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1

Quantifying RORA Protein Levels

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Total proteins were extracted from MSB1 cells 48 h post-transfection using radio immunoprecipitation assay (RIPA) lysis buffer supplemented with protease and phosphatase inhibitors. The concentration of proteins was determined by the BCA assay (BCA Protein Assay Kit, Beyotime, Shanghai, China), and 20 μg protein per sample was denatured in loading buffer by boiling for 3~5 min, and separated by 10% SDS-PAGE. The resulting bands were electro-transferred to polyvinylidene difluoride (PVDF) membrane at 100 mA over 1.5 h. After blocking with 4% BSA for 1 h, the membranes were incubated overnight with primary antibodies against RORA (1:1000, Abcam, ab60134) and β-actin (1:1000, Abcam, ab8226), followed by HRP-conjugated anti-rabbit IgG (1:1000) and anti-mouse IgG (1:1000) (Bayotime) respectively. The positive proteins bands were detected using a chemiluminescence system (Bio-Rad Clarity Western ECL; Bio-Rad Laboratories Inc.), and the grayscale values were quantified using ImageJ. The density of the RORA bands was standardized to that of β-actin.
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2

Protein Isolation and Western Blot Analysis

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Organoids were collected and protein was isolated using RIPA-buffer (#sc-24948) according to the manufacturer’s protocol. Protein concentration was measured using the Pierce BCA Protein Assay Kit (#23225). Proteins were blotted on nitrocellulose membranes using a Trans-Blot TurboTM Transfer System (Bio-Rad, Hercules, CA, USA). Blots were washed with 1×TBS and blocked with 5% milk for 1 h. Membranes were incubated with primary antibodies for CK8 (Abcam, Cambridge, UK, ab53280, 1:10,000), CK5 (Abcam, Cambridge, UK, ab52635, 1:10,000), AR (Santa Cruz, sc-816, 1:200), GAPDH (Cell Signaling, Danvers, MA, USA, 5174, 1:1000), or Tubulin (Sigma, T5168, 1:1000) O/N. Membranes were washed and incubated with secondary antibodies (Cell Signaling, 7076S & 7074S, 1:1000) for 1 h. Protein was detected using Bio-Rad Clarity Western ECL (Bio-Rad, Hercules, CA, USA), according to manufacturer’s protocol.
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3

Protein Extraction and Western Blot Analysis

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Total protein was extracted from cells using RIPA buffer (150 mM NaCl, 1.0%
IGEPAL® CA-630, 0.5% sodium deoxycholate, 0.1% SDS, and 50 mM Tris, pH 8.0)
(Sigma-Aldrich) and protease inhibitor cocktail (Thermo Fisher Scientific). Protein
concentrations were measured using a commercially available assay (Bio-Rad Laboratories)
according to the manufacturer’s protocol. Primary human AKR1D1 (dilution 1/250;
HPA057002, Atlas Antibodies AB, Bromma, Sweden), GILZ (sc-133215, Santa Cruz
Biotechnology), β-tubulin (#15115, monoclonal) (Cell Signaling), β-actin
(#3700, monoclonal) (Cell Signaling), CYP8B1 (#PA5-37088, polyclonal) (ThermoFisher
Scientific) and secondary antibodies (P044801-2, polyclonal) from Dako (Agilent) were used
at a dilution of 1/1000 (primary) and 1/2000 (secondary) respectively, unless stated
otherwise. Bands were visualised with Bio Rad Clarity Western ECL and ChemiDocXS imager
(Bio Rad). Western blots were quantified by densitometry analysis using ImageJ (https://imagej.nih.gov/ij/), normalised to β-tubulin to correct for
variability in gel loading.
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4

Western Blot Analysis of PCV-2 Cap Protein

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Recombinant PCV-2 Cap protein (10 μg) was resolved on a 12% sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) gel and transferred to polyvinylidene (PVDF) membranes. The transferred nitrocellulose blot was blocked with 5% skim milk (BD Pharmingen, San Diego, CA, USA) in PBST [phosphate buffer solution (PBS) containing 0.1% Tween-20] at 4 °C overnight. After being washed with PBST solution three times, the membrane was incubated with PCV-2 positive serum (1/1000 dilution in PBS) at 4 °C overnight, and hybridized with HRP-conjugated goat anti-pig IgG (Solarbio, Beijing, China) (1/2000 dilution in PBST) for 1 h at room temperature. At last, the detection was performed using Enhanced Chemiluminescence Plus Kit (Bio-Rad Clarity Western ECL; Bio-Rad Laboratories Inc.).
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5

Protein Extraction and Western Blot Analysis

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Protein samples were prepared using lysis buffer (50 mM Tris-HCl [pH 7.4], 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.25% sodium deoxycholate,) with protease and phosphatase inhibitors. Immunoblots were incubated in primary antibodies: SLC5A2 (Abcam; ab37296), GLUD1 (Abcam; ab166618) or β-Actin (Cell Signaling; #8457L) and visualized using Bio-Rad Clarity Western ECL (Bio-Rad; 170-5061).
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6

