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7 protocols using coomassie plus bradford assay

1

Temsirolimus Treatment of GFb Cells

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GFb cells were plated onto 55 cm2 petri dishes at 3 × 105 per dish and incubated. Subconfluent cells (about 5.5 × 106) were treated with 50 nM CCI-779 (temsirolimus) for 12 h, collected with trypsin, washed 3 times with cold PBS, and lysed in buffer that contained 20 mM Tris (pH 8.0), 137 mM NaCl, 100 g/L glycerol, 50 g/L Triton X-100, 2 g/L Na2VO4, and 4 g/L EDTA; 10 ml PMSF (0.1 M) and 10 ml ALT (10 g/L) were added per 1 ml lysis buffer immediately before use. The cell lysates were put on ice for 15 min and centrifuged at 15,000 rpm at 4 °C for 20 min, and the supernatant was transferred to new tubes.
The concentrations of the lysates were measured by Coomassie Plus (Bradford) Assay (Thermo Scientific). Equal amounts (40 μg) of protein were electrophoresed on 12 % (w/v) sodium dodecylsulfate polyacrylamide gels. Proteins were transferred to Hybond-polyvinylidene difluoride membranes (Amersham) and incubated with the primary antibodies overnight at 4 °C and peroxidase-conjugated secondary antibodies at room temperature for 1 h. Enhanced chemiluminescence (ECL) (Amersham) was used to detect the signals.
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2

Protein Isolation and Quantification

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Following the removal of RNA from the phenol-chloroform extraction, DNA was removed with ethanol and protein was precipitated with isopropanol overnight at −80°C. Precipitated total protein was washed 3 times with 0.3M guanidine hydrochloride in 95% ethanol for 20 minutes each, followed by 1 wash with 100% ethanol per the manufacturer's protocol for dual RNA and protein isolation. Protein pellets were then solubilized in 8M urea solution containing 1% protease inhibitor cocktail (Sigma, St Louis, Mo) at 55°C for 20 minutes. Urea was then gradually exchanged for a Tris-HCl buffer with 1% Triton-X through serial dilution and concentration in a 3-kDa Amicon ultra centrifuge filter (Millipore, Darmstadt, Germany).
The Coomassie Plus Bradford Assay (Thermo Scientific, Rockford, Ill) was used to quantify total protein following standard protocol. Briefly, a standard curve was prepared by dilution of bovine serum albumin (BSA) protein (Sigma, St Louis, Mo) in Tris-HCl buffer. Five microliters of standard or isolated total protein was mixed with 150 μL of Coomassie Plus reagent (Thermo Scientific) in a microtiter plate and absorbance was assessed at 570 nm.
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3

Utrophin Expression in mdx Muscles

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Western blots were performed on whole muscle lysates as previously described [26 (link)]. Briefly, the gastrocnemius muscles treated mdx4cv muscles and contralateral controls (n = 4) were ground in liquid N2 and homogenized in extract buffer (50 mM Tris-HCl, 150 mM NaCl, 0.2% SDS, 24 mM Na deoxycholate, 1% NP40, 47.6 mM Na Fluoride, 200 mM Na Orthovanadate, Roche, Basel, CH). Protein concentration of whole muscle was determined by Coomassie Plus Bradford Assay (Thermoscientific, Rockford, IL). Equal amounts of protein (20 μg) were resolved on a 4–12% SDS polyacrylamide gel. The blots were incubated in N-terminal anti-utrophin (1:1000; kind gift from Stanley C. Froehner) overnight at 4°C. The GAPDH antibody (1:50,000; Sigma, St. Louis, MO) was used as a loading control as its expression was unchanged when comparing the treated and untreated mdx4cv muscles. The primary antibodies were detected with IgG HRP secondary antibodies (1:25,000; Jackson ImmunoResearch Labs). The blots were developed with ECL plus (Thermoscientific, Rockford, IL) and scanned with the Storm 860 imaging system (GE Healthcare Lifesciences, Piscataway, NJ). The band intensity was measured using Image J software (NIH).
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4

