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20 protocols using envision 2104 plate reader

1

In Vitro Human Translation Assay

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The reconstitution system for human translation has been described previously (Iwasaki et al., 2019 (link); Machida et al., 2018 (link); Yokoyama et al., 2019 (link)). The in vitro translation reaction and luciferase assay were performed as previously described (Iwasaki et al., 2019 (link)) with some modifications. The final concentrations of mRNA and the eIF4A protein were 60 ng/µl and 2.16 µM, respectively. The translation mixture was incubated for 2.5 hr. The fluorescence signal was detected using the Renilla-Glo Luciferase Assay System (Promega) and measured in an EnVision 2104 plate reader (PerkinElmer).
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2

Compound Screening in MV4-11 Cells

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MV4;11 cells expressing luciferase-FKBP12F36V were plated at 2000 cells per well in 50 µL of appropriate media in 384-well white culture plates (Thermo Fisher Scientific). 100 nL of compound in DMSO from compound stock plates was added to each well using a Janus Workstation pin tool (PerkinElmer). After addition of compound, plates were incubated for 16 hours at 37 ºC, prior to luminescence assessment. Plates were brought to room temperature prior to reagent addition. 25 µL Fluc buffer (as described above for the FKBP12WT and FKBP12F36V dual luciferase assay) was added to each well for 10 minutes at room temperature, and luminescence was measured on the Envision 2104 plate reader (PerkinElmer). Luminescence values were then normalized by setting DMSO only wells to 100%. Data were analyzed and plotted using GraphPad PRISM v6 using the ‘log(inhibitor) vs. response -- Variable slope (four parameters)’ analysis module.
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3

Quantitative Cell Viability Assay

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Cell viability was assayed in 2D-adherent or ultra-low adherent 3D-spheroids using CellTiter-Glo (Promega)6 (link),15 (link). Luminescence was measured on an Envision 2104 plate reader (PerkinElmer) and Fluostar Omega Reader (BMG Labtech) and data was analyzed using GraphPad PRISM v8. Synergy assessments were performed using CellTiter-Glo (Promega) with the following modifications to the protocol described in the ref. 34 (link). In brief, EWS502 cells were plated at 1000 cells per well in 50 µL of appropriate media in 384-well white culture plates (Corning) allowed to adhere overnight, and 100 nL of compounds were added using a Janus Workstation pin tool (PerkinElmer) for 72 h. Cell viability was measured by addition of 10 µL of CellTiter-Glo (Promega), followed by incubation for 15 minutes at room temperature. Luminescence was measured on an Envision 2104 plate reader (PerkinElmer) and data was analyzed using GraphPad PRISM v8.
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4

Quantifying Cellular Luciferase Activity

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For luciferase assays, cells were lysed, after washing twice with 1xPBS, by adding passive lysis buffer (Promega) directly onto the plates following the manufacturer’s protocol. Extracts were collected and centrifuged at 14000 rpm for 5 min. 50 µl of cleared extract was transferred into each well of a 96 well plate (#655083, Greiner Bio-one) containing 50 µl of 2 x Luciferase Buffer (50 mM Tris/phosphate (pH 7.8), 16 mM MgCl2, 2 mM DTT (dithiothreitol), 30% (v/v) glycerol, 1 mM ATP, 1% BSA, 0.25 mM luciferin and 8 μM sodium pyrophosphate) and the data was obtained using an Envision 2104 plate reader (PerkinElmer). Protein concentration, determined by BCA Protein Assay Reagent (Pierce), was used for data normalisation.
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5

Cell Viability Assay Protocol

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Cells were plated at 1000 cells/well in 50 µL/well of media in 384 well white culture plates (Thermo). NMC797 cells were allowed to adhere overnight before adding 100 nL of compound in DMSO from compound stock plates using a Janus Workstation pin tool (PerkinElmer). After addition of compound, plates were incubated for 72 hours at 37°C. Cell viability was read out using the ATPlite kit (PerkinElmer). Plates were brought to room temperature prior to reagent addition. Lyophilized powder was resuspended in lysis buffer and diluted 1:2 with DI water. 20 µL of this solution was added to each well and plates were incubated for 15 min at room temperature before signal was read on an Envision 2104 plate reader (Perkin Elmer).
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6

