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17 protocols using d12345

1

Hypericin Incubation Optimization for U-87 MG Spheroids

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All preparation steps were performed in the dark. Stock solutions of hypericin (PhytoLab GmbH & Co.KG) in DMSO (Molecular Probes™ D12345) with concentrations of 0.1 mM, 0.25 mM, 0.125 mM, 0.05 mM, and 0.005 mM were prepared and frozen at − 20 °C. Aliquots of this stock were freshly thawed for each experiment. After thawing, a 1:100 dilution of hypericin (1 µM, 2.5 µM, 1.25 µM, 0.5 µM, 0.05 µM) in complete cultivation medium and additional 10% FBS was prepared. This procedure was adopted from [15 (link)]. Excess medium was removed from each single well and the hypericin/MEM mixture was added at a final concentration of 1 µM for incubation time experiments. Spheroids were incubated for 5 min, 30 min, 125 min, 10 h + 30 min, and 35 h + 15 min in the hypericin cultivation medium, respectively. Varying hypericin concentrations (2.5 µM, 1.25 µM, 0.5 µM, 0.05 µM) were incubated for a predefined time period of 30 min. Non-hypericin-incubated control spheroids were treated with a 1:100 dilution of DMSO in complete cultivation medium and additional 10% FBS for 30 min. Afterwards, the hypericin and control incubation were disrupted by removing the incubation medium and applying three washing steps with phosphate buffered saline (PBS). Following the washing steps, U-87 MG spheroids were directly preserved by fixation. All experiments were executed in triplicate.
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2

Calcium Flux Assay for Piezo1 Mutants

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Fluo-4 AM NW dye and probenecid (Molecular Probes, 36206) were prepared according to manufacturer’s instructions. The dye was further supplemented to a final 4 mM CaCl2 concentration. Yoda1 was prepared as 10 mM stock in 100% DMSO (Molecular Probes, D12345). 24 h after HEK293TΔP1 cells were seeded in 96-well plates (Corning, 3603) and transfected with Piezo1-myc, S260R-myc, or S2211L-myc constructs. Media was aspirated to reduce background and adherent cells were loaded with dye/probenecid solution for 40 min at 37 °C and 8% CO2. On loading, baseline fluorescence was measured for 5 min, and activation by 20 µM Yoda-1 (in 0.2% DMSO) or 0.2% DMSO alone was measured for 18 min. Maximal calcium signal was determined by addition of A23187 ionophore (Millipore Sigma, C7522) and assayed for 25 min. All Relative Fluorescence Unit (RFU) measurements were performed on a BioTek Synergy H1 at 37 °C with excitation 488 nm and emission 518 nm, and 70 s between reads. Normalized RFU = (signal RFU - baseline RFU) / (maximal post-A23187 - baseline RFU). Signal RFU = mean well RFU at t = 24 min, baseline RFU = mean well RFU at t = 5 min, maximal post-A23187 = mean signal at t = 52 min. Data point represents n = 9 to 15 normalized wells. Each well is plated, transfected, treated, and assayed independently, and as such, represents individual experiments.
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3

Preparation and Application of Plant Extracts

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The stocks were prepared weighing 3–6 mg of crude extract into a micro centrifuge tube. The crude extract was dissolved in DMSO (dimethyl sulfoxide anhydrous from Life technologies cat # D12345) to reach a 60 mg/mL final concentration and stored at −20 °C. For the assay, a different amount of stock material (from 1 to 20 µL) was added to 21 mL of medium to make a working extract. Different concentrations were tested for cell/tissue toxicity and one concentration was chosen for further work (data not shown). Specifically, to obtain “low” (0.007 mg/mL) and “high” (0.015 mg/mL) functional concentrations, 2.45 µL or 5.25 µL of stock extract (60 mg/mL) were added to 21 mL of medium, respectively. The final concentration of DMSO was 0.012% and 0.025% in the “low” and “high” extract concentrations, respectively. The extracts were sterilized using a 0.22 µm filter.
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4

