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25 protocols using 384 well microplate

1

Organoid-Based Compound Screening

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Organoids were mechanically dissociated by pipetting before being resuspended in 5% BME/AO media (15–20,000 organoids ml−1) and dispensed into 384‐well microplates (Greiner).

Each compound was dispensed at 1–100 μM using a TECAN D300e Digital Dispenser, and after 5 days, cell viability was assayed as described above.

Paclitaxel (T7402), methotrexate (A6770), crizotinib (PZ0240), and cisplatin (C2210000) were obtained from Sigma; Nutlin‐3a (10004372) was obtained from Cayman chemicals; erlotinib (S1023) from Santa Cruz; alpelisib (A‐4477) from LC Laboratories; and gefitinib (S1025) from Selleck Chemicals. Averages of IC50s from at least three independent experiments were calculated and visualized using GraphPad Prism, version 6.0, Morpheus (https://software.broadinstitute.org/morpheus) and CorelDraw X7.
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2

High-throughput Cell Painting Assay

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Cells were seeded at 800–1500
cells per well in 50 μL into 384-well microplates (Greiner,
#781091) for 24 h. Compounds were then added as 8-point semi-log dose
responses from 10 μM before being incubated for a further 48
h.
For morphological and nuclei count readouts, the Cell Painting
protocol was applied, which uses multiplexed fluorescent dyes to visualize
cellular and subcellular organelle and cytoskeletal morphology.12 (link),13 (link) Cells were fixed in 4% formaldehyde before permeabilization in 0.1%
Triton-X100 (v/v). Finally, the staining solution was added in 1%
bovine serum albumin in PBS (w/v) and incubated for 30 min before
being washed out. (Supporting Table 8).
Four fields of view were captured per well using a 20× objective
and five filters (Supporting Table 8).
For the expanded panel of EAC cell lines, data CellTitre-Glo (promega)
was added according to the manufacturer’s instructions and
incubated for 10 min at room temperature before being read. For caspase-dependent
apoptosis assays, we monitored caspase activity at sequential time
points following compound treatments using the Incucyte imaging instrument
and caspase-3/7 biosensor according to the manufacturer’s instructions
(Sartorius).
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3

Fluorescence Polarization Assay for Protein-Nucleic Acid Binding

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Equilibration reactions were performed using same protocol as for EMSAs. Reactions were transferred to 384 well microplates (Greiner Bio-One Monroe, NC). The apparent fluorescence polarization was determined using a Clariostar monochromator microplate reader with fluorescein-sensitive filters and polarizers. Polarization values were normalized relative to saturation polarization value. For each experiment, values of three reads were averaged. Average values and standard errors from at least three technical replicates were calculated and plotted against each protein concentration. These data were fit to a quadratic equation (Equation 1, where b is the base polarization, m is the maximum polarization, R is the labeled nucleic acid concentration, and P is the total protein concentration) as in (Pagano et al., 2011 (link)), to calculate the apparent dissociation constant. The reported values are the dissociation constants calculated using the polarization values averaged from all technical replicates. The reported errors are standard error values calculated from the dissociation constant of each individual technical replicate. ϕ=b+(mb)×[R+P+Kd,app(R+P+Kd,app)2(4RP)2R]
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4

Pyrophosphatase-based Counterscreening Assay

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Counter-screens
carried out to exclude false positive compounds were performed in
50 μL reactions containing 0.5 U/mL pyrophosphatase and 2 μM
pyrophosphate in 100 mM Tris-HCl, pH 7.6, buffer containing 1 mM MgCl2 and 1 mM TCEP for 2 h at room temperature in 384-well microplates
(Greiner Bio-One). Control reactions were performed in the absence
of the pyrophosphatase. The reactions were terminated by addition
of 50 μL BIOMOL Green (Enzo Life Sciences), and product formation
was measured by absorbance (650 nm) using a PHERAstar microplate reader
(BMG Labtech) following incubation for 20 min. Liquid dispensing was
performed using a Thermo Scientific Matrix Wellmate, and data were
processed and analyzed using ActivityBase (IDBS).
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5

Measuring α2-Adrenoceptor Arrestin Recruitment

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Investigation of α2AAR and α2BAR stimulated β-arrestin-2 recruitment was performed applying an assay which is based on fragment complementation of β-galactosidase (PathHunter assay, DiscoverX, Birmingham, UK) as described (79 (link)). In detail, HEK293T cells stably expressing the enzyme acceptor (EA) tagged β-arrestin-2 were cotransfected with human α2AAR or α2BAR each fused to the ProLink-ARMS2-PKS2 fragment for enzyme complementation and GRK2 (cDNA Resource Center) at equal amounts and subsequently transferred into 384 well microplates (Greiner) after 1 day. After incubation for further 24 hours cells were incubated with test compounds for 60 min (α2AAR) or 90 min (α2BAR), arrestin recruitment was stopped by adding detection regent and the resulting chemoluminescence was monitored with a Clariostar plate microreader. Data were normalized relative to buffer (0%) and the maximum effect of norepinephrine (100%). Three to nine repeats for α2AAR (three to six for α2BAR) in duplicate were measured.
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6

