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1

Protein Expression Analysis in Nuclear and Cytoplasmic Fractions

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Total protein was extracted by RIPA (Solarbio, Beijing), and the concentration was measured by bicinchoninic acid (Solarbio). The nuclear and cytoplasmic fractions were isolated by a Nuclear Extraction Kit (Solarbio, Beijing, China) according to the manufacturer‘s instruction. 80 μg/well proteins were loaded onto 10% SDS-PAGE for each sample, and proteins were transferred onto equilibrated polyvinylidene difluoride membranes (Millipore Corporation, Billerica, MA, USA) by electroblotting. Membranes were blocked with TBST containing 5% milk and incubated overnight at 4°C with primary antibodies against HO-1 (Bioworld Tech, LP, USA), Wnt1 (Abcam, Cambridge, MA, USA), Wnt5a (Novus Biologicals, Littleton, USA), β-catenin, GSK-3β, phospho-GSK-3β (Ser9) (ProteinTech Group, Chicago, USA), and NFAT5 (Santa Cruz, CA, USA). After incubation with the secondary antibody (ProteinTech), proteins expression was corrected by the amount of β-actin (ProteinTech) in the same sample. Lamin A (ProteinTech) and tubulin (ProteinTech) were used as the marker for nuclear and cytosolic proteins, respectively. The bands were quantified by scanning densitometry using Quantity One 4.6.3 software (Bio Rad).
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2

Sensitive PCR Detection of Toxoplasma gondii in Soil

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The PCR method based on T. gondii-conserved gene internal transcribed spacer 1 (ITS-1) as target gene for soil detection was conducted according to previously reported [6 (link)]. To standardize the sensitivity, diluted T. gondii tachyzoites at the concentration of 1 × 105, 1 × 104, 1 × 103, 5 × 102, 1 × 102, 5 × 101, 1 × 101, 1 × 100 were mixed respectively with 0.5 g blank soils. The negative control with only blank soil was set. Then the total DNA of the mixture and negative control were extracted by the commercial E.Z.N.A TM Soil DNA Kit (OMEGA, USA) according to the manufacturer’s instructions and was used as template for the PCR.
The PCR products were then loaded onto 1% agarose gels (Sigma–Aldrich, St. Louis, MO, USA). The resulting DNA fragments were visualized by the Gel Doc XR System and analyzed using Quantity One 4.6.3 software (Bio-Rad, Hercules, CA, USA). The size of the amplified PCR products was estimated by comparison with the DL2000 DNA Marker (TaKaRa, Dalian, China).
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3

Quantifying Protein Purity and Concentration

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Protein purity was quantified by densitometry of SDS-PAGE bands using the BioRad GS-800 densitometer and Quantity One 4.6.3 software (BioRad, Hercules, CA, USA). The relative percentage of the target protein band was calculated by Equation (1):
Total protein concentration was measured by the DC Protein Assay Lowry method (BioRad, Hercules, CA, USA) and the concentration of the target protein was calculated using the values of relative quantity according to the Equation (2): target mg/mL=relative quantity %× protein concentration100
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4

Notch and ADAM10 Expression Analysis

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For Notch expression, mRNA was extracted from non-stimulated, non-transfected p6 HUVEC. cDNA was obtained using VERSO cDNA kit (Invitrogen) following the manufacturer’s instructions. PCR for each fragment was performed with Superscript (Invitrogen) for 40 cycles on a Biorad thermocycler, ran on a 1.5% agarose gel and visualized on QuantityOne 4.6.3 software (Biorad). For ADAM10 knockdown, mRNA was extracted 48 hours after siRNA transfection, reverse-transcribed with VERSO kit (Invitrogen). 100 ng of cDNA were run with Taqman primers and FastTaq on a QuantStudio3 (Applied Byosistems) following the manufacturer’s instructions. Beta actin was used as a housekeeping gene. For primer sequences and catalog numbers see Table2.
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5

SDS-PAGE and Western Blot Analysis

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The protein concentration of each sample was measured using a bicinchoninic acid (BCA) protein assay kit (Bioteke, China). Equal amounts of total protein (50 μg) from each sample were separated in a 10% SDS-PAGE gel and transferred to a PVDF membrane at 120 V for 2 h at room temperature (RT). The blot was blocked with 5% nonfat dry milk suspended in 1x TBS (25 mM Tris, 137 mM NaCl, and 2.7 mM KCl) for 1 h at room temperature. Membranes were incubated with primary antibodies against STAT6 and GAPDH (Cell Signaling Technology, USA). The resulting blots were incubated with 1:1,000 rabbit–mouse secondary antibodies (Cell Signaling Technology, 4414/4410, USA). Bands were scanned using a densitometer (Bio-Rad) and quantified using the Quantity One 4.6.3 software (Bio-Rad).
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6

Extracting Soluble and Insoluble Protein Fractions from Brain Tissue

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To extract the soluble protein fraction, brain tissue or cells were isolated and homogenized in 1× STEN buffer (50 mM Tris (pH 7.6), 150 mM NaCl, 2 mM EDTA, 0.2% NP-40, 0.2% BSA, 20 mM PMSF and protease cocktail inhibitor), centrifuged at 10,000 g for 20 min at 4°C and the supernatant containing the soluble protein fraction was collected. To extract insoluble Aβ1-42, the pellet was re-suspended in 30% formic acid and centrifuged at 10,000 g for 20 min at 4°C and the supernatant was collected. Extracts were analyzed by WB on SDS NuPAGE 4-12% Bis-Tris gel (Invitrogen, NP0301BOX). β-actin was probed (1:1000) with polyclonal antibody (ThermoScientific, PA121167). Autophagy antibodies, including Beclin-1 (1:1000) and LC3-B (1:1000) were used to probe according to autophagy antibody sampler kit (Cell Signaling, Inc. Cat# 4445). Tau antibodies were used as we previously described [14 (link), 18 (link)]. WBs were quantified by densitometry using Quantity One 4.6.3 software (Bio Rad).
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7