RH1 Reduction Assay Protocol

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For studies of RH1 reduction, cells were grown in 22 cm2 cell culture dishes. Cells were scraped off and suspended in 500 μL of buffer containing 25mM Tris-HCl (pH 7.4) and 250mM sucrose. Cells were disrupted with an ultrasonic homogenizer (Bandelin Sonopuls HD 2070, Berlin, Germany) and protein concentration was measured with a Coomassie Plus Bradford Assay (Thermo Scientific, Vilnius, Lithuania). Cell lysates were diluted to a concentration of 1 mg/ml with the same buffer which has been used for cell disruption. The RH1 reduction rate was measured in the presence of the NADPH regeneration system or by adding 500 μM NMeH (reduced N-methylnicotinamide, Santa Cruz Biotechnology, Heidelberg, Germany). For the NADPH regeneration system we used 20 μM NADPH, 10 mM glucose-6-phosphate and 10 µ/mL glucose-6-phosphate dehydrogenase. The reactions were followed spectrometrically using a Hitachi 557 UV-Vis spectrometer at 37 °C. The RH1 reduction was monitored at 328 nm with the NADPH regeneration system or at 318 nm (NMeH isosbestic point) when NMeH was used as a cosubstrate. NMeH oxidation was monitored at 380 nm. Spectral data was first processed with R Studio and then statistical analysis was performed with MS Excel software.
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5

Isolation and Characterization of hESC-MSC Extracellular Vesicles

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The hESC‐MSC EVs were prepared as previously described (Lai et al., 2016). Briefly, immortalized hES‐ MSCs were grown in a chemically defined medium for 3 days and CM was harvested and pre‐cleared with a 0.22 µm syringe filter. The CM was concentrated 100× for exosomes by tangential flow filtration (Sartorius; MWCO 100 kDa) and stored in −20°C freezer until use. The EVs were assayed for protein concentration using Coomassie Plus (Bradford) Assay (Thermo Fisher Scientific) per manufacturer's instruction and characterized for particle size distribution and concentration by Zetaview (Particle Metrix) according to the manufacturer's protocol. Follow‐up experiments from subsequent batches of hESC‐MSC EVs (posterior to batch AC83) yielded identical results.
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6

Purification of CIAptB and CIAptR Proteins

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E. coli cells were transformed with either pET30-ctbciA or pET30-rsbciA, and single colonies were used to inoculate 1 L LB broth supplemented with kanamycin (30 µg/ml). Protein expression was induced at an OD600 of 0.6 upon addition of isopropyl β-D-thiogalactopyranoside (IPTG) to a final concentration of 0.5 mM. The culture was incubated for an additional 16 hours at 30°C and cells were harvested by centrifugation. The cell pellet was resuspended in Buffer A (50 mM Tris-HCl, 100 mM NaCl, 5 mM imidazole, pH 8.0) and cells were lysed by sonication. The supernatant was clarified by centrifugation at 15 000×g for 20 minutes and the soluble portion was loaded onto a 5 ml HisTrap FF column (GE Healthcare, Piscataway, NJ) which was equilibrated with Buffer A. The protein was eluted from the column over a linear gradient to 100% Buffer B (50 mM Tris-HCl, 100 mM NaCl, 250 mM imidazole, pH 8.0) over 20 column volumes. The resulting fractions were analyzed by SDS-PAGE to assess protein purity. Fractions determined to be >95% pure were pooled and the protein concentration was determined by Coomassie Plus Bradford assay (Thermo Scientific, Rockford, IL).
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7

Immortalized MSC Exosome Isolation

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MSC exosome was prepared as previously described [35, 36, 39 . Briefly, immortalized human embryonic stem cell-derived MSCs were grown in a chemically defined medium for 3 days and the conditioned medium was harvested and 0.22-mm filtered. The conditioned medium was concentrated 100 × for exosomes by tangential flow filtration (Sartorius; MWCO 100 kDa) and stored in -20°C freezer until use. The exosomes were assayed for protein concentration using Coomassie Plus (Bradford) Assay (Thermo Fisher Scientific), as per manufacturer's instruction, and characterized for particle size distribution and concentration by Zetaview (Particle Metrix) according to the manufacturer's protocol. The mean protein and particle contents of the exosome preparations were 1.9 mg/mL and 1.9 × 10 11 particles/mL.
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