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25 protocols using i control

1

Illumina Gene Expression Profiling

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Extraction of RNA was performed using Ambion Tempus RNA Spin kit (Thermo Fisher, Asheville, NC, USA) according to manufacturer instructions. RNA concentrations and A260/280 ratio (Tecan iControl, Life Sciences, Switzerland) and sample quality (Agilent Bioanalyzer 2100 RNA Nano assay, Agilent, Santa Clara, CA, USA) was determined. Each sample was linearly amplified by TotalPrep-96 RNA Amplification Kit for Array Analysis (Illumina, San Diego CA, USA). On the same day, all samples were hybridization to Illumina Human HT-12 Expression BeadChips using the Whole-Genome Gene Expression Direct Hybridization Assay (Illumina). BeadChips were scanned on the Illumina HiScan to determine raw probe fluorescence intensity.
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2

Quantifying Amine-Modified PLGA Nanoparticles

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PLGA and PLGA-NH2 NPs
or ratios were dissolved at concentrations of 1 mg/mL in PBS. Fluorescamine
(Sigma-Aldrich, Israel) was dissolved at 9 mg/mL in acetone, and 50
μL was added to the NPs and incubated at 37 °C for 5 min.
After incubation, the particles were centrifuged at 20 817g for 30 min, the supernatant was discarded, and the pellet
was resuspended in PBS. Fluorescence (excitation: 390 ± 9 nm,
emission: 475 ± 20 nm) was measured in triplicate with a Tecan
Infinite M200 PRO (Tecan, Austria) and the software Tecan i-control
(Tecan).
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3

Antibacterial Potency Screening of Compounds

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AST was performed on the compounds (1–29) (Supplementary Table 1) (Yele et al., 2020 (link), 2021 ) concerning the standard protocol (CLSI, 2017 ). The lowest concentration of a compound at which inhibition of bacterial growth was observed is termed MIC. The microbroth dilution method in Hi-media, Mueller Hinton Broth (MHB), was used to calculate the MIC. Bacterial cultures were diluted at a ratio of 1:1,000 MHB to achieve turbidity of 0.5 McFarland. DMSO and ciprofloxacin were used as a negative and positive control, respectively. The bacterial inoculum was added into a series of 96-well plates containing various test compounds ranging from 0.625 to 20 μg/mL. Plates were incubated for 20–24 h at 37°C. The absorbance was recorded at 600 nm of wavelength using Tecan-i-control, 1.7.1.12. MIC determinations for each compound were carried out in triplicate using a duplicate sample each time (Eloff, 1998 (link); Agyare et al., 2012 (link)).
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4

Colorimetric Quantification of Liver Lipid Peroxidation

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Quantification of lipid peroxidation in liver tissue was performed using a lipid-peroxidation malondialdehyde (MDA)-assay kit (Abcam). Lipid peroxidation forms MDA and 4-hydroxynonenal as natural byproducts. MDA in the sample reacts to form an adduct with thiobarbituric acid, which can be quantified colorimetrically (λ=532 nm). The minimum detectable amount of MDA by this colorimetric method is 1 nmol/well.
The homogenate was prepared in lysis buffer containing butylated hydroxytoluene provided by the manufacturer (20 mg of liver tissue per 300 μL of MDA lysis buffer). Further steps were performed in accordance with the manufacturer’s protocol, including an additional step of filtering samples through a 0.22 μm syringe filter to reduce turbidity. Measurements were performed with an Infinite® 200 Pro microplate reader with I-Control™ software (Tecan, Männedorf, Switzerland).
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5

Multimodal Cellular Analysis Protocol

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For phase-contrast microscopy, CellSens Entry (Hamburg, Germany) version 1.18 was used. BD (Franklin Lakes, NJ, USA) FACSDiva™ (6.1.3) was used to operate the BD (Franklin Lakes, NJ, USA) FACSCanto™ II system. FlowJo (Franklin Lakes, NJ, USA) version 10.7.1 was used for further analysis of flow cytometry data. The TECAN multimode-microplate reader was operated with the software i-control™ (Männedorf, Schweiz) version 3.22. Rotor-Gene Q series (Hilden, Germany) version 2.3.4) was used to operate the Rotor Gene Q PCR-cycler and to analyze the results of the RT-qPCR. Cardiomyocyte beating analysis was performed with the in-house developed software CardioVision described in Section 3.3.
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6

