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6 protocols using pierce detergent compatible bradford assay

1

Protein Extraction and SDS-PAGE Analysis

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Cells treated with DMSO (the negative control) or terfenadine (1, 2, 3 μM) cells were harvested after 48 h and processed to obtain a total protein extract according to an earlier report [54 (link)]. Briefly, the parasites were collected by cooling and posterior centrifugation at 1973× g for 10 min at 4 °C. The cells were lysed with RIPA buffer (sodium chloride, 150 mM, Tris-HCL, 50 mM, Nonidet P-40 1%, sodium deoxycholate 0.5%, SDS 0.1%) supplemented with complete protease inhibitor (Roche), PMSF (Sigma-Aldrich St. Louis, MO, USA), and sodium orthovanadate (Sigma-Aldrich St. Louis, MO, USA) and were incubated on ice for 30 min. Protein concentration was determined using a Bradford assay (Pierce Detergent Compatible Bradford Assay, Thermo Fisher Scientific). Readings were made using a microplate reader at 595 nm (Multiskan SkyHigh Microplate Spectrophotometer, A51119500C, Thermo Scientific, Waltham, MA, USA). Protein extracts (25 µg) were separated under reducing conditions by electrophoresis (polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate, SDS-PAGE) (10%) [55 (link)]. The electrophoretic separation of the proteins was carried out at a constant voltage of 120 V for 2 h. Visualization of protein bands was carried out by incubating the gel with a Coomassie staining solution.
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2

Quantifying Cellular cGAMP in Thymocytes

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To measure total cellular cGAMP DN3/4 thymocytes were expanded in OP9-DL1 culture for 3 days. Cells were then harvested, washed with PBS, and lysed in 100 µl MPER buffer (ThermoFisher Scientific) for 15 min at room temperature. Lysates were cleared by centrifugation at 16,000 × g for 15 min. Total protein content for lysates was determined using Pierce Detergent-Compatible Bradford Assay (ThermoFisher Scientific) for normalization of cGAMP. cGAMP ELISAs performed using the 2′,3′-cGAMP ELISA (Cayman Chemicals) according to the manufacturer’s recommended protocol.
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3

Zafirlukast-Induced Protein Quantification

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Cells were seeded in a 6-well plate, grown to confluence and incubated with zafirlukast for a determined amount of time depending on the experiment. Total cellular extracts were prepared in M-PER extraction buffer (Thermo Scientific, Waltham, MA) and total protein calculated using Pierce Coomassie Plus (Bradford) Assay Reagent (Thermo Scientific, Waltham, MA). Proteins were separated via SDS-PAGE and transferred to a PVDF membrane. Membranes were blocked with 5% nonfat milk in Tris Buffered Saline (TBS) and probed with the appropriate primary and HRP-coupled secondary antibodies in 3% bovine serum albumin (BSA) in TBS with 0.1% Tween 20.
Tumor lysates were prepared from 10–20 mg of flash frozen tumor tissue in 1% Triton X-100 buffer, and total protein calculated using the Pierce Detergent Compatible Bradford Assay (Thermo Scientific, Waltham, MA). Samples were electrophoresed and transferred as described above. Membranes were probed with anti-PDI and anti-ERp57 followed by an HRP-coupled antirabbit secondary antibody.
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4

Proteomic Profiling of Nematode Excreted/Secreted Proteins

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The obtained antigen fractions were separated by SDS-PAGE using 20 µg of total or trans-cuticular ES and 2 µg CSO per lane and visualized by silver staining. To determine protein contents, Bradford Assay (Pierce™ Detergent Compatible Bradford Assay, Thermo Fisher Scientific, Waltham, MA, USA) and spectrophotometric quantification (NanoDrop™ 1000 spectrophotometer, PEQLAB Biotechnologie, Erlangen, Germany) were performed.
As the RPMI medium initially contained 2000 mg/L glucose, the residual glucose content after worm cultivation was measured (Glucose Colorimetric Detection Kit, Thermo Fisher Scientific, Schwerte, Germany) to determine glucose absorption during in vitro cultivation and to check for possible interference with Ussing chamber measurements. Furthermore, amino acid and ammonia contents of lyophilized native RPMI medium as well as lyophilized medium after worm cultivation were analysed by custom service (Gesellschaft für Lebensmittel-Forschung, Berlin, Germany).
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5

Total Protein Extraction and Immunoblot Analysis

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Total protein extraction was carried out according to published protocol [68 (link)] with minor modifications. Briefly, 10–12 SAMs per sample were grounded in liquid nitrogen and homogenized in 50 μL of E buffer (125 mM Tris-HCl pH = 8.8, 50 mM Na2S2O5, 1% w/v SDS, 10% v/v Glycerol, 1% v/v HALT Protease Inhibitor Cocktail (Thermo Scientific)). Protein extracts were centrifuged at 15000g for 10 minutes and supernatants were collected. Protein concentrations were quantified using the Pierce Detergent Compatible Bradford Assay (Thermo Scientific) according to the manufacturer’s instructions. Samples were diluted with the appropriate amount of 4X NuPAGE LDS Sample Buffer (Thermo Fisher Scientific). Immunoblot analysis was carried out using rabbit αGFP antibody (1:2000; ab6556, Abcam) to detect VENUS:AREB3, rabbit αUGPase antibody (1:2000; AS05086, Agrisera) to detect UGPase, and goat αRabbit-Peroxidase (1:10000; A0545, Sigma-Aldrich, Merck) as secondary conjugated antibody.
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6

Quantifying ECM Components in Tissue Samples

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hSVs before and after SDS treatment (n = 6 per treatment group) were compared with regard to content of hydroxyproline (Sigma), elastin (FastinTMElastin kit, Biocolor) and glycosaminoglycans (GAGs, Blyscan Assay Kit, Biocolor). Assays were performed according to manufacturer’s instructions on approximately 10 mg of tissue following treatment with 0, 0.01, 0.025, 0.025, 0.075 and 0.1% w/v SDS. All data were normalised to the total wet protein content of tissue, as determined by Pierce Detergent Compatible Bradford Assay (ThermoFisher, UK). In addition, FFPE transverse sections (5 µm thick) through the conduit were stained with picrosirius red (PSR), elastin van gieson (EVG) and alcian blue for evaluation of collagen, elastin and GAGs respectively. The percentage area of tissue staining for elastin, collagen and GAGs was determined by counting the number of pixels stained for each ECM component, within four quadrants in four transverse sections, and counted using automated image analysis software (ImageJ).
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