Sunitinib and Mitochondrial Dynamics Assay

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Stock solutions (10 mmol/l) of Sunitinib malate (S-8803, LC Laboratories, Woburn, Massachusetts) were prepared in dimethyl sulfoxide (DMSO) (D12345, Life Technologies, Thermo Fisher Scientific) and were remade every 6 months to ensure biological activity. Stock solutions were diluted at least 1:1000 in media for experiments to avoid any DMSO-induced toxicity. Samples treated with DMSO at the same volume per volume percentage were used as control samples (vehicle). Microtissues treated with 1 μmol/l Staurosporine (Sigma Aldrich, St. Louis, Missouri) were used as a positive control for apoptosis (27) (link). Carbonyl cyanide m-chlorophenyl hydrazone (CCCP) (Sigma Aldrich) was used a positive control for mitochondria membrane potential disruption (28) (link) at a concentration of 50 μmol/l and was incubated with cells for 30 min at 37⁰C. In a subset of experiments, 5-aminoimidazole-4-carboxamide 1-β-D-ribofuranoside (AICAR) (Sigma Aldrich) was administered concurrently with sunitinib at a concentration of 1 mmol/l.
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5

Fluorescent Collagen Labeling Protocol

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Type I collagen solution (5026-50ML, TeloCol, Advanced BioMatrix) was used for the study and labeled with AF488 (Alexa Fluor 488 TFP ester, A37570, Invitrogen) as described previously.11 ,14 (link) Briefly, collagen monomers were diluted in 10 mM HCl to 1  mg/mL and then mixed 1:1 with 0.2 M sodium carbonate–bicarbonate buffer (24095, Polysciences) containing 1 M sodium chloride (S671-3, Fisher Scientific). AF488 was dissolved in dimethyl sulfoxide (D12345, Life Technology) to a concentration of 0.5  mg/mL and added to collagen solution in excess amount to achieve at least two fluorophores on average on each collagen monomer. The reaction mixtures were stirred for 3 h at room temperature. Labeled monomers were dialyzed in dialysis cassettes (Slide-A-Lyzer, 3.5K MWCO, 3 mL) for 3 days in 10 mM HCl. Collagen concentration was measured using DC Protein Assay (Bio-Rad). AF488 concentration was measured using Beer–Lambert law. Degree of labeling was measured as moles of fluorophore per mole of collagen.
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6

Fluorescent Labeling of Bovine Collagen

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Bovine collagen solution (5026-50ML, TeloCol, Advanced BioMatrix) was diluted to 1 mg/ml using 10 mм hydrochloric acid (SA56-1, Fisher Scientific), and then mixed 1:1 with 0.2 M sodium carbonate-bicarbonate buffer (24095, Polysciences) containing 1 M sodium chloride (S671-3, Fisher Scientific). The labelling protocol was carried out at pH 7.5, 8.0, and 8.5 to probe the effect of pH on efficiency of labeling. Lysine residues are most efficiently labeled at pH values of 8.5-9.5; however, the lower pH range was selected to increase the probability of attaching one fluorophore to the N-terminal [45] and improve the average distance between fluorophores on each collagen molecule. Next, AF488 (A37570, Alexa Fluor 488 TFP ester, Invitrogen) was diluted to 0.5 mg/mL using dimethyl sulfoxide (D12345, Life Technology) and slowly added to collagen solution in 1x to 15x molar excess. The labeling reaction was carried at room temperature and gently stirred for 3 hours.
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7

Fluorescent Labeling of Bovine Collagen

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Bovine collagen solution (5026-50ML, TeloCol, Advanced BioMatrix) was diluted to 1 mg/ml using 10 mм hydrochloric acid (SA56-1, Fisher Scientific), and then mixed 1:1 with 0.2 M sodium carbonate-bicarbonate buffer (24095, Polysciences) containing 1 M sodium chloride (S671-3, Fisher Scientific). The labelling protocol was carried out at pH 7.5, 8.0, and 8.5 to probe the effect of pH on efficiency of labeling. Lysine residues are most efficiently labeled at pH values of 8.5-9.5; however, the lower pH range was selected to increase the probability of attaching one fluorophore to the N-terminal [45] and improve the average distance between fluorophores on each collagen molecule. Next, AF488 (A37570, Alexa Fluor 488 TFP ester, Invitrogen) was diluted to 0.5 mg/mL using dimethyl sulfoxide (D12345, Life Technology) and slowly added to collagen solution in 1x to 15x molar excess. The labeling reaction was carried at room temperature and gently stirred for 3 hours.
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8

