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407 protocols using synergy h1 plate reader

1

Antioxidant Capacity Measurement by DPPH Assay

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The 2,2-Diphenyl-1-picrylhydrazyl (DPPH)-free-radical scavenging activity was measured according to the method described by Schaich et al. [31 (link)], with modifications for a 96-well microplate scale. The stock solution (600 μM) was prepared in methanol and stored in the dark at −20 °C. A daily DPPH solution was prepared by dilution with methanol to achieve an absorbance of 0.600 ± 0.100 at 515 nm. For the assay, 25 μL of sample (biocompatible concentrations of 0.12 g/L for the delivery system and 0.005 g/L (15 µM) for curcumin, determined in our previous work [21 (link)]), Trolox (7.5–240 μM), ascorbic acid (0.05 g/L, 280 μM) or solvent were added to 175 μL DPPH daily solution. The mixture was incubated for 30 min at 25 °C and the absorbance was measured at 515 nm with a Synergy H1 plate reader ( Agilent, Santa Clara, CA, USA). The scavenging activity was expressed as percentage (%) reduction in absorbance related to the control. Regression equations between DPPH scavenging and Trolox concentration were calculated, and the results expressed as µmol TE (Trolox equivalent) per gram of sample. The DPPH scavenging effect percentage was determined according to Equation (4): DPPH scavenging effect%=AcontrolAsampleAcontrol×100
where Acontrol and Asample are the absorbances at 515 nm of control and sample, respectively.
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2

Virus Entry Assay with BlaM-Vpr

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A549 cells were seeded in phenol red-free DMEM with 10% FBS the day before infection. BlaM-Vpr containing HIV-1 particles (50 pg p24) pseudotyped with wild-type or GPc were bound to cells by centrifugation at 1550xg for 30 min, 4°C. Cells were washed with cold phenol red-free DMEM with 10% FBS and 20 mM HEPES (GE Healthcare Life Sciences) to remove unbound viruses and incubated at 37°C to initiate virus-cell fusion. Cells were then placed on ice, loaded with the CCF4-AM BlaM substrate (Life Technologies), and incubated at 11°C overnight to allow substrate cleavage. The cytoplasmic BlaM activity (ratio of blue to green fluorescence) was measured using a Synergy H1 plate reader (Agilent Technologies, Santa Clara, CA, USA).
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3

Cytochrome-C Release Assay in BAEC

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Quantification of cytochrome-C released in response to AEA treatment in BAEC challenged with LPS was carried out using the Promega Cytochrome-C Assay (Promega, Madison, WI, USA). Briefly, BAEC were cultured in white 96-well plates following the experimental design and the assay was carried out following manufacturer’s recommendations. Luminescence was read on a BioTek Synergy H1 plate reader (Agilent, Santa Clara, CA, USA).
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4

Quantification of Cellular PIP2 Levels

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Cells were transfected with GFP-PLCδ-PH or Tubby-YFP expression plasmid as a PIP2 reporter, and GFP and YFP images were obtained by confocal microscopy [35 (link)]. Alternatively, cellular lipids were extracted, and PIP2 amounts were determined using a PIP2 Mass ELISA Kit (#K-4500, Echelon Biosciences) following the manufacturer’s protocol [36 (link)]. Absorbance was measured at 450 nm using a BioTek Synergy H1 Plate Reader (Agilent Technologies, Santa Clara, CA, USA). PIP2 was quantified from a standard curve fitted by four-parameter nonlinear regression.
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5

Bacterial Growth Conditions and Monitoring

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Bacteria were grown in lysogeny broth (LB) (Sezonov et al., 2007 (link)) and brain heart infusion (BHI) (Rosenow, 1919 )‐rich medium or in Spizizen (SM) (Anagnostopoulos & Spizizen, 1961 (link)), C‐Glc (Commichau, Herzberg, et al., 2007 (link); Commichau, Wacker, et al., 2007 (link); Dormeyer et al., 2019 (link)), and CGXII (Keilhauer et al., 1993 (link)) minimal medium. agar plates were prepared with 15 g agar/l (Roth, Germany). Growth in liquid medium was monitored using 96‐well plates (Microtest Plate 96‐Well, F Sarstedt, Germany) at 37°C and medium orbital shaking at 237 cpm (4 mm) in a Synergy H1 plate reader (Agilent, USA) equipped with the Gen5 software, and the OD600 was measured in 10–15 min intervals. Single colonies were used to inoculate 5 mL overnight LB cultures that were incubated at 220 rpm and 30°C. The OD600 was adjusted to 0.1, and 150 μL of the cell suspensions were transferred into 96‐well plates. Bacteria were cultivated in the Synergy H1 plate reader as described above.
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6

