by 5% (w/v) nonfat dry milk in TBS-Tween (0.2%) for 1 h. Membranes were probed with rabbit anti-rat α-SMA (1:400, Abcam) overnight at 4°C. After several washes in TBS-Tween, membranes were incubated with goat anti-rabbit HRP-conjugated secondary antibody (1:2000, ZSGB-BIO, China). The subsequent visualization was performed using SuperSignal West Pico Chemiluminescent Substrate (Thermo) by the ChemiDoc XRS+ with image Lab software (Bio-Rad).
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6

Integrin Expression Quantification in Ishikawa Cells

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Ishikawa cells which had received the different treatments were scraped from the six-well plates and lysed with RIPA lysing buffer (Beyotime; Nantong, China) containing 1 mM PMSF and a protease inhibitor cocktail (Beyotime). The lysed cells from each treatment group were centrifuged at 16,000g for 20 min, and the supernatant fractions were collected. Next, a 20 μg sample of supernatant protein was separated by 8 % SDS-PAGE, and then semi-dry blotted onto PVDF (polyvinylidene fluoride) membranes (Millipore, Bedford, MA, USA). After being blocked for 2 h with TBST containing 5 % non-fat dry milk, the membranes were incubated overnight at 4 °C with a primary rabbit monoclonal antibody to integrin β1 (1:5000) or integrin β3 (1:5000); after which, they were incubated with the HRP-labeled secondary antibody (1:10,000; Cwbiotech, Beijing, China) for 1 h at room temperature. HRP-labeled β-actin (1:10,000; Sigma-Aldrich) was used as an internal control protein. The protein blots were developed using Beyo ECL Plus reagent (ThermoFisher Scientific; Waltham, MA, USA), and the results were recorded with a gel imaging system. The relative expression levels of integrins β1 and β3 in the different samples were calculated using a Gel-Pro-Analyzer (Media Cybernetics; Rockville, MD, USA).
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7

ROCK-1 Expression Analysis in Cells

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Cells were lysed using RIPA lysing buffer (Beyotime, Beijing, China), and protein concentration was measured using a BCA protein assay kit (Beyotime, Beijing, China). Proteins were separated using SDS-PAGE and blotted onto PVDF membranes, which were incubated with primary ROCK-1 antibodies (1:1000, Abcam) for 12 h at 4°C and then with secondary antibodies for 1 h at 37°C. Bands were imaged using the FluorChem E data system (ProteinSimple, CA, USA). The relative density values were determined based on the GAPDH expression level. Each assay was repeated at least three times.
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8

Protein Expression Analysis in Heart Tissues

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Total protein from heart tissues or cells was extracted by use of RIPA Lysing Buffer (Beyotime, Shanghai, USA). Protein was incubated with the primary antibodies anti-LC3, anti-beclin1, anti-acetyl-histone 3 (Lys9), anti-histone 3, anti-β-actin (Cell Signaling Technology, Danvers, MA, USA); anti-SIRT1, anti-FOXO1, anti-cleaved caspase 3 (Abcam); anti-acetyl-FOXO1 (Lys259, Lys262, Lys271; Santa Cruz Biotechnology, Santa Cruz, CA, USA); anti-p62 and anti-Rab7 (Sigma-Aldrich), then horseradish peroxidase-conjugated AffiniPure goat anti-rabbit and antimouse IgG secondary antibodies. Bands were revealed by use of the FluorChem E data system (Cell Biosciences, Santa Clara, CA, USA) and quantified by densitometry with Quantity One 4.52 (Bio-Rad, Hercules, CA, USA). Each assay was repeated at least three times.
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9

Western Blot Analysis of Hippo Pathway

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Total protein from A498 and 786O cells was extracted using RIPA Lysing Buffer (Beyotime). Protein was separated by electrophoresis in 12% SDS-PAGE and transferred to PVDF membranes, blocked with 5% milk in Tris-buffered saline with Tween 20, and probed with the primary antibodies against YAP1 (ab52771), LATS1 (ab70562), LATS2 (ab110780), TEAD2 (ab92279), TEAD3 (ab75192) and β-actin antibody (MAB8929, 1:1000; R&D systems). After incubation with peroxidase-conjugated secondary antibodies, bands were visualized with enhanced chemiluminescence (Millipore). The relative band intensities were quantified using a ChemiDoc XRS imaging system.
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10

Western Blot Analysis of Protein Expression

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Total cellular protein was isolated with RIPA Lysing Buffer (Beyotime, Jiangsu, China). The protein concentrations were measured with a BCA Protein Assay Kit (Pierce, Rockford, IL, USA). The membrane was probed with specific primary antibodies against SIRT1, ARHGAP5 (Abcam, Cambridge, MA, USA), and c-JUN (Cell Signaling, Danvers, MA, USA) and then with a horseradish peroxidase-conjugated anti-mouse or anti-rabbit IgG antibody. The protein bands were developed using the ECL system (Millipore, Boston, MA, USA). β-Actin (Cell Signaling) or GAPDH (Proteintech, Rosemont, IL, USA) served as the loading control.
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