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9 protocols using biomek fx laboratory automation workstation

1

EPAC1-CNB and EPAC2-CNB Competitive Assay

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Optimisation of 8-(2-[7-nitro-4-benzofurazanyl] aminoethylthio) adenosine-3′,5′-cyclic monophosphate (8-NBD-cAMP) competition assay was performed with purified EPAC1-CNB and EPAC2-CNB GST-fusion proteins, using modified assay conditions that were previously described21 (link). Optimisation of assay conditions was performed in 96 well black assay plates (Greiner). Comparison of reference molecules, dose response curves and pilot screen were done in black, low volume 384 assay plates (Greiner). Liquids were dispensed using a Biomek Fx laboratory automation workstation with a 96-multichannel pipetting head (Beckman Coulter) for optimisation, whereas the Echo® Liquid Handler (Labcyte) and Wellmate automated dispenser (Thermo Matrix) were employed for pilot screens (see library screening). Plates were incubated for four hours before 8-NBD-cAMP fluorescence intensity at 480/535 nm (ex/em) was measured using the Envision multi-label plate reader (Perkin-Elmer).
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2

Automated Solubility Profiling Workflow

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Solubility assays were carried out on a Biomek FX Laboratory Automation Workstation (Beckman Coulter, Inc., Fullerton, CA) using SOL Evolution software (pION Inc., Woburn, MA). The detailed method was as follows. A 10 μL aliquot of 10 mM compound stock (in DMSO) was added to 190 μL of 1-propanol to make a reference stock plate. From this plate, a 5-μL aliquot was mixed with 70 μL of 1-propanol and 75 μL of citrate phosphate-buffered saline (PBS; isotonic) to make the reference plate, and the UV spectrum (250–500 nm) of the reference plate was read. Then, 6 μL of 10 mM test compound stock was added to 594 μL of buffer in a 96-well storage plate and mixed. The storage plate was sealed and incubated at room temperature for 18 h. The suspension was then filtered through a 96-well filter plate (pION Inc.), and 75 μL of filtrate were mixed with 75 μL of 1-propanol to make the sample plate. The UV spectrum of the sample plate was then read. Calculations were carried out with μSOL Evolution software, based on the area under the curve (AUC) of the UV spectra of the sample and reference plates. All compounds were tested in triplicate.
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3

High-Throughput Drug Screening in Cancer Cells

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Tumor cells were seeded in 384-well plates. For a detailed method of cell culture condition, tumor dissociation and cell density optimization, see Supplementary Material. 2 to 24 hours after seeding, 87 compounds in 10 concentrations dose–response were pin-transferred to plates using the Biomek FX Laboratory Automation Workstation (Beckman Coulter, Inc.). 0.08% DMSO and 1.6 μmol/L staurosporine were used as negative and positive controls, respectively. 7 days after treatment, cell proliferation was measured using CellTiter-Glo reagent (Promega, G7375). For the anchor-based combination screen, cells were drugged with a single dose IC20 value of the anchor, 5 μmol/L ribociclib or 132 nmol/L JQ1, or 0.08% DMSO against up to 87 compounds in dose–response. IC50 values of the 87 compounds, with or without the anchor, were computed using RISE (Robust Investigation of Screening Experiments), an in-house program. To evaluate synergy, cells were drugged with ribociclib and the drug partner (JQ1 or the PI3K/mTORi paxalisib) in dose–response and data were analyzed using Bivariate Response to Additive Interacting Doses (BRAID) response surface model (13 (link)). For more details of the high-throughput screen (HTS), washout experiment, cell cycle, Annexin V analysis and immunoblotting methods, see Supplementary Material.
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4

Automated PAMPA Permeability Assay

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Our parallel artificial membrane permeability assay (PAMPA) was conducted with a Biomek FX Laboratory Automation Workstation (Beckman Coulter, Inc., Fullerton, CA) and PAMPA Evolution 96 Command software (pION Inc., Woburn, MA). The detailed method for this assay was as follows. First, 3 μL of 10 μM test compound stock in DMSO was mixed with 597 μL of citrate PBS (isotonic) to make a diluted test compound. Then, 150 μL of diluted test compound was transferred to a UV plate (pION Inc.), and the UV spectrum of this reference plate was read. The membrane, on a pre-loaded PAMPA Sandwich (pION Inc.), was painted with 4 μL of GIT lipid (pION Inc.). The acceptor chamber was then filled with 200 μL of ASB (acceptor solution buffer; pION Inc.), and the donor chamber was filled with 180 μL of diluted test compound. The PAMPA Sandwich was assembled, placed on the Gut-Box stirring device, and stirred for 30 min. The aqueous boundary layer was set to 40 μm for stirring. The UV spectrum (250–500 nm) of the donor and the acceptor were then read. The permeability coefficient was calculated using PAMPA Evolution 96 Command software, based on the AUCs of the reference plate, the donor plate, and the acceptor plate. All compounds were tested in triplicate.
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5