Immunoblotting of S100A8 and S100A9

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Healthy and tumor parts of fresh frozen samples were homogenized in RIPA buffer containing proteinase inhibitors, followed by protein concentration measurement using Bio-Rad Protein Assay Dye Reagent (Bio-Rad Laboratories Inc.). 50 μg protein was loaded onto reducing 15% SDS gel, followed by transfer onto PVDF membrane. Membranes were blocked with 5% nonfat dry milk in PBS-0.05% Tween-20 for overnight at 4° C. Immunoblotting was performed with primary antibodies anti-S100A8 and anti-S100A9 (R&D Systems) diluted in blocking solution incubating the membrane for 1 h at room temperature, followed by incubation with HRP conjugated anti-mouse secondary antibody (Sigma) for 1 h at room temperature. Signal was detected by Bio-Rad Clarity western ECL (Bio-Rad Laboratories Inc.) and autoradiography.
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7

Analyzing HBV Proteins in Transfected Cells

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Transfected HepG2-NTCP and HepG2.2.15 cells were washed with PBS (Eurobio Scientific) and lysed with radioimmunoprecipitation assay buffer (150 mM NaCl, 50 mM Tris-HCl pH 7.5, 1 mM EDTA pH 8.0, 1% Nonidet P-40, 1% sodium deoxycholate, 0.1% SDS, protease inhibitor cocktail [Roche]) for 30 min at 4°C followed by centrifugation at 12,000 × g to remove cell debris. Protein concentrations were measured using a BCA assay kit (Life Technologies). Equal amount of total protein was subjected to SDS-PAGE using 4%–20% mini-PROTEAN TGX stain-Free Precast Gel or 3%–8% Criterion XT Tris-Acetate (BioRad Laboratories). Immunodetection was done using anti-HBs (Abbott H166 mouse monoclonal), anti-Ku80 (ab119935, Abcam), and anti-Cas9 (C15310258 Diagenode) primary antibodies followed by incubation with horseradish peroxidase conjugated secondary antibodies. Signals were detected using Bio-Rad Clarity Western ECL and the Chemidoc XRS (Bio-Rad Laboratories).
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8

Western Blot Analysis of RORA Protein

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Total proteins were extracted from MSB1 cells 48h post-transfection using radio immunoprecipitation assay (RIPA) lysis buffer supplemented with protease and phosphatase inhibitors. The concentration of proteins was determined by the BCA assay (BCA Protein Assay Kit, Beyotime, Shanghai, China), and 20µg protein per sample was denatured in loading buffer by boiling for 3~5 min, and separated by 10% SDS-PAGE. The resulting bands were electro-transferred to polyvinylidene di uoride (PVDF) membrane at 100 mA over 1.5h. After blocking with 4% BSA for 1h, the membranes were incubated overnight with primary antibodies against RORA (1:1000, Abcam, ab60134) and β-actin (1:1,000, Abcam, ab8226), followed by HRP-conjugated anti-rabbit IgG (1:1000) and anti-mouse IgG (1:1000) (Bayotime) respectively. The positive proteins bands were detected using a chemiluminescence system (Bio-Rad Clarity Western ECL; Bio-Rad Laboratories Inc.), and the grayscale values were quanti ed using ImageJ. The density of the RORA bands was standardized to that of β-actin.
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9

Western Blot Analysis of RORA Protein

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Total proteins were extracted from MSB1 cells 48h post-transfection using radio immunoprecipitation assay (RIPA) lysis buffer supplemented with protease and phosphatase inhibitors. The concentration of proteins was determined by the BCA assay (BCA Protein Assay Kit, Beyotime, Shanghai, China), and 20µg protein per sample was denatured in loading buffer by boiling for 3~5 min, and separated by 10% SDS-PAGE. The resulting bands were electro-transferred to polyvinylidene di uoride (PVDF) membrane at 100 mA over 1.5h. After blocking with 4% BSA for 1h, the membranes were incubated overnight with primary antibodies against RORA (1:1000, Abcam, ab60134) and β-actin (1:1,000, Abcam, ab8226), followed by HRP-conjugated anti-rabbit IgG (1:1000) and anti-mouse IgG (1:1000) (Bayotime) respectively. The positive proteins bands were detected using a chemiluminescence system (Bio-Rad Clarity Western ECL; Bio-Rad Laboratories Inc.), and the grayscale values were quanti ed using ImageJ. The density of the RORA bands was standardized to that of β-actin.
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10

Western Blot Protein Extraction Protocol

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For extracting total protein, cells were resuspended in lysis buffer containing 150mmol/L NaCl, 1%SDS, and 50 mmol/L Tris-Cl pH 8, 2ug/mL aprotinin 2ug/mL leupeptin, 40mg/mL of phenylmethylsulfonyl uoride (PMSF), 2mmol/L dithiothreitol (DTT). Palate centrifuged at 12000 rpm for 15 min and supernatant were then quickly frozen at -80 C until use.
The protein concentration was distincted by the Bradford assay (Biorad, Hercules, and CA). Thirty micrograms of cell extracted protein from B16F10 were loaded onto a 10% SDS-polyacrylamide gel subjected to electrophoresis and electro-transferred onto a nitrocellulose membrane. The immunoblot was incubated 1 h at room temperature with 5% nonfat milk, and then the membrane was then probed with the primary antibody overnight at 4 C. The next day, Blots were washed twice with Tris buffered saline/Tween 20(TBST) and the secondary appropriate antibody at room temperature was added for 1 h. Blots were again washed with TBST before development. The visualization blot of the signal was obtained using ECL (Bio-Rad Clarity Western ECL). Band densitometry was measured by Image J software, Protein Simple and semi quantitative data were normalized for GADPH and Tubulin.
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