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Protein Expression Analysis by Western Blot

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Protein concentrations were measured using BCA kit (BioVision K813-5000 Milpitas, CA). Protein samples (15-40 μg) were subjected to SDS-PAGE electrophoresis and then were electro-transferred to a 0.45 μm polyvinylidene difluoride membrane (Merck Millipore Ltd, IPVH00010, Ireland). The membrane was blocked and incubated with primary antibodies, secondary horseradish peroxidase-conjugated antibody, and visualized with an ECL kit (Applygen, p1020, Beijing, China). For Co-IP assay, 200 μg of cellular protein was incubated with primary antibody, and precipitated using agarose beads (Santa Cruz biotechnology, sc-2003, USA). Antibodies were shown in Supplementary Table S1.
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2

Protein Expression Analysis in U2OS Cells

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48 h after cell transfection, log-phase U2OS cells were harvested, and total cellular protein was extracted by using RIPA Buffer (Auragene, Changsha, China). The BCA protein quantitative kit (Thermo, USA) was applied to determine protein concentration. Equal amount of protein samples were resolved by using SDS-PAGE analysis and then transferred to a polyvinylidene fl uoride (PVDF) membrane. The membrane was then blocked with 5 % fat-free milk at room temperature for 1 h. Subsequently, the membrane was incubated with a primary antibody (anti-β-actin 1 : 1000; anti-p53 1 : 1000; anti-p21 1 : 1000; anti-TP73 1 : 1000; anti-Bcl-2 1 : 1000; anti-Bax 1 : 1000) at 4 °C overnight, then washed three times with TBST solution, followed by incubation with a HRPconjugated secondary antibody (Anti-rabbit IgG, HRP-linked Antibody; 1 : 5,000) at room temperature for 1 h. To visualize the protein bands, an ECL kit (Applygen, Beijing, China) was applied following the manufacturer's protocol.
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3

Western Blot Analysis of Antioxidant Proteins

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We performed Western blot, as previously recorded ((Zhang et al., 2016 (link); Fei et al., 2020 (link))). The proteins extracted from renal tissues or cells were lysed in a RIPA buffer containing protease and phosphatase inhibitors, and the protein content was detected by using the BCA protein assay kit (Beyotime). Protein samples (50 ug) from each group were electrophoresed in 10% SDS-PAGE gel and then transferred to a PVDF membrane. After blocking with 5% nonfat dry milk, the blots were incubated with the primary antibodies against GPX4 (1: 1000, DF6701, Affinity), ACSL4 (1: 1000, A14439, Ablonal), Nrf2 (1: 1000, AF7904, Affinity), SIRT-1 (1: 1000, DF6033,Affinity), and or β-actin (1: 200, ab181602, Abcam) overnight at 4°C. Subsequently, the blots were washed in TBST and incubated with a secondary antibody for 2 h at room temperature. The bands were determined with an ECL system applying an ECL kit (Applygen), and band intensities were checked by BandScan software.
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4

Protein Expression Analysis of Adipose Tissue

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Adipose tissue samples were lysed with cold RIPA lysis buffer (0.5% Nonidet P-40, 0.1 M NaCl, 0.03 M HEPES with pH 7.6, protease inhibitors), and then the lysate was centrifuged at 13,000× g rpm, 4 °C for 15 min. The supernatants were collected and the concentration of the total proteins was measured using a BCA protein detection kit (Applygen Technologies, Beijing, China). Following this, 25 μg of protein were separated using SDS-PAGE gel and were moved onto NC membranes (Applygen Technologies, Beijing, China). Subsequently, the membranes were blocked with 2.5% nonfat milk and were incubated overnight with primary antibodies against anti-rabbit GPX4 (ABclonal, Wuhan, China), anti-rabbit SLC7A11 (ABclonal, Wuhan, China), anti-rabbit TFR1 (Invitrogen, Carlsbad, CA, USA), anti-rabbit L-ferritin (Abcam, Cambridge, UK), anti-rabbit H-ferritin (Abcam, Cambridge, UK), and anti-mouse β-actin (Cell Signaling Technology, Boston, MA, USA). After being washed three times, the membranes were treated with a corresponding horseradish peroxidase-conjugated secondary antibody (EASYBIO, Beijing, China). Finally, the protein bands were identified using an ECL kit (Applygen Technologies, Beijing, China). β-actin was served as the loading control.
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5

