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1

Western Blot Analysis of Protein Signaling

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Total protein was lysed from TKE2 cells in RIPA buffer. Samples were run on 12% SDS-PAGE gels for 2 h at 110 V and then transferred to a PVDF membrane (Millipore, Billerica, MA). The blots were blocked in 5% non-fat dried milk in TBST for 1 h at room temperature, and incubated overnight with primary antibodies against p-Akt (1:2000), total Akt (1:2000, Epitomics), p-ERK1/2 (1:1000, abcam), total ERK1/2 (1:1000, abcam), p-p38 (1:300, abcam), total p38 (1:1000, abcam), p-mTOR (1:2000, abcam) and total mTOR (1:1000, abcam) at 4°C. After three washes with TBST, the blots were incubated with a horseradish peroxidase (HRP)-conjugated secondary antibody (Amersham Biosciences, Piscataway, NJ) and visualized via enzyme-linked chemiluminescence using the ECL kit (Chemicon, Temecula, CA). The blots were analyzed by Image J software with total Akt, ERK1/2, p38 or mTOR as control.
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2

Western Blot Analysis of Angiogenic Signaling

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Total protein was extracted from the lysed samples of mouse TG or cultured neurons in RIPA buffer. Samples (total protein concentration: 40 μg for mouse TG and corneal tissue or10 μg for cultured neurons) were run on 12% SDS-PAGE gels and then transferred to a PVDF membrane (Millipore, Billerica, MA). The blots were blocked with 5% non-fat dry milk for 1 h at room temperature and incubated overnight at 4 °C with primary antibodies, including VEGF-B (1:500; R&D),VEGFR-1 (1:1000; Abcam), NRP-1 (1:1000; Abcam), p-Akt (1:2000; Abcam), Akt (1:5000; Abcam), p-ERK (1:1000; CST), ERK (1:1000; CST) p-GSK3β (1:2000; CST), GSK3β (1:2000; CST), p-mTOR(1:1000, CST), mTOR(1:1000, CST), p-S6K (1:2000; CST), S6K (1:2000; CST) and GAPDH (1:3000; Abcam). Finally, the blots were incubated with the horseradish peroxidase-conjugated secondary antibody (1:3000; Amersham Biosciences, Piscataway, NJ) and visualized via the enzyme-linked chemiluminescence using the ECL kit (Chemicon, Temecula, CA).
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3

Western Blot Analysis of Nur77 and GFP

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Cells were lysed in 150 mM NaCl, 10 mM Tris (pH 7.5), 5 mM EDTA, 1% Triton X-100, 1 mM PMSF, 10 mg/ml leupeptin, 10 mg/ml pepstatin, and 10 mg/ml aprotinin for 30 min on ice. Equal amounts of lysates (50 μg) were separated by 8–12% SDS-PAGE and transferred onto Immobilon-P transfer membranes (Millipore, Billerica, MA). Non-specific binding sites were blocked by incubating membranes in 5% (w/v) solution of nonfat dried milk in TBST (50 mM Tris–HCl (pH 7.4), 150 mM NaCl, 0.1% Tween 20). Blocked membranes were probed with specific antibodies against Nur77 (1;1000, Abcam, Cambridge, UK), GFP (1;1000, eBioscience, San Diego, CA), or β-actin (1;5000, BioVision, Mountain View, CA) in TBST. Membranes were washed 3 times with TBST and then incubated for 2 h at room temperature in TBST containing HRP-linked anti-rabbit or anti-mouse immunoglobulin. After 3 washes in TBST, HRP was visualized by chemiluminescence using the ECL kit (Chemicon, Temecula, CA). The protein concentration was quantified using the BCA protein assay (Merck, Darmstadt, Germany).
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4