Kinome-wide siRNA Screening for Therapeutic Targets

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A kinome-wide siRNA library targeting 715 human kinases (Dharmacon, Lafayette, CO, USA) was used. Four different siRNAs targeting each kinase gene were spotted as a pool on 384-well plates (CELLSTAR; Greiner Bio-One, Monroe, NC, USA) using a Biomek FX Laboratory Automation Workstation (Beckman Coulter, Brea, CA, USA). Lipofectamine RNAiMAX (Invitrogen, Carlsbad, CA, USA) dissolved in Opti-MEM (Gibco, Gaithersburg, MD, USA) was added to the assay plates to perform reverse transfection. The final total siRNA concentration was 15 nM (3.75 nM for each siRNA targeting each kinase gene). The 92.1 cells were suspended and seeded onto the assay plates using a MultiFlo Microplate Dispenser (BioTek, Winnoski, VT, USA) at 850 cells/well with a final culture volume of 50 μL. The cells were incubated for 120 h, and then Cell Counting Kit-8 reagent (CCK8; Dojindo Molecular Technologies, Rockville, MD, USA) was added for 2 h to measure the cell viability. Viable cells were quantitated by measurement of the absorbance at 450 nm. Genes with Z-scores < −2.5 were considered therapeutic targets.
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6

RNA Extraction and qRT-PCR Analysis

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Total RNA was isolated using the RNeasy Mini Kit (Qiagen, Valencia, CA) according to the manufacturer's protocol, tested for quality, and stored at −80°C until use. The VILO kit (Life Technologies/Invitrogen, Grand Island, NY) was used to reverse transcribe 150 ng of total RNA. Primers (Qiagen) were diluted 1∶20 with molecular-grade water, and 5 µL/well were added to 384-well plates using a Biomek FX Laboratory Automation Workstation (Beckman Coulter, Inc., Brea, CA). The plates were left to dry overnight in a sterile hood and stored covered at −20°C until use. qRT-PCR was performed using SYBR Green (Qiagen) and a 7900HT Real-Time PCR System (Life Technologies/Applied Biosystems, Foster City, CA) operated in standard mode. All of the runs contained a dissociation step. The samples were amplified in duplicate in a total volume of 5 µL. The results are expressed as the relative copy number (RCN), defined as RCN = 2−ΔCq×100, where ΔCq is the difference Cq(target) – Cq(reference) [27] (link). As a reference for normalization, we used the median Cq values of three endogenous controls (beta-2 microglobulin, GAPDH and RPL13). Data were were uploaded to Gene Expression Omnibus (GSE56327).
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7

High-Throughput Screening for HPA Inhibitors

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Screening was performed on
a Beckman Coulter Biomek FX Laboratory Automation Workstation (Fullerton,
CA, USA) integrated with a Beckman Coulter DTX880 plate reader with
UV/Vis capability. The screening assay was run in 384-well plates
containing a 60 μL volume of 50 mM sodium phosphate, 100 mM
sodium chloride buffer (pH 7.0), HPA (1 μg mL–1), and the commercially available HPA substrate 2-chloro-4-nitrophenyl
α-maltotrioside (1 mM; KM = 3.6
mM). Triton X-100 (0.01%) was included to minimize detection of nonspecific
inhibitors. The natural product extract samples were present as DMSO
solutions that contained 5 mg mL–1 of dried methanolic
extract, which were tested at a dilution of 60 nL in a final assay
volume of 60 μL. HPA was found to be unaffected by the addition
of this small amount of DMSO (0.1%) and Triton X-100 (0.01%). The
integrity of the assay was tested through the use of two test plates
run as the first and last plate of each batch and which contained
a serial dilution of the known HPA inhibitor acarbose. Validation
of hits from the primary screen was performed manually on a UV/Vis
spectrophotometer. Among the hits examined in this secondary screen,
the natural extract from the sea anemone Stoichactis helianthus proved to have the highest activity against HPA. A more detailed
account of the screening methodology used can be found in Tarling
et al. 2008.17 (link)
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8

Chronic TGF-β Inhibition Assay in Py2T Cells

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For the chronic inhibition experiment, Py2T cells were seeded in 96-well plates (Techno Plastic Products AG) with a seeding density of 1,800 cells per well in 80 μl of growth cell media. Only the 60 inner wells were used for analysis. To acquire sufficient sample size, five 96-well plates were used for single condition. After seeding, cells were allowed to recover for 36 h to reach 50% confluence. Cells were treated simultaneously with TGF-β1 or vehicle (PBS) and small-molecule inhibitor or vehicle (DMSO) for 5 d, and medium was changed daily. All pipetting procedures were performed at room temperature using a Biomek FX Laboratory Automation Workstation (Beckman Coulter) supplied with 96-well pipetting pod.
In addition to experimental conditions treated with small-molecule inhibitors, at least five ‘uninhibited’ control conditions and five ‘untreated’ control conditions were included on each 96-well plate. Uninhibited control conditions were those in which TGF-β was applied to induce EMT in absence of any inhibitor. Untreated control conditions were those in which neither TGF-β nor inhibitor was applied and no EMT was induced.
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9

Yeast cDNA Amplification and Purification

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The yeast colonies were picked and digested with 20 μl of 0.02 N NaOH. After 5 min of boiling, 2 μl of the solution was used as a template to amplify the inserted cDNA with the forward primer 5′-ATGGCTGACAAACAAAGATCTGGT-3′ and the reverse primer 5′- GCGGCCGCACCACTTTGTACAAGAAA-3′. The reaction buffers were mixed and aliquoted with a Biomek FX Laboratory Automation Workstation (Beckman Coulter, Brea, CA) into 384-well PCR plates. PCR was performed with I-5 2× High-Fidelity Master Mix (Catalog No. I5HM-200, MCLAB, TSINGKE Biological Technology) according to the manufacturer’s instructions. For each amplification, 3 μl of the PCR products was mixed and purified using a QIAquick PCR Purification Kit (Catalog No. 28104, Qiagen).
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