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35 protocols using m1000 microplate reader

1

Quantifying Cell Viability and Apoptosis

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The cell viability IC50 of each compound was determined using Promega CellTiter-Glo Luminescent Cell Viability Assay kit by measuring the total ATP levels to quantify the number of metabolically active cells upon drug treatment as described in [42 (link)]. Briefly, the compounds were suspended in DMSO at 10 mM and diluted in 384 plates (20 μl/well in DMSO) in triplicate by a 14-point titration (12 nM to 100 μM). 50 μl of HeLa cells or patient derived glioblastoma cells (HK-309) (2000 cells/well) were then treated with the prepared dilutions of the drugs (0.5 μl) and incubated at 37°C and 5% CO2. 72 hours later 50 μl of CellTiter-Glo reagent was added to each well followed by 2 minutes shaking and a 10-minute incubation to lyse the cells. The relative luminescent intensity units (RLU) of each well was measured using a Tecan M1000 microplate reader (Tecan Group Ltd.) with its green filter and 1 second integration time. Similarly, to measure caspase activity in response to 24 hour compound treatment we used the Caspase-Glo 3/7 assay from Promega as described above for the CellTiter-Glo assay.
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2

Quantifying Peroxidase Activity in Cells

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Peroxidase activity in neutrophils and adipose tissue was measured by the chemiluminescence assay using luminol plus near-infrared quantum dots, as previously described (18 (link)). Briefly, epididymal WAT and neutrophils were homogenized with RIPA buffer containing 1 mmol/L Na3VO4, 1 µg/mL leupeptin, and 1 mmol/L phenylmethylsulfonyl fluoride. Protein concentration was determined using the bicinchoninic acid method. The protein concentrations of homogenates were adjusted to 2 mg/mL and 1 mg/mL, respectively. Eighty microliters protein lysate were placed in a Costar 96-well black plate with 80 µL 2.3 mmol/L luminol (Thermo Fisher, Rockford, IL) and 1 µL 8 μmol/L QD800 (Invitrogen, Grand Island, NY). Then, 80 μL 2 mmol/L H2O2 were added to the mixtures to trigger production of HOCl. Luminescence was recorded for 20 seconds after the H2O2 addition to estimate peroxidase activity by using an M1000 microplate reader (Tecan Group Ltd., Männedorf, Switzerland).
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3

Quantification of 5' Thiolated pre-tRNA

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To generate a standard curve, increasing concentrations of thG in 20 mM Tris-HCl (pH 7.5) were aliquoted into a 384-well black microplate (Nunc) and fluorescence intensity was recorded using a Tecan M1000 microplate readerexc, 380 nm; λem, 452 nm). Relative fluorescence units were determined by subtracting the background fluorescence of blanks lacking thG, and RFU was then plotted against concentration of thG to generate a linear curve-fit (Excel). This standard curve was subsequently used to determine the concentration of thG in pre-tRNACys (Figure S1). To investigate if there was any quenching associated with thG present at the 5' terminus of pre-tRNACys, we compared the fluorescence of thG-initiated pre-tRNACys before and after alkaline hydrolysis, and found that the fluorescence values were nearly indistinguishable (data not shown). This finding lends confidence to the estimates of % 5'-modified RNAs that were determined from the thG-based standard curve.
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4