Rapamycin-Induced Luminescence Assay

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G1ER cells were harvested, pelleted at 125 g × 5 min at 4°C, and plated into a white-walled 96-well plate in fresh G1ER medium at 105 cells/well in 80 μL. Cells were treated with 100 nM rapamycin or vehicle in 2 μL for 60, 30, 15, or zero min at 37°C before addition of Nano-Glo substrate (Promega N1110) in 80 μL. The well plate was then shaken at 300 rpm for 3 min before being read using a Synergy H1 plate reader (Aglient, v2.04.11). Luminescent values were recorded using a gain of 200 and an integration time of 1 s.
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7

Fluorescent Labeling of TTDN1 Protein

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TTDN1 has a cystine residue at the C terminus; therefore, we used 5-iodoacetamido-fluorescein (Thermo 62246) to label TTDN1. The pH 11-soluble fraction of TTDN1 was brought to 10 mg/ml in SEC buffer, and 1/50th volume of 20 mg/ml 5-iodoacetamido-fluorescein in DMF was added. After 2 h at room temperature, the samples was passed over a PD10 desalting column (Cytiva) equilibrated with SEC buffer. The sample was further purified on a Superdex 200-Increase 10/300 column (Cytiva) equilibrated with SEC buffer. Purified, labeled TTDN1 was quantified by comparison to known standards on a Coomassie stained gel. Labeled TTDN1 (2.5 nM) was incubated with Dbr1 (3-fold dilution from 2.8 μM to 1 nM) or Drn1 (225 nM) in black 96-well half-area plates (Costar 3694). Proteins were diluted with SEC buffer. The fluorescence polarization was measured with a BioTek Synergy H1 plate reader equipped (Agilent). Plotting and curve fitting was performed with GraphPad (Prism).
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8

Quantifying Cardiac Collagen Content

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A hydroxyproline assay kit (Sigma, Burlington, MA #MAK008) was used to quantify total collagen content in the heart. After 20 weeks, hearts were harvested and a portion of the ventricle, ∼20 mg, was frozen and homogenized in ultrapure water. The ventricular tissue was hydrolyzed in 12 M HCl, and after 3 h at 120°C in pressure-tight capped vials, samples were centrifuged at 10,000 g for 3 min at room temperature. Subsequently, 10 μl (HFpEF samples) or 40 μl (control samples) of supernatant was transferred to the 96-well plate and dried overnight at 60°C. After drying, the Chloramine T/Oxidation Buffer Mixture provided with the hydroxyproline kit was added to both the sample and standard curve wells and incubated at room temperature. After 5 min, diluted 4-(dimethylamino)benzaldhyde reagent provided with the kit was added to all wells and incubated at 60°C for 90 min. Finally, absorbance was read at 560 nm using a Synergy H1 plate reader (Agilent Technologies, Santa Clara, CA). Hydroxyproline content was calculated using the standard curve and was normalized to tissue weight.
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9

PIP5Kγ Silencing and Verteporfin Treatment

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After seeding into 6-well plates (1000 cells/well), cells were repeatedly treated with UNC3230 (100 nM), verteporfin (1 μM), and/or DMSO as a vehicle control at 2 to 3 d intervals. Cells were treated with control or PIP5Kγ siRNA every 3 days under the indicated conditions. After 10 d, the cells were stained with 0.5% crystal violet following fixation with a mixture of acetic acid and methanol at 25 °C, as described previously [33 (link)]. Cell colonies were counted using ImageJ software. Cell viability was evaluated using an EZ-CYTOX assay kit (Daeil Lab Service, Seoul, Republic of Korea) according to the manufacturer’s protocol. Briefly, cells seeded in 96-well plates (10,000 cells/well) were treated with PIP5Kγ siRNA and/or verteporfin (1 μM) as described above. After 7 d, formation of the water-soluble tetrazolium salt was measured at 450 nm using a BioTek Synergy H1 Plate Reader (Agilent Technologies, Santa Clara, CA, USA).
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10

High-throughput Src-3CL protease inhibitor assay

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3x106 293 T were seeded per well in a 6-well dish. 24 hours later, they were transfected with 2 μg of the wild-type Src-3CLpro-Tat-Luc or mutants thereof with TransIT-LT1 (Mirus, catalog number MIR 2304). Four hours after transfection, cells were washed with PBS, trypsinized, resuspended in medium and counted. 2x105 cell per well were seeded in 50 μl medium in a flat-bottom 96-well plate (Greiner). Inhibitor dilution series were added in 2-fold excess to required concentrations in 50 μl medium. After 44 hours, medium was removed and 50 μl of Bright-Glo reagent (Promega) added to each well. Cells were incubated for five minutes in the dark and then transferred to a white flat 96-well plate (CLS3600, Corning) for measuring luminescence on a Synergy H1 plate reader (Agilent). The percent inhibition was calculated with the following formula. %inhibition=100(100/relative luminescence)
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