High-Throughput Cellular Viability Assay

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293T and NIH/3T3 cells were plated at 1000 cells per well in 50 µL of appropriate media in 384-well white culture plates (Thermo Fisher Scientific). Cells were allowed to adhere overnight before adding 100 nL of compound in DMSO from compound stock plates using a Janus Workstation pin tool (PerkinElmer). After addition of compound, plates were incubated for 72 hours at 37 ºC, and ATPlite 1 Step Luminescence Assay System (PerkinElmer) was used to determine ATP-dependent luminescence as an approximation of cellular viability. Plates were brought to room temperature prior to reagent addition. Lyophilized powder was resuspended in lysis buffer and diluted 1:3 with deionized water. 20 µL of this solution was added to each well, plates were incubated for 15 minutes at room temperature, and luminescence was measured on an Envision 2104 plate reader (PerkinElmer). Cell viability values were calculated by normalizing to DMSO treated wells for each cell line. Data were analyzed and plotted using GraphPad PRISM v6 and the ‘log(inhibitor) vs. response -- Variable slope (four parameters)’ analysis module.
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7

FKBP12 Binding Inhibition Assay

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In 384-well AlphaPlates (PerkinElmer), 90 nM GST-FKBP12 (WT or F36V) and 62.5 nM bio-SLF were diluted in 20 µL assay buffer (PBS containing 0.1% BSA and 0.01%Triton X-100) containing competitor compound or DMSO. Following a 30-minute incubation, 20 µL detection solution containing Streptavidin Donor Beads and Glutathione Acceptor Beads diluted to 20 ng/µL in assay buffer was added to each well. After a one hour incubation at room temperature, luminescence was measured on an Envision 2104 plate reader (PerkinElmer). Percent activity values were calculated by setting the average background (no protein wells) to 0% and the average DMSO wells to 100% activity. Data were analyzed and plotted using GraphPad PRISM v6 and IC50 values were determined using the ‘log(inhibitor) vs. response -- Variable slope (four parameters)’ analysis module.
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8

Dual Luciferase Assay for FKBP12 Variants

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Dual luciferase assays were performed using 293FT FKBP12WT-Nluc and FKBP12F36V-Nluc cells6 (link). In brief, cells were plated at 2000 cells per well in 20 µL of appropriate media in 384-well white culture plates (Corning), allowed to adhere overnight, and 100 nL of compounds were added using a Janus Workstation pin tool (PerkinElmer) for 24 h at 37 °C. To evaluate Fluc signal, plates were brought to room temperature, 20 µL of Dual-Glo Reagent (Promega) was added for 10 min and luminescence was measured on an Envision 2104 plate reader (PerkinElmer). Subsequently, 20 µL of Dual-Glo Stop & Glo Reagent (Promega) was added for 10 min and luminescence was again measured to capture Nluc signal. DMSO-normalized ratios of Nluc/Fluc signal was analyzed and plotted using GraphPad PRISM v86 (link).
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9

Quantifying SMAD3, p38, ERK, JNK Phosphorylation

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The phosphorylation state of SMAD3, p38, ERK1/2, and JNK1/2/3 was quantified using Amplified Luminescence Proximity Homogenous Assays (Perkin Elmer Waltham, Massachusetts, USA). A total of 12,000–15,000 cells/well were seeded in a 24-well plate. Forty-eight hours after plating, the cells were starved overnight in total absence of fetal bovine serum. They then were stimulated with different concentrations of TGF-β1 (0–100 ng/mL) for 1 hour, washed with phosphate-buffered saline, and lysed for 20 minutes at room temperature using 200 μL/well of AlphaScreen SureFire Ultra lysis buffer supplemented with protease inhibitors. The quantifications were performed in 384-well plates (Proxiplate; Perkin Elmer), according to protocol guidelines and measured with the EnVision 2104 plate reader (Perkin Elmer). For each condition, Six independent measurements were performed for each cell line and experiments were repeated four times.
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10

Wnt Signaling Pathway Luciferase Assay

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HEK293 cells (4 × 10
4/cm
2) were seeded in 12-well plates. 24 h later, 200 ng of SuperTOPFlash, 20 ng of Renilla luciferase (Promega, E2261), and 100 ng of GFP or PAWS1-GFP plasmids were co-transfected as described above. After 24 h, cells were treated with L-Wnt3A or L-conditioned medium for 6 h. Cells were washed with PBS and lysed in Passive Lysis Buffer (Promega, E194A). Firefly and Renilla luciferase activities were measured as described previously
17 (link). Briefly, extracts were mixed 1:1 with 2x Luciferase Buffer (50 mM Tris/phosphate (pH 7.8), 16 mM MgCl
2, 2 mM DTT (dithiothreitol), 30% (v/v) glycerol, 1 mM ATP, 1% BSA, 0.25 mM luciferin and 8 μM sodium pyrophosphate) and light emission was measured using a Envision 2104 plate reader (PerkinElmer). An equivalent volume of 3x Renilla Assay Buffer (45 mM Na
2EDTA, 30 mM sodium pyrophosphate, 1.425 M NaCl, 60 µM PTC124, 10 µM h-Coelenterazine) was then added, and Renilla luciferase emission was measured. The firefly luciferase counts were normalised to Renilla for each sample.
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