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1

Western Blot Protein Detection Protocol

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Cells were harvested, and proteins were extracted using RIPA lysis buffer containing the protease inhibitor phenylmethylsulfonyl fluoride. Protein concentrations were measured using a spectrophotometer (Beckman, Fullerton, CA, United States). Equivalent amounts of protein were separated by sodium dodecyl sulfate polyacrylamide gel electrophoresis and transferred to polyvinylidene fluoride membranes by electroblotting. The membranes were blocked in 5% (w/v) skimmed milk for 1 h at room temperature. After blocking, the membranes were incubated with appropriate primary antibodies overnight at 4°C. Subsequently, the membranes were washed three times with PBS and incubated with the corresponding horseradish peroxidase-conjugated secondary antibodies at room temperature for 1 h. Then, the ECL working solution (Millipore, MO, United States) was added to the membranes. Finally, proteins were visualized and detected using a chemiluminescence system (Bio-Rad Laboratories).
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Western Blot Protein Detection Protocol

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After the cells were lysed in RIPA buffer containing the protease inhibitor PMSF, the protein concentration was determined, and 4× Laemmli sample buffer (Catalog: 161074, Bio‐Rad) was added to the sample. Electrophoresis and semidry transfer electrophoresis were performed. After the membrane was sealed and the antibody was added, the membrane was incubated at 4°C with shaking overnight. Diluted second antibody was added and incubated for 1.5 hours. The membrane was covered with the ECL working solution (Millipore, St. Louis, Missouri) and placed in the imaging system (Bio‐Rad) to obtain images.
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3

Western Blot Analysis Protocol

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After the cells were lysed in RIPA buffer containing the protease inhibitor PMSF, the protein concentration was determined, and 4 × Laemmli sample buffer (Catalog: 161074, BIO-RAD) was added to the sample.
Electrophoresis was performed at 150 V with 4-20% gradient gels. Semidry transfer electrophoresis was performed for 7 minutes at 2.5 V. After the membrane was sealed, the antibody was added to detect the target protein, and the membrane was incubated at 4°C with shaking overnight. The membrane was washed with PBS, diluted second antibody was added and incubated for 1.5 hours, and the membrane was washed again. The ECL working solution (Millipore, MO, USA) was prepared by mixing solutions A and B at a ratio of 1:1. The membrane surface was covered with working solution, placed in the imaging system (Bio-Rad, USA), and pictures were taken.
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4

Western Blot Protein Analysis Protocol

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Cells were lysed with enhanced radio immunoprecipitation assay lysis appended to protease inhibitor (BOSTER Biological Technology Co., Ltd., Wuhan, Hubei, China). The protein concentration was measured by the Bicinchoninic Acid Assay Kit (BOSTER). Following electrophoresis separation, the protein was transferred onto polyvinylidene difuoride membrane. After blocked with 5% bovine serum albumin for 2 h to inhibit non-specific binding, membranes were incubated with diluted primary antibodies (Supplementary Table 3) overnight at 4 °C. The membranes were then incubated with the horseradish peroxidase (HRP)-labeled secondary antibody (1: 2000) (Supplementary Table 3) at room temperature for 1 h. The membrane was developed with ECL working solution (EMD Millipore) for 1 min with the results analyzed with ImageJ software.
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5

Western Blot Protein Detection Protocol

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The protein extracts were subjected to electrophoresis separation, and then the separated protein was electrotransferred to polyvinylidene fluoride membrane which was blocked with 5% bovine serum albumin (BSA) at ambient temperature for 1 hour. Then, the membrane was incubated with diluted primary antibodies: CUL3 (10450, 1/1000; Cell Signaling Technology (CST)), PD-L1 (NBP1-76769, 1/1000; Novus Biologicals), SPOP (16 750–1-AP, 1/1000; Proteintech), Flag-tag (MA1-91878, 1/1000; Sigma), GAPDH (sc-47724, 1/2000; Santa Cruz, internal reference), and HA-tag (sc-7392, 1/1000; Santa Cruz) overnight at 4°C as well as with anti-Mouse-HRP secondary antibody (7076, 1/5000; CST) or anti-Rabbit-HRP secondary antibody (7074, 1/5000; CST) for 1 hour at ambient temperature. Subsequently, the membrane was developed with ECL working solution (EMD Millipore). ImageJ analysis software was run to quantify the gray levels of each group of bands.
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Quantitative Protein Analysis of Retinal Tissues