Small Molecule Compound Preparation

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Commercially available small molecules used in this study were NU7026 (SIGMA, T8552), Trichostatin A (SIGMA, T8552), MLN4924 (Adooq BioScience, A11260), NSC 19630 (Calbiochem, 681647), NSC 15520 (ChemBridge, 6048069), AICAR (SIGMA, A9978), RS-1 (Calbiochem, 553510), Resveratrol (Selleckchem, S1396), SCR7 (XcessBio, M60082-2s), L755507 (TOCRIS, 2197), B02 (SIGMA, SML0364), and STL127685 (Vitas-M). STL127685 is a 4-fluorophenyl analog of the non-commercially available STL127705. Stocks of 15 mM (or 10 mM for NU7026) were made using dimethylsulfoxide (DMSO) (Thermo Scientific, D12345). Solubility is a limiting factor for NU7026 concentration. Suitable working solutions for different concentrations were made so that addition of each small molecule accounts for a final concentration of 0.08% (or 0.2% for NU7026) DMSO in the media. Addition of all small molecules would lead to a final concentration of 0.7% DMSO.
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9

Transwell Migration Assay with M344

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The cells were plated at 2 x 105 cells/well on the day before treatment. On the following day, the cells were treated for 24 hours with 1 μM or 10 μM M344 in the experimental wells and with a corresponding volume of 0.1% dimethyl sulfoxide (DMSO; D12345, Thermo Fisher Scientific) in the control wells. Following this incubation, the cells were re-plated in 8-micron inserts at a concentration of 1x105 cells in base maintenance medium (without fetal bovine serum but in the presence of 1 μM M344 or 10 μM M344 or 0.1% DMSO), and the cells were allowed to move to high fetal bovine serum (15%)-containing base maintenance medium for 24 hours. The inserts were then washed 3 times with cold phosphate-buffered saline (PBS), stained using the HEMA 3TM STATpack (Thermo Fisher Scientific), and placed onto slides. Three random fields of each insert were photographed and counted to obtain the average number of migrating cells.
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10

Fluorescent Antibody Conjugation Protocol

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Mouse IgG2a kappa monoclonal CD99 antibody (3B2/TA8) labeled with FITC and mouse IgG1 kappa monoclonal CD117 antibody (YB5.B8) labeled with PE were bought from Invitrogen. Mouse IgG2a kappa isotype control (eBM2a) labeled with FITC and mouse IgG1 kappa isotype control (P3.6.2.8.1) labeled with PE (Invitrogen) were recommended (by Invitrogen) and used as isotype controls. A chimeric monoclonal antibody against GD2 (Dinutuximab-beta, Qarziba, Laupheim, Germany) was conjugated to Alexa Fluor™ NHS ester 647 (Invitrogen). The Alexa Fluor (AF) NHS esters were dissolved in anhydrous dimethylsulfoxide (DMSO) (Invitrogen, D12345, Carlsbad, CA, USA), and the reaction was carried out in 0.5 M Hepes buffer (15630–056, Gibco, Carlsbad, CA, USA), pH 8.0, at room temperature for two hours. 0.1 M Tris was added to quench the reaction. The antibody-fluorophore conjugate was purified twice using a gel filtration column (Zeba Spin Desalting Column, 40 MWKO, Thermo Fisher Scientific, Waltham, MA, USA). The degree of labeling (DoL) was calculated by measuring the protein concentration and fluorophore concentration using the NanoDrop™ One (Thermo Fisher Scientific, Waltham, MA, USA). A DoL around 1–1.5 was considered successful as this is generally recommended for FGS probes [31 (link)].
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