Gelatin Zymography for MMP-2 Activity

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MMP-2 activity in culture media samples was assayed using a 0.05% gelatin zymography gel, as described previously (5 (link)). Briefly, 10 µl of each sample was mixed with an equal amount of Laemmli sample buffer (62.5 mM Tris-hydrogen chloride, 25% glycerol, 2% SDS and 0.01% bromophenol blue, pH 6.8) and separated on a 10% SDS-PAGE gel copolymerized with 0.05% gelatin. Enzyme activity was regained by removing the SDS, whereby gels were washed three times for 1.5 h in total in 2.5% Triton X-100 at room temperature following electrophoresis. Washed gels were then bathed in proteolysis buffer (50 mM calcium chloride, 0.5 M sodium chloride and 50 mM Tris, pH 7.8) and incubated at 37°C for 15 h. Following incubation, gels were rinsed in a 2.5% Triton X-100 solution and stained at room temperature with Coomassie blue (45% methanol, 44.75% H2O, 10% acetic acid and 0.25% Coomassie blue R-250) for 1 h on a rotator. Gels were then destained with a 40% methanol, 7.5% acetic acid and 52.5% H2O solution until white bands were clearly visible against the Coomassie blue background. Bands were scanned with a densitometer (GS-800; Bio-Rad Laboratories, Inc.) and quantification was performed using Quantity One 4.6.3 software (Bio-Rad Laboratories, Inc.). The experiment was repeated three times, and the relative density values were subjected to statistical analysis.
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8

Western Blot Analysis of Protein Interactions

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Whole-cell lysate and the Co-IP supernatant were mixed with 5× SDS-PAGE Plus sample buffer (GenStar, Beijing, China) and then incubated in a boiling water bath before separation by SDS-PAGE and subsequent transfer to PVDF membrane (Millipore, Bedford, MA). The membrane was blocked with 5% skim milk (Solarbio, Beijing, China) for 3 h then incubated with primary antibody overnight at 4°C. The membrane was washed thrice for 10 min each time using Tris-buffered saline and 0.1% Tween-20 (Solarbio, Beijing, China) and incubated with the appropriate secondary antibody. The primary antibodies used for Western blot were β-catenin rabbit polyclonal antibody (1:2,000) (ab6302, Abcam, Cambridge, UK), Myc-tag rabbit monoclonal antibody (1:5,000) (AE070, ABclonal), and HA-tag rabbit monoclonal antibody (1:1,000) (C29F4, Cell Signaling). β-actin rabbit monoclonal antibody (1:2,000) (AF5003, Beyotime) was used as a loading control. The secondary antibody was goat anti-rabbit IgG (1:5,000) (A0208, Beyotime). The blot signal was visualized using ECL reagent (Thermo Fisher Scientific, Carlsbad, CA). The protein expression level was quantified by the band density using Quantity One 4.6.3 software (Bio-Rad Laboratories, Hercules, CA) and normalized by β-actin.
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9

Western Blot Analysis of ER Stress and MMP14

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The concentration of each sample protein was measured by the bicinchoninic acid (BCA) protein assay kit (Bioteke, Beijing, China). Equal amounts of total protein (50 μg) from each sample were separated in a 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) gel for 3 h at room temperature and transferred to a polyvinylidene fluoride (PVDF) membrane at 110 V for 2 h on ice. The blot was blocked with 5% nonfat dry milk suspended in 1× Tris buffered saline with Tween (TBST) (25 mM Tris, 2.7 mM KCl, and 137 mM NaCl, 0.05% Tween-20) for 40 min in the incubator at 37 °C. Then, the blot was incubated with ER stress antibody (1:1000, Cell Signaling Technology, Danvers, MA, USA) and MMP14 (1:1000, Abcam) at 4 °C for 12 h, followed by incubation with goat anti-rabbit IgG-HRP (1:10,000, Lianke, Hangzhou, China) for 1 h at room temperature. The blot was washed three times with 1× TBST for 10 min between the first and second incubation. A densitometer (Bio-Rad) to scan the bands and a Quantity One 4.6.3 software (Bio-Rad) was used for quantification. This experiment was repeated four times.
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10

Muscarinic Receptor Expression Analysis

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Total RNA (2 µg per reaction) extracted from rat bladder tissues using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA) and cDNA synthesis was performed using the SuperScript III First-Strand kit (Invitrogen) according to the manufacturer's instructions. Synthesized cDNA fragments were amplified by a PCR process in thermal cycler (S1000 Thermal Cycler; BIO-RAD Laboratories, CA, USA).
M2, 3-muscarinic receptors in our study were used published primers (6 (link)15 (link)). PDZ-RhoGEF, LARG, and p115RhoGEF were used published primers (16 (link)). And β-actin primer was designed bound on exon-exon base. The β-actin in the diabetic disease research has been used as a house-keeping gene because the expression of β-actin is not affected by the glucose. Each PCR reaction was carried out with the Maxime PCR PreMix I-StarTaq (iNtRON Biotechnology, Korea) using cDNA equal to 100 ng total RNA, under the following conditions: 94℃ for 2 min and 35 cycles at 94℃ for 30 sec, 60℃ for 30 sec and 72℃ for 30 sec, followed for 7 min. The reaction products were analysed by electrophoresis on agarose gels. Densitometric analysis of band intensity was detected by Gel Documentation System (Gel Doc XR; BIO-RAD Laboratories, CA, USA) and measured using Quantity One 4.6.3 software (BIO-RAD, CA, USA).
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