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RB tissues and normal retinal tissues or cells were lysed to isolate total protein. Proteins were separated by 10% sodium dodecyl sulfide-polyacrylamide gel electrophoresis (SDS-PAGE), and then electrotransferred to nitrocellulose membrane (Millipore, Temecula, CA, USA) and blocked with 5% BSA at room temperature for 2 h to block nonspecific binding. Primary rabbit anti-p38 MAPK, anti-P-p38 MAPK, USP22, SIRT1, SOST, and GAPDH (ab128915; 1: 10000, Abcam) were incubated with the membrane overnight at 4°C. The membrane was then incubated with HRP-labeled goat anti-rabbit secondary antibody (ab6702; 1:2000, Abcam) for 1 h at room temperature, developed using ECL working solution (EMD Millipore, USA) and exposed. Image J analysis software was used to quantify the gray scale of each band in the Western blot Image. GAPDH was taken as internal reference.
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7

Western Blot Analysis of Hippo Pathway Proteins

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Total protein was extracted from mouse liver tissue using precooled RIPA buffer (Biosesang) containing protease inhibitor (Sigma-Aldrich; Merck KGaA), and the concentration was determined using a BCA kit (Beyotime Institute of Biotechnology). Then, 10 µg protein was separated via SDS-PAGE on a 12% gel. The proteins were then transferred to a PVDF membrane, which was blocked with 5% non-fat milk for 1 h at room temperature. The membranes were incubated with primary antibodies against mammalian STE20-like protein kinase 1 (MST1; cat. no. ab79199; 1:500; 56 kDa), large tumour suppressor kinase 1 (LATS1; cat. no. ab70561; 1:5,000; 127 kDa), YAP (cat. no. ab52771; 1:5,000; 70 kDa) and TAZ (cat. no. ab119373; 1:1,000; 44 kDa) overnight at 4°C. A HRP-conjugated rabbit anti-mouse immunoglobulin G (cat. no. ab6728; 1:2,000) secondary antibody was added for 1 h at room temperature followed by exposure, development and visualization using an ECL working solution (EMD Millipore). β-actin (cat. no. ab8226; 1:1,000; 42 kDa) was used as an internal reference. All antibodies were purchased from Abcam. Protein bands were analysed using ImageJ2× software (version 2.1.4.7; National Institutes of Health).
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8

Western Blot Analysis of Autophagy Markers

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Cells were collected after trypsin digestion and lysed with enhanced RIPA buffer containing protease inhibitor (Boshide Co., Ltd., Wuhan, China), and protein concentration was determined by a BCA Protein Assay Kit (Boshide Co., Ltd., Wuhan, China). Equal amounts of protein were separated by 10% SDS-PAGE and transferred to a PVDF membrane, followed by blockade of nonspecific binding with 5% BSA at room temperature for 2 hours. Subsequently, membranes were incubated at 4°C overnight with primary rabbit antibodies to HDAC3 (Ab32369, 1 : 2000, Abcam), LC3B (ab51520, 1 : 2000, Abcam), ULK1 (ab203207, 1 : 2000, Abcam), Beclin-1 (ab207612, 1 : 1000, Abcam), and Ac-FOXO1 (AF2305, 1 : 1000; Affinity Biosciences, Jiangsu, China). The membranes were the incubated with HRP-conjugated goat anti-rabbit secondary antibody (ab205719, 1 : 2000, Abcam) at room temperature for 1 hour. ECL working solution (EMD Millipore, USA) was applied for 1 minute at room temperature to visualize membranes. ImageJ was used to quantify the gray levels of each band, with GADPH (rabbit, ab181602, 1 : 10000) as the loading control. The experiment was repeated three times.
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9

Protein Expression Analysis of Tumor Samples

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First, we lysed the samples digested and collected from tumor tissues of each group with enhanced RIPA Lysis Buffer containing protease inhibitors (Wuhan Boster Biological Technology). The protein concentration was measured using a BCA protein assay kit (Wuhan Boster Biological Technology) to ensure equal protein loading. Subsequently, protein samples were separated via SDS-PAGE and then electro-transferred onto PVDF membranes. On the PVDF membranes, we blocked with 5% BSA at room temperature for 1 h to prevent non-specific binding, then added diluted primary antibodies, including β-actin (ab8226, 1/5000, Abcam), NDUFAF6 (ab110244, 1/1000, Abcam), NRF2 (SAB4501984, 1/1000, Sigma), and PD-L1 (ab213480, 1/1000, Abcam) and incubated overnight at 4 °C for specific protein binding. Afterward, the PVDF membrane was washed three times with PBST for 5 min each, then incubated with Anti-Mouse-HRP secondary antibody (Cat # 7076, 1/5000, CST) or Anti-Rabbit-HRP secondary antibody (Cat # 7074, 1/5000, CST) at room temperature for 1 h. Finally, an appropriate amount of ECL working solution (EMD Millipore, USA) was added to the transferred membrane and incubated at room temperature for 1 min. Excess ECL reagent was removed, sealed with plastic wrap, placed in a dark box, and exposed to X-ray film for 5–10 min, followed by development and fixation.
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