Evaluating IgG1-LALA Fc Effector Function

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Example 15

    • a. To test the potency of a LALA mutation in the constant part of an IgG1 antibody in diminishing antibody-mediated effector function, e.g. ADCC, a Jurkat effector cell reporter cell line based assay (Promega ADCC Bioassay, #G701A) has been applied according to manufacturer's instruction and using HEK-Blue-CD40L™ cells as target cells. 5000 HEK-Blue-CD40L™ cells were seeded per well in a white flat-bottom 384-well assay plate in 25 μl DMEM+10% FCS and incubated 20 h at 37° C., 5% CO2. Medium was replaced with 8 μl RPMI medium containing 4% low-IgG FCS before 4000 effector cells per well were added in 8 μl of the same medium. Finally, CP-870,893 anti-CD40 antibodies, either containing an IgG1 or an IgG1-LALA Fc-part, were added in 8 μl medium at concentrations ranging from 10000 to 0.002 ng/ml. The plate was incubated for 6 h at 37° C., 5% CO2. Effector cell luciferase activity was measured using BioGlo Luciferase assay reagents (Promega) according to the manufacturer's instructions. Luminescence was read using a Tecan M1000 microplate reader. Fold of induction was calculated with the formula RLU (antibody treatment−background)/RLU (vehicle−background). Fitting curves were obtained by using Excel (Microsoft) and XLfit (IDBS). FIG. 20 demonstrates that the LALA mutation in IgG1 abrogates Fc-receptor mediated signaling in effector cells.

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5

Binding Affinity of Anti-CD40 Antibodies

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Example 4

Binding of humanized anti-CD40 IgG1-LALA monoclonal antibodies to cynomolgus monkey-CD40 protein was tested in a biochemical ELISA. Recombinant cyno-CD40 protein (Acro Biosystems) was incubated in a 384-well Nunc™ MaxiSorp™ plate at a concentration of 0.5 μg/ml in PBS for one hour at room temperature. After washing three times with wash buffer (PBS, 0.1% Tween), plates were blocked with PBS, 2% BSA, 0.05% Tween for one hour at room temperature. Plates were washed again three time with wash buffer and antibodies at concentrations ranging from 500 to 0.03 ng/ml in PBS, 0.5% BSA, 0.05% Tween were incubated for one hour at room temperature. After 3 washes in wash buffer, wells were incubated with 12.5 μl of a 1:3000 dilution of anti-human peroxidase-linked, species specific F(ab)2 Fragment from goat (AbD Serotec) in ELISA buffer for one hour at room temperature. Wells were washed six times with wash buffer and 15 μl/well TMB substrate solution (Invitrogen) were added. After 10 minutes at room temperature 15 μl Stop solution (1M HCl) were added per well and absorbance at 450 and 620 nm wavelength was measured using a Tecan M1000 microplate reader. Fitting curves and EC50 calculation were obtained by using Excel (Microsoft) and XLfit (IDBS). As shown in FIG. 4, most antibodies bind to cyno-CD40 with EC50 values between 8 and 31.8 ng/ml.

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6

Evaluating Fc-Mediated Effector Functions of Anti-IL1R3 Antibodies

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Example 21

To test the activity of IgG-1 and IgG1-LALA versions of a humanized anti-IL1R3 antibody in eliciting Fc-mediated effector cell functions such as ADCC, MAB-16-0030 was produced as an IgG1 or IgG1-LALA antibody. hIL1R3 expressing target cells SK-MEL-30 cells were seeded in a 384-well tissue-culture treated plate at a density of 2500 cells/well in 25 μl RPMI medium containing 10% FCS. 24 h after seeding, 4000 effector cells/well (ADCC Bioassay Effector cells, Jurkat, Promega Cat. #G701A) were added in RPMI medium containing 4% low-IgG-FCS. Antibodies were then added to final concentrations ranging from 10000 to 0.002 ng/ml and the plate was incubated for 6 hours at 37° C. and 5% CO2. Activation of NF-kB signaling in luciferase gene reporter Jurkat cells was measured according to manufacturer's instructions (Bio-Glo Luciferase Assay) and using a Tecan M1000 microplate reader. “Fold of induction” values represent RLU (antibody treated−background)/RLU (no antibody control−background). Fitting curves and EC50 calculation were obtained by using Excel (Microsoft) and XLfit (IDBS). As shown in FIG. 24, only the IgG1-version of MAB-16-0030 induces NF-kB signaling in effector Jurkat reporter cells, while effector cell activation with the IgG1-LALA version is abolished.