Western Blot Analysis of Cellular Proteins

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Total protein was extracted from CHON-001 cells and tissues with cell extraction kit (Thermo Scientific, Waltham, MA, USA) by centrifuging samples at 4°C, 6,000 × g for 10 min. A BCA kit was used to determine the concentration of extracted protein. Total protein (20 µg) and a pre-stained protein ladder (Thermo Fisher Scientific, Inc.) were separated by 10% SDS-PAGE and transferred to polyvinylidene difluoride membranes (Sigma-Aldrich; Merck KGaA). Membranes were stained with 1X ponceau-S (Beijing Solarbio Science & Technology, Co. Ltd.) following transfer to ensure consistent loading of total protein per lane. The protein membranes were blocked with 5% bovine serum albumin (Sigma-Aldrich; Merck KGaA) at room temperature. Primary antibodies (Table II; Cell Signaling Technologies, Inc.) were applied and membranes were incubated at 4°C overnight. Secondary antibodies (cat. nos. 7074 and 7076; Cell Signaling Technologies, Inc.) were applied for 2 h at room temperature. Primary and secondary antibodies were diluted with TBST with Tween-20, as specified by the supplier. An ECL kit (Sigma-Aldrich; Merck KGaA) was employed to visualize proteins. Stains were developed with X-ray film (Fuji, Tokyo, Japan). The densitometry was performed using the Bio-Rad ChemiDoc system with Image Lab software version 6.0 (Bio-Rad Laboratories, Inc., Hercules, CA, USA).
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5

Western Blot Protein Analysis Protocol

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Cells or tissues were lysed in RIPA buffer (BioVision, Shanghai, China) solution with protease inhibitor and phosphatase inhibitor cocktail (Sigma-Aldrich). Cell lysates were collected and quantified. Total proteins (25–40 µg per condition) were separated via 10–12.5% SDS-PAGE, and subsequently transferred to a PVDF membrane (EMD Millipore). Then, the membrane was blocked in 10% milk PBST solution (for 45 min) and incubated at 4 °C overnight with the applied primary antibody. Then, the membrane was incubated with HRP-conjugated secondary antibody. HRP signaling was detected by an ECL kit (Sigma). The uncropped blotting images were listed in Fig. S1.
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6

Western Blot Analysis of Phosphorylated Proteins

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Protein samples were boiled for 5 min with Laemmli sample buffer (Bio-Rad Laboratories) and loaded into pre-poured Tris-HCl-glycine SDS-PAGE gels (stacking gel 4%, resolving gel 6% or 8%). Gels run at 150 V for 1.5 hours following transfer to a polyvinylidene difluoride membrane (PVDF, Bio-Rad Laboratories) at 40 mA constant current for 2 h. Blots were blocked with 5% BSA in 1xTBST, primary and secondary antibodies were dissolved in TBST. Following primary antibodies were used. R & D Systems: human phopho-AXL (Y779) mAb (Clone 713610), Cell Signaling: anti-AXL C89E7 rabbit mAb, phospho-MET (Tyr1234/1235) rabbit mAb (D26) XP®. Santa Cruz: Gas6 antibody (C-20). Sigma Aldrich: mouse monoclonal β-actin antibody (clone 1A4). Immunocomplexes were visualized using a second HRP-conjugated anti-rabbit or anti-mouse antibody (Pierce Biotechnology). For development we used ECL Kit (Sigma). ImageJ Software was used for densitometry analysis. Reported values were first normalized to the loading control and then multiplied by a constant to reach the lowest whole integral. Each western blot was carried out with a negative control consistent of sample diluent or beads incubated with antibody and sample diluent only.
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7

Homoisoflavanone-1 Modulates Apoptotic Signaling

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A549 cells were seeded in 6-well plates for 12 h, and then treated with either homoisoflavanone-1 (12.5, 25, 50, or 100 µg/ml) or DMSO for 24 h. Cellular proteins were harvested and immunoblotting was carried out as previously described (21 (link)) with appropriate modifications. Cells were resuspended in lysis buffer (1% Triton-X100, 50 mM Hepes pH 7.4, 2 mM sodium orthovanadate, 1 mM edetic acid, 100 mM sodium fluoride, 1 mM PMSF, 10 µg/ml of leupeptin and 10 µg/ml of aprotinin), and the supernatants of the lysates were collected after centrifugation at 14,000 g for 10 min at 4°C. The protein concentration was determined using a protein concentration kit. Proteins were separated with 12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis and transferred to polyvinyldene fluoride membranes. The membranes were blocked in 5% skimmed milk for 2 h at room temperature. Protein was detected with antibodies against active caspase 3, caspase 3, PARP, Bcl-2, Bak, p-Cdc2, Cdc2, p-P38, P38, P53 or β-actin at 4°C. The membranes were washed three times with TBST before incubation with the horseradish peroxidase-conjugated secondary antibody at room temperature for 1 h. Immunoreactive bands were visualized using an ECL kit (Sigma-Aldrich; Merck KGaA). Protein levels were quantified relative to the control group.
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8