Mitochondrial Proteome Analysis in Kidney

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The proteins of renal cortex tissue were lysed with Protein Extraction Kit (P0033, Beyotime, Jiangsu, China), the proteins of mitochondria and cytoplasmic were extracted with Tissue Mitochondria Isolation Kit (C3606, Beyotime, Jiangsu, China) and quantified by BCA protein assay kit (P1511, Applygen, Beijing, China). Total tissues lysates were fractionated by sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) and then transferred to nitrocellulose membranes. Afterward, the membranes were blocked with 5% BSA for 1 h at room temperature and followed by incubation with the primary antibodies anti-Parkin (SC-32282, Santa, Dallas, USA), anti-PINK1 (DF7742, Affinity, Ohio, USA), anti-LC3 (2775, CST, Boston, USA), SQSTM1/p62 antibody (5114, CST, Boston, USA), anti-Caspase-3 (9662S, CST, Boston, USA), anti-Cyt c (11940S, CST, Boston, USA), and anti-Nephrin (ab136894, Abcam, Cambridge, UK) overnight at 4 ℃. After washing, the corresponding HRPconjugated secondary antibodies were used. Finally, we used an ECL Kit (P1010, Applygen, Beijing, China) and a multi-functional imaging system to detect positive binding. Image-Pro Plus 6.0 software was used to quantify all protein bands.
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6

Western Blot Analysis of Vascular Proteins

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Arteries or cells were placed into RIPA lysis buffer containing protease inhibitor cocktail (Roche Diagnostics, Indianapolis, IN, USA). Protein samples (30 μg) were separated with 7.5% SDS-PAGE and transferred to polyvinylidene difluoride membranes (Amersham Biosciences, Piscataway, NJ, USA). The membrane was blocked with blocking buffer (TBS, 0.1% Tween-20, 5% non-fat milk or 2% BSA) for 2 hours at room temperature and incubated with primary antibodies against eNOS (1:1000, Cell Signaling Technology, Danvers, MA, USA), p-eNOS (ser1177) (1:1000, Abcam, Cambridge, MA, USA), arginase I (1:1000, Abcam, Cambridge, MA, USA), arginase II (1:1000, Santa Cruz Biotechnology, Santa Cruz, CA, USA), UT-B (1:1000, a kindly gift from Dr. Trinh-Trang-Tan, INSERM, Paris, France), β-actin (1:5000, Santa Cruz Biotechnology, Santa Cruz, CA, USA). Goat anti-rabbit IgG horseradish peroxidase (1:10000, Abcam, Cambridge, MA, USA) or goat anti-mouse IgG horseradish peroxidase (1:5000, Santa Cruz Biotechnology, Santa Cruz, CA, USA) were incubated for 60 minutes at room temperature the next day, respectively. The blots were developed with ECL kit (Applygen Technologies Inc, Beijing, China) and finally exposed to X-ray films. Relative protein expression levels were quantified by optical density analysis (Quantity-One software, Bio Rad Gel Doc 1000, Milan, Italy) and normalized to β-actin.
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7