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7

Liposome Permeabilization Assay for Bax Activation

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The liposome permeabilization assay was performed as previously described60 (link). Briefly, unilamellar liposomes (48% phosphatidylcholine, 28% phosphatidylethanolamine, 10% phosphatidylinositol, 10% dioleoyl phosphatidylserine, and 4% tetraoleoyl cardiolipin (Avanti)) were encapsulated with the quencher, p-xylene-bis-pyridinium (DPX, 45 mM, Life Technologies) and the fluorescent dye, aminonaphthalene1,3,6-trisulfonic acid (ANTS, 12.5 mM, Life Technologies) in assay buffer (10 mM Hepes (pH 7.2), 200 mM KCl, 1 mM MgCl2).
The release of encapsulated ANTS dye (excitation at 355 nm and emission at 520 nm) from liposomes (1 mg/mL) was measured on a Tecan M1000 microplate reader to assess activation of Bax via Bax-mediated pore formation. Background (F0) was recorded for 30 min at 37 °C in the presence of 0.04 mg/mL liposomes and the indicated compounds and proteins (DMSO [1%], BDA-366, ABT-199, Bcl-xL, Bcl-2ΔTMD and Bim or cBid). Afterwards Bax was added (t0) and change in fluorescence (F) was examined for 2 or 3 h at 37 °C. Finally, the liposomes were permeabilized with Triton-X-100 (0.2%) and fluorescence was measured during 5 min to estimate F100. The % release is calculated as follows: [(F − F0)/(F100 − F0)] × 100%.
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8

In vitro Biofilm Formation Assay

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In vitro biofilm formation assays were performed according to a published protocol (50 (link)). Briefly, overnight A. oris cell cultures were used to inoculate fresh cultures (1:100 dilution) in 1.5 ml of HIB containing 1% sucrose and kanamycin in 24-well plates. After incubation in a CO2 incubator at 37°C for 48 h, the biofilms were gently washed with PBS and dried before staining with 1% crystal violet. After washing the unbound dye, the stained biofilms were subject to ethanol treatment before being quantified by absorbance measurement at 580 nm with a Tecan M1000 microplate reader.
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9

Measuring miRNA Regulation of CACT 3'UTR

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The 3′ untranslated region (UTR) of the rat CACT gene was fused behind the firefly gene in the pmirGLO expression construct (Promega). This construct also contained a Renilla luciferase gene, which was used to normalize for transfection efficiency, according to the manufacturer’s directions. INS-1 832/3 cells were transfected with pmirGLO with or without cotransfection of either Ad-GFP, Ad-miR-132, or Ad-miR-375 (MOI 10) 24 h after seeding. We measured luminescence in INS-1 cells 48 h later using a Tecan M1000 microplate reader.
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10

Mitochondrial Membrane Potential Assay in Cells

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The mitochondrial membrane potential of cells was monitored by tetramethylrhodamine, ethyl ester (TMRE) Mitochondrial Membrane Potential Assay Kit, according to manufacturer protocol (BioVision, Milpitas, CA). Briefly, HepG3 cells were seeded at a density of 2.5 X 104 cells/well in a 96-well clear bottom black plate and incubated ON at 37°C in a 5% CO2 incubator. For HEK293T cells, 1 X 104 cells/well were seeded in poly D-lysine coated black 96-well plate to avoid washing off the cells. The next day, cells were treated with medium only (control), 100 μM NRH for 1, 4, and 24 h. Carbon cyanide 4-(trifluoromethoxy) phenylhydrazone (FCCP, BioVision) at 30 μM was used as a negative control and incubated at 37°C for 20 min before dosing all samples with TMRE (200 nM) for 25 min at 37°C. Following incubation, media containing dye was discarded, and the cells were washed twice with PBS and replaced the final wash with PBS to read fluorescence with Tecan M1000 microplate reader at Ex/Em = 549/575 nm. Hoechst 33342 (Life Technologies) stain (1:1000 dilution) was used to normalize the experimental fluorescence values with cell density variation. The obtained values for the treated samples were compared relative to the control values, and the fluorescence intensity was expressed as the average of the three biological replicates ± SEM.
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