Protein Extraction and Western Blot Analysis

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The protein we used was extracted by utilizing RIPA Lysis and Extraction Buffer (Thermo Fisher Scientific, Waltham, MA, USA). And Bicinchoninic acid (BCA) Protein Assay Kit (Thermo Scientific, Rockford, IL, USA) was used for assessing the content of the proteins. Loaded equal amounts of proteins on SDS-GAGE and then transferred to polyvinylidene difluoride (PVDF) membrane (Millipore, Billerica, MA). Next, the membranes were blocked with 5% non-fat milk for 1 h, and incubated with applied primary antibody (dilution, 1:1000) overnight at 4°C, after that, using HRP-conjugated secondary antibodies (dilution, 1:1000) to incubate for 1 h. Subsequently, the membranes were visualized by using ECL kit (Sigma). After all, corresponding internal parameters were analyzed by Image LabTM Software (Bio-Rad Laboratories). Uncropped figures of the Western Blot Assay were shown in Supplementary figures S1-7.
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9

Western Blot Analysis of Apoptotic Markers

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Post-garcinol treatment, C6 cells were pelleted and lysed in chilled RIPA buffer and were supplemented with a phosphatase and protease inhibitor (Sigma-Aldrich, Missouri, United States) cocktail for 30 min. A BCA protein estimation kit (Sigma-Aldrich, Missouri, United States) was used to quantify the protein concentration in various groups. The proteins were then separated through SDS-PAGE and subsequently transferred onto PVDF membranes (Millipore Corporation, Massachusetts, United States). Non-specific binding was prevented by incubating the PVDF membrane with blocking buffer, constituted by 5% non-fat milk for 2 h. Thereafter, the membrane was incubated overnight with primary antibodies at 4 °C. Post-incubation, the membrane was again incubated with horseradish peroxidase (HRP)-conjugated secondary antibodies for 2 h at room temperature and were then washed with TBST buffer. The expression of NF-κB, cleaved caspase-9, cleaved caspase-3, and surviving genes were evaluated by detecting changes in the chemiluminescence levels using an ECL kit (Sigma-Aldrich, Missouri, United States) following the manufacturer’s manual. Subsequently, the level of protein expression was normalized to relative internal standard and further quantified using ImageJ software (National Institutes of Health, Maryland, United States).
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10

Osteogenic Differentiation: Protein Analysis

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After 7 days of osteogenic induction, cells were washed with PBS and total protein was obtained by RIPA lysis buffer (Beyotime, China). Quantitative analysis was performed using BCA (Sigma, USA). Next, proteins were isolated on NuPAGE 10–12% polyacrylamide gel and transferred to a PVDF membrane (Millipore, USA). The membrane was blocked with 5% milk for 2 h and then incubated with primary antibodies overnight. The following primary antibodies were used: ALP (ABCAm, 1:400), RUNX2 (ABCAm, 1:400), total-β-catenin (ABCAm, 1:1000), active-β-catenin (Cell Signaling, 1:500), GSK-3β (ABCAm, 1:1000), p-GSK-3β (Santa Cruz, 1:500) and GAPDH (Cwbiotech, 1:500). The secondary antibody (Corning, 1:5000) was incubated according to the source of primary antibody, and the chemiluminescence ECL kit (Sigma, USA) was used for protein detection. ImageJ was used to analyze the corresponding spectral band intensity of scanned images.
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