Quantification of Total Phenolic Content in Essential Oils

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The total phenolic content (TPC) of the EO sample was performed with an adapted Folin–Ciocalteu method, as previously described [40 (link),41 (link)] with minor modifications. Briefly, 15 mg of the EO sample was weighted and mixed with 1 mL methanol. The mixture was vortexed and combined in a 1:5 ratio sample with Folin–Ciocalteu reagent (diluted 1:10 in distilled water to obtain a 0.25 N concentration) and left for five minutes in the dark at room temperature; after this, an equal volume of 7.5% sodium carbonate solution with Folin–Ciocalteu reagent was added, mixed, and left for 1 h in the dark at room temperature. The samples were plated in triplicate in 96-well plates, and the absorbance was measured at 725 nm with a spectrophotometer Tecan i-control, 1.10.4.0 infinite 200Pro. TPC was expressed in gallic acid equivalents (mg GAE/g sample) calculated after a propyl gallate calibration curve with concentrations between 0.375 mg/mL to 0.732 µg/mL.
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7

Binimetinib IC50 Determination in Melanoma

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Half-maximal inhibitory concentrations (IC50) of binimetinib (Selleckchem, MEK162) were determined for each cell line using CellTiter-Glo (CTG) luminescent cell viability assay (Promega). Cells were seeded at density of 10,000 (SKMEL2, SKMEL28, IPC298) or 5,000 (SKMEL5, A375, RPMI-7951) cells/well in a 96-well plate and allowed to adhere overnight. Cells were then treated with binimetinib or DMSO as a vehicle control in fresh medium for 72h and assayed. All viability data was acquired using a Tecan plate reader Infinite 200 with Tecan icontrol version 1.7.1.12. IC50 values were calculated using a four-parameter logistic curve in Prism 9.0.0.
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8

Proliferation and Cell Cycle Analysis

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Cells were diluted and seeded into a 96-well plate, with 2000 cells per well and three replicates for each time point. Then, the CCK-8 reagent was added to each well at 24, 48, 72, and 96 h post-seeding, according to the manufacturer′s protocol. After incubation for 2 h at 37 °C, the optical densities at 450 nm and 600 nm were separately measured for individual wells using a microplate reader (Tecan i-control).
For cell cycle analysis, cells were centrifuged at 500 × g for 4 min. Then, the cell pellets were washed once using 1 × PBS and resuspended using 1 × PBS containing 0.03% Triton X-100 and 50 μg/ml propidium iodide. After incubation at room temperature for 10 min, the cell cycle assay was performed on the BD Flow Cytometer.
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9

Cell Viability and Cell Cycle Assay

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After selection by puromycin, the survival (transfected) cells were trypsinized and counted using hemocytometer. Then cells were diluted and seeded into a 96-well plate, with 2000 cells per well and three replicates for each time point (add CCK-8 reagent at 24 hrs, 48 hrs, 72 hrs and 96 hrs according to the manufacturer’s protocol). After each treatment, cells were incubated for two hours at 37 °C, then the optical density (OD) at 450 nm and 600 nm were measured respectively for each well by microplate reader (Tecan i-control).
For cell cycle analysis, cells were trypsinized, then centrifuged at 500g for four minutes (mins). Cell pellets were washed once with 1×PBS and resuspended with PBS containing 0.03% Triton X-100 and 50μg/ml Propidium Iodide (PI), and incubate for 10 mins. The cell cycle assay was then performed on the BD Flow Cytometer.
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10

Cytochrome C Oxidase Activity Assay

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Cultures were lysed and homogenised by freeze-thaw with dry ice and sonication in cold buffer. COX activity was evaluated using a COX Activity Assay Kit (760151, Cayman Chemical). Samples were prepared as indicated by manufacturer’s instructions and readings were obtained with the Tecan i-control, software 1.10.4.0 (Tecan, Crailsheim, Germany).
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