Functional Coupling of FFA2 Receptors

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Yeast strain YIG69 was constructed by chromosomal integration of pRS306GPD-hFFA2 into the ura3 locus of MMY23. Strain YEG5 was produced by introducing episomal expression construct p426GPD-rFFA2 into MMY24 (Brown et al. 2003 (link)). MMY23 contains a chimeric Gpa1/Gαi1 subunit, whereas MMY24 contains Gpa1/Gαi3 (Brown et al. 2000 (link)), allowing functional coupling of hFFA2 or rFFA2 to the pheromone response pathway. Receptor activation was measured as described previously (Brown et al. 2011 (link)) by 24 h growth assays in 384-well microplates (50 μL/well; Greiner, Stonehouse, UK) with fluorescein di-β-d-galactopyranoside (10 μmol/L). Fluorescence was measured on an Envision plate reader (PerkinElmer). Signal:basal ratios were optimized by varying 3-aminotriazole (3AT), and final assay conditions were 5 mmol/L 3AT (YIG69) or 20 mmol/L 3AT (YEG5) except where otherwise indicated.
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7

SARS-CoV-2 Inhibitor Screening Assay

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HEK293T-ACE2-GFP cells were seeded in white, solid bottom 384-well microplates (Greiner BioOne) at 6,000 cells/well in 15 μl medium and incubated at 37°C with 5% CO2 overnight (~16 h). Compounds were titrated 1:3 in DMSO and dispensed via pintool at 23 nl/well to assay plates. Cells were incubated for 1 h at 37°C 5% CO2 before 15 μl/well of media was added. The plates were then incubated at 37°C for 48h at 37°C 5% CO2. After incubation, 30 μl/well of ATPLite (PerkinElmer) was added to assay plates and incubated for 15 min at room temperature. The luminescence signal was measured using a Viewlux plate reader (PerkinElmer). Data were normalized with wells containing cells as 100%, and wells containing media only as 0%.
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8

Measuring G Protein Signaling of α2-Adrenergic Receptors

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Determination of G protein–mediated signaling by human α2AAR, murine α2AAR, and human α2BAR was performed applying an IP accumulation assay (IP-One HTRF, Cisbio, Codolet, France) according to the manufacturer’s protocol and in analogy to previously described protocols (77 (link), 78 (link)). In brief, HEK 293T cells were cotransfected with the cDNA for a receptor and the hybrid G protein Gαqi (Gαq protein with the last five amino acids at the C terminus replaced by the corresponding sequence of Gαi) (gift from The J. David Gladstone Institutes, San Francisco, CA), respectively, in a ratio of 1:2. After 1 day, cells were transferred into 384-well microplates (Greiner) and incubated for further 24 hours. On the day of the experiment, cells were incubated with test compounds for 90 min (α2AAR) or 120 min (α2BAR), and accumulation of second messenger was stopped by adding detection reagents (IP1-d2 conjugate and Anti-IP1cryptate TB conjugate). After 60 min, TR-FRET was monitored with a Clariostar plate reader. FRET-signals were normalized to buffer (0%) and the maximum effect of norepinephrine (100%). Three to nine (murine α2AAR, α2BAR) or 4 to 11 repeats (human α2AAR), respectively, were performed for each test compound all done in duplicate.
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9

FRET Assay for Protein-Protein Interactions

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FRET assay experiments were carried out using a CLARIOstar® microplate reader (BMG Labtech, DE) following the protocol for measuring a three-way protein-protein interaction using FRET from Martin et al (2008)32 (link) and Kopp et al (2018)22 for apo protein. In brief, a mixture containing 30 μM of each fluorescent protein (CFP-IRE1 LD and YFP-BiP), and increasing concentrations of CH1 were made into a volume of 160 μL in buffer E. Next, 50 μL was transferred to a 384 well microplate (Greiner Bio-one, AT). The protocol was adapted for nucleotide experiments to include a 30 min incubation at RT with 1mM nucleotide in the reaction mixture. Calculation of Ki was based on the protocol from Martin et al (2008)32 (link). The data were plotted using percentage inhibition as a function of the CH1 concentration and fitted to an exponential curve (two phase association), from which 50% dissociation value or IC50 (equivalent to half-life) for each phase were measured in GraphPad prism 8. These values were then used to calculate the Ki for each phase.
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10

FRET Assay for Protein-Protein Interactions

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FRET assay experiments were carried out using a CLARIOstar® microplate reader (BMG Labtech, DE) following the protocol for measuring a three-way protein-protein interaction using FRET from Martin et al (2008)32 (link) and Kopp et al (2018)22 for apo protein. In brief, a mixture containing 30 μM of each fluorescent protein (CFP-IRE1 LD and YFP-BiP), and increasing concentrations of CH1 were made into a volume of 160 μL in buffer E. Next, 50 μL was transferred to a 384 well microplate (Greiner Bio-one, AT). The protocol was adapted for nucleotide experiments to include a 30 min incubation at RT with 1mM nucleotide in the reaction mixture. Calculation of Ki was based on the protocol from Martin et al (2008)32 (link). The data were plotted using percentage inhibition as a function of the CH1 concentration and fitted to an exponential curve (two phase association), from which 50% dissociation value or IC50 (equivalent to half-life) for each phase were measured in GraphPad prism 8. These values were then used to calculate the Ki for each phase.
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