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63 protocols using protease and phosphatase inhibitor cocktail

1

Tubulin Fractionation from Rat Cardiomyocytes

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Free tubulin was separated from cold-labile microtubules using a protocol adapted from Tsutusi et al., 1993 and Ostlud et al., 1979 . Isolated rat cardiomyocytes were washed once with PBS and homogenized with 250 ul of microtubule stabilizing buffer using a tissue homogenizer. The homogenate was centrifuged at 100,000 xg for 15 minutes at 25°C and the resulting supernatant was stored at -80°C as the free tubulin fraction. The pellet was resuspended in ice-cold microtubule destabilizing buffer and incubated at 0°C for 1 hour. After centrifugation at 100,000 xg for 15 minutes at 4°C the supernatant containing the cold-labile microtubule fraction was stored at -80°C.
Microtubule stabilizing buffer: 0.5 mM MgCl2, 0.5 mM EGTA, 10mM Na3PO4, 0.5 mM GTP, and 1X protease and phosphatase inhibitor cocktail (Cell Signaling #5872S) at pH 6.95 Microtubule destabilizing buffer: 0.25 M sucrose, 0.5 mM MgCl2 10 mM Na3PO4, 0.5 mM GTP, and 1X protease and phosphatase inhibitor cocktail (Cell Signaling #5872S) at pH 6.95
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2

Antioxidant and Cytotoxic Assays Protocol

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Eagle’s minimum essential medium (MEM), Ham’s F12, Trypsin-EDTA, and trypan blue were purchased from Gibco BRL (USA). Fetal bovine serum (FBS; PAA Laboratories, Australia), 3-(4,5-dimethylthiazole-2-yl)-2,5-diphenyltetrazolium bromide (MTT), 1, 1-diphenyl, 2-picrylhydrazyl (DPPH), ascorbic acid, glutathione (GSH), glutathione reductase (GR) and β-NADPH were purchased from Sigma (USA), 2′,7′-dichlorofluorescein diacetate (H2DCFDA) was purchased from Invitrogen (USA). Protease and phosphatase inhibitor cocktail, rabbit monoclonal anti-caspase-3, rabbit polyclonal anti-phospho-p53, mouse monoclonal anti-β-actin antibodies, biotinylated protein ladder, HRP-conjugated secondary anti-rabbit, and anti-mouse antibodies were purchased from Cell Signaling Technology (USA). Rabbit polyclonal anti-Nrf-2 (H-300) antibody was purchased from Santa Cruz Biotechnology (USA). Enhanced chemiluminescence (ECL) detection system was obtained from Pierce (USA). Polyvinylidene difluoride (PVDF) membrane and H2O2 were purchased from MERCK Millipore (Germany).
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3

ERK1/2 Activation in HT-1080 Cells

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200,000 HT-1080 cells/well were grown overnight in a 6-well tissue culture plate. Cells were washed with 1 mL HBSS and the media was replaced with serum-free DMEM High Glucose media containing 1% Pen/Strep. After 16 h serum starvation, HT-1080 cells were stimulated with serum-containing media ± U0126 (5 μM) or trametinib (250 nM) for 30 min, washed with 1 mL HBSS and lysed in 100 μL of 9 M urea containing protease and phosphatase inhibitor cocktail (Cell Signaling Technology). Samples were analyzed by Western blotting as described above. Rabbit monoclonal antibodies directed against the diphosphorylated (Thr202/Tyr204) form of ERK1/2 (p42/44 MAPK, Cell Signaling Technology, dilution: 1:1000) and total ERK1/2 (Cell Signaling Technology, dilution: 1:1000) were the primary antibodies.
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4

ER Stress Signaling Pathway Evaluation

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The lysates of HK-2 cells were prepared with RIPA lysis buffer containing Protease and Phosphatase Inhibitor Cocktail (Cell Signaling Technology, Boston, USA). Then the concentrations of total protein were measured by BCA method (Thermo Fisher Scientific, USA). 30 μg protein were subjected to SDS-PAGE (10%), and then transferred to polyvinylidenedifluoride (PVDF) membranes (Millipore, Beford, MA, USA). After blocking with5% bovine serum albumin, the membranes were incubated with appropriate primary antibodies at 4°C overnight, followed by incubation with HRP-conjugated secondary antibody (1:5000, Beyotime, Shanghai, China) at room temperature for 1 h. Following antibodies were used: anti-PERK (1:1000), anti-p-PERK (1:1000), anti-GPR78 (1:1000), anti-CHOP (1:1000), anti-cleaved Caspase12 (1:1000), anti-cleaved Caspase3 (1:1000) (Cell Signaling Technology, USA), anti-GAPDH (1:3000), anti-p-eIF-2α (1:1000), anti-eIF-2α (1:1000), anti-Bax (1:1000), anti-Bcl-2 (1:1000) (Abcam, Cambridge, MA, USA). GAPDH was selected as the loading control. The blots were detected using the enhanced chemi-luminescence (ECL) detection kit (KeyGen Biotech, Nanjing, China).
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5

Western Blot Analysis of JUND Protein

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The experiment involved extracting total proteins from cells using RIPA lysis buffer (Thermo Fisher Scientific) that contained a Protease and Phosphatase Inhibitor Cocktail (Cell Signaling Technology CST). The proteins were then separated using 10% SDS-PAGE and transferred to 0.45 µm nitrocellulose membranes (Merck Millipore USA). These membranes were then blocked using a blocking buffer and then incubated with primary antibodies overnight at 4°C. The primary antibodies used were anti-JUND (ab181615; Abcam) and anti-β-actin antibody (ab8226; Abcam). Afterward, the membranes were incubated with secondary antibodies for 1 hour at room temperature, and the detection of protein signals was done using chemiluminescence.
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6