Protein Expression Analysis in A549 Cells and Tumor Tissues

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Using RIPA lysis buffer (Beijing Solarbio Science & Technology Co., Ltd.), total proteins were extracted from A549 cells and tumor tissues. Protein concentration was determined by a BCA kit (Beyotime Institute of Biotechnology). The proteins (25 µg) were separated in 10% SDS-PAGE gels and then transferred to PVDF membranes, which were blocked with 5% non-fat dry milk for 1 h at room temperature. After incubation with specific primary antibodies (all purchased from Abcam) at 4°C overnight, the membranes were washed thrice with 1X 0.05% TBST for 10 min and incubated with goat-anti-rabbit IgG H&L secondary antibodies (1:2,000; cat no. ab6721; Abcam) at room temperature for 1 h. Protein bands were visualized by an ECL reagent (Applygen Technologies, Inc.). The primary antibodies were as follows: NPM1 (1:400; cat no. ab183340), phosphorylated (p)-EGFR (1:1,000; cat no. ab40815), EGFR (1:5,000; cat no. ab52894), p-MEK (1:2,500; cat no. ab96379), MEK (1:2,500; cat no. ab32091), p-ERK (1:1,000; cat no. ab201015), ERK (1:10,000; cat no. ab184699), GAPDH (1:2,500; cat no. ab9485). The protein bands were visualized using an ECL kit (Applygen Technologies, Inc.), and the relative protein levels were quantified using ImageJ software 1.8.0 (National Institutes of Health).
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8

Western Blot Analysis of EMT Markers

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After specific treatment, total cellular proteins from SW1990 cells were extracted by using RIPA Buffer (Auragene, Changsha, China). BCA protein quantitative kit (Thermo Fisher Scientific, Inc.) was carried out to measure the concentration of protein samples. Equal amount of protein samples were resolved by 12% SDS-PAGE and then transferred onto PVDF membranes. The membranes were blocked with 5% non-fat milk at room temperature for 1 h, followed by incubated with primary antibodies (anti-E-cadherin, cat no. 3195; anti-ZEB1, cat no. 3396; anti-TWIST1, cat no. 46702; dilution for all, 1:1,000; Cell Signaling Technology, Inc., Danvers, MA, USA) at 4°C overnight. Subsequently, membranes were incubated with a HRP-conjugated secondary antibody (anti-rabbit IgG, HRP-linked antibody, cat no. 7074; 1:5,000) at room temperature for 2 h. To visualize the protein blots, an ECL kit (Applygen Technologies, Inc., Beijing, China) was used to visualize the protein blots according the manufacturer's protocol.
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9

Western Blot Analysis of Stem Cell Markers

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Cells were lysed in RIPA buffer on ice, and protein concentration was quantified by the BCA method (Sigma, MO, USA). 20 μg protein was resolved by SDS-PAGE and transferred onto PVDF membrane (Millipore, MA, USA). After brief blocking with 5% milk, the membrane was probed with primary antibodies: rabbit anti-Sox2 (#2748, Cell Signaling Technology, MA, USA), rabbit anti-Bmi1 (#6964, Cell Signaling Technology, MA, USA), rabbit anti-Lin28 (#3695, Cell Signaling Technology, MA, USA), rabbit anti-Nanog (#8822, Cell Signaling Technology, MA, USA), rabbit anti-ADGB (ab204085, Abcam, Cambridge, UK), rabbit anti-β-actin (#4970, Cell Signaling Technology, MA, USA) at 4 °C overnight. After washing, membranes were hybridized with secondary antibodies for another hour. The blots were detected with ECL Kit (APPLYGEN, Beijing, China) and visualized on LI-COR system (Biosciences, Lincoln, NE, USA).
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10

Protein Expression Analysis in Lens Capsules

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Dispersion of lens capsules under a microscope was followed by extraction of the proteins with lysis buffer (Beyotime Biotechnology, Shanghai, China). Protein extract was separated by electrophoretic 10% or 12.5% SDS‐PAGE (EPizyme, Shanghai, China). Then, it was transferred to PVDF membranes. The blots were incubated with the primary antibodies of LC3II/I (Abcam, ab192890), P62 (Abclonal, A19700), Lamp1 (Abclonal, A16894), Cln5 (Abclonal, A12886), Gla (Abclonal, A1700) and Lipa (Abclonal, A6385). The blots were incubated with a secondary antibody (ZSGB‐Bio, ZB‐2301), and then they were visualized using enzyme‐linked chemiluminescence using the ECL kit (Applygen, Beijing, China).
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