Protein Expression Analysis in Aortic Tissue

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The frozen aortic tissues underwent homogenization through the utilization of an automated bead homogenizer. Total proteins were subsequently extracted from the aortic tissues by employing a RIPA buffer that contained a protease and phosphatase inhibitor cocktail (Cell Signaling Technology, 9806, Danvers, MA, USA). Following this, all of the protein samples for each experimental group were subjected to a 5 min heating process at 95 °C. Subsequently, equal quantities of protein were loaded and electrophoretically separated onto 12% sodium dodecyl sulfate-polyacrylamide (SDS) gels. Afterward, all proteins were transferred onto a polyvinylidene fluoride membrane. The membrane was then subjected to an overnight incubation at 4 °C with specific primary antibodies, namely SM22α (Abcam ab14106, 1:10,000), αSMA (Abcam ab124964, 1:1000), αTubulin (Abcam ab52866, 1:5000), and GAPDH (CST, 5174S, 1:5000). Following the primary antibody incubation, the membranes were exposed to the corresponding secondary antibodies. Protein bands were subsequently visualized using a chemiluminescent reagent (Thermo, 34580, Waltham, MA, USA) in conjunction with the Chem-iDoc™ Imaging System (12003153 BioRad, Hercules, CA, USA).
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7

Western Blot Analysis of HAECs

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After the indicated stimulation, cell lysates were prepared from HAECs using a commercial cell lysis containing protease and phosphatase inhibitor cocktail (#5872, Cell Signaling Technology, USA). Protein concentration was measured using the BCA method (Thermo Fisher Scientific, USA). Protein from each group (20 μg) was subjected to 10-12% sodium dodecylsulphate polyacrylamide gel electrophoresis (SDS-PAGE). Separated proteins were then transferred to a PVDF membrane (Bio-Rad, USA), then blocked with 5 % fat skim milk in TBST. The PVDF membrane was then sequentially probed with primary antibodies overnight at 4° C and horseradish peroxidase (HRP)-conjugated secondary antibody for 1 h at RT. Blots were developed with enhanced chemiluminescence (ECL) western blot substrate (Thermo Fisher Scientific, USA) and exposed on X-ray film (#4741019291, Fujifilm). The following antibodies were used in this study: GPR30 (1:1000, #ab39742, Abcam, USA), KLF2 (1:1000, #ab139699, Abcam, USA), p-ERK5 (1:1000, #3371, Cell Signaling Technology, USA), β-actin (#1:10000, #4970, Cell Signaling Technology, USA), anti-rabbit IgG, HRP-linked secondary antibody (1:3000, #7074, Cell Signaling Technology, USA); anti-mouse IgG, HRP-linked antibody (1:3000, #7076, Cell Signaling Technology, USA).
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8

Protein Extraction and Turnover Analysis

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After treatment, cells were lysed in cell lysis buffer (25mM Tris7.4, 300mM NaCl, 1mM EDTA, 1% Triton) supplemented with protease and phosphatase inhibitor cocktail (Cell Signaling #5872). For xenograft tumor samples, tissues were homogenized in SDS lysis buffer (100mM Tris-HCl buffer, pH7.4, 10% Glycerol and 1% SDS) supplemented with protease and phosphatase inhibitor cocktail. 4μg of lysates were loaded for immunoblotting following standard procedures. For protein halflife studies, U2OS cells were first treated with DMSO or AZD5153 for 30 minutes before addition of 10 μg/ml of cycloheximide (Cell Signaling #2112). Cell extracts were collected after various amounts of time, and the expression levels of proteins of interest were examined by western blot analysis following standard procedure.
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9

Western Blot Analysis of Retinal Proteins

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Protein samples were obtained from whole retinas homogenized in RIPA lysis buffer (ThermoFisher Scienific) containing protease and phosphatase inhibitor cocktail (5872S; Cell Signaling Technology, Danvers, MA, USA). Proteins were separated in a 12% Mini-PROTEAN TGX Precast gel (BioRad) and transferred to a polyvinylidene difluoride (PVDF) membrane (GenHunter Corp., Nashville, TN). To block non-specific staining, membranes were incubated in 5% nonfat dry milk in Tris buffered saline containing 0.3% Tween-20 (TBST) for 2 hours. Membranes were incubated with the antibodies-containing solution overnight at 4°C. Blots were then washed in TBST and incubated with horseradish peroxidase-conjugated secondary IgG (1:1000) for 1 hour at room temperature. Antibody-bound protein was visualized using Pierce ECL Western blotting substrate (32106; ThermoFisher Scienific, Waltham, MA). To visualize loading controls, blots were also stained with antibodies against actin. Images were captured using the Azure C500 (Azure Biosystems, Dublin, CA). Densitometry of protein bands was performed using ImageJ software (https://imagej.nih.gov/ij/).
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10

Protein Extraction and Western Blot Analysis

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Samples were lysed in a radio immunoprecipitation assay buffer (Beyotime, China) with a protease and phosphatase inhibitor cocktail (Cell Signaling Technology, United States). The protein samples were measured by a BCA protein assay kit (Beyotime, China). Fifty micrograms of liver MAM protein were separated by SDS-PAGE and transferred to a polyvinylidene difluoride membrane. After blocking with 5% skim milk in Tris-buffered saline containing 0.05% Tween-20, membranes were incubated with appropriate primary antibodies overnight at 4°C and then incubated with the HRP-conjugated secondary antibody for 1.5 h at room temperature. The primary antibodies were listed in Supplementary Table S1. The membranes were developed with an ECL kit (Tanon, China) using an Amersham Imager 600 (General Electric Company, United States).
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