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5 protocols using perfect focus system

1

Visualizing Actin Dynamics in PtK1 Cells

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PtK1 cells were electroporated with EmeraldGFP-tagged LifeAct using the Neon transfection system and plated on acid-treated glass coverslips. Cells were cultured for 48-hours at 37 °C, 5% CO2 and imaged using a Nikon Ti motorized inverted microscope with Perfect Focus System, Yokagawa CSU-X1 spinning disk confocal and Spectral Applied Research Borealis modification, 491 solid-state laser, 100× 1.45 N.A. objective, Hamamatsu ORCA-AG cooled CCD camera, and Metamorph software. Cells were in L-15 medium containing 10% FBS, 20 mM HEPES, and 0.03 U/ml Oxyrase. Experiments using U0126 were carried out using a Nikon TE2000 inverted microscope with Perfect Focus System, Yokogawa CSU-10 spinning disk confocal, 488 solid-state laser, 60× 1.4 N.A. objective, Andor Clara cooled CCD camera, and NIS Elements software.
Cells were imaged for 10 minutes before perturbation and 20 minutes following perturbation (30 min total). PtK1 cell boundaries were detected from the fluorescence microscopy data using a threshold method. Once identified, the edge was then subdivided into 1 micron long segments and their respective velocities were calculated as described previously (25 (link)). For inhibitor-treated experiments, results were obtained from 3–4 independent experiments. For BrafV600E overexpression experiments, results were obtained from 2 independent experiments.
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2

Monitoring Antibiotic-Treated Cell Recovery

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Growth and fluorescence of OFL-treated cells and untreated controls during recovery from antibiotic treatment on LB agar supplemented with 50 μg/mL kanamycin (KAN) for plasmid retention, as well as untreated cells recovered on LB-KAN agar containing ~0.2 ng/mL OFL, were monitored using a fully motorized Nikon Ti-E inverted microscope with Perfect Focus System equipped with Yokogawa spinning disc (CSU-21). Sample preparation, microscope setup, and image analysis are detailed in the Supplementary Methods.
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3

Imaging border cell migration in Drosophila

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Border cell migration was observed in egg chambers expressing rk RNAi (VDRC, line v29931) driven by slbo-Gal4. Cell membranes were visualized with a Gap43-mCherry marker (Martin et al., 2010 (link)), which labels the membranes of all cells, with especially strong signal surrounding the polar cells. Females were fed yeast for 40 h prior to dissection. Individual ovarioles were dissected out of the ovary, and the germaria and older egg chambers were removed from these ovarioles. Dissection was performed in media previously described (Prasad et al., 2007 (link); Domanitskaya et al., 2014 (link)). Droplets of media containing dissected ovarioles were imaged with a Nikon Ti-E spinning disc confocal microscope equipped with a Perfect Focus System, a Yokogawa spinning disc, and a Hamamatsu detector. We imaged border cell cluster detachment and early migration for approximately 4–6 h in rk RNAi expressing egg chambers, and wild type egg chambers expressing the Gap43-mCherry membrane marker as a control. A 561 nm laser was utilized to detect the mCherry signal. 10–20 μm Z stacks were imaged to capture the whole border cell cluster, with Z stacks containing 1 μm steps taken every 3 min.
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4

Live-cell imaging of OSER structures

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U2-OS cells were grown on #1.5 35-mm glass bottom dishes (MatTek) in McCoy’s 5A medium supplemented with GlutaMAX (Thermo Fisher) and 10% fetal bovine serum (Thermo Fisher) and transfected with 0.5 μg of pCytERM-mAvicFP1 and pCytERM-mEGFP plasmid DNA using fuGENE (Promega) 24 hours prior to imaging. Before imaging, the growth medium was replaced with FluoroBrite DMEM supplemented with 5% FBS (Thermo Fisher). Image acquisition was performed in a full environmental enclosure (37°C, 5% CO2; Okolab) on a Nikon Ti-E microscope with Perfect Focus System, a Spectral Borealis-modified spinning disc confocal (Yokogawa X1), and an Orca Flash v3 sCMOS camera (Hamamatsu). OSER data were acquired with a 40× Plan Fluor 1.3 NA objective lens, and live time-lapse imaging was acquired with a 100× Plan Apo VC 1.4 NA objective (162-nm and 65-nm pixel size, respectively). Green fluorescence was excited with a 491-nm solid state laser (Cobolt) and a Di01-T405/488/568/647 (Semrock) dichroic; emission was selected with an ET525/50m filter (Chroma). Hardware was controlled with MetaMorph (v7.8.13). For time-lapse experiments, single-plane images were acquired every second. For OSER acquisition, a uniform grid of images was acquired covering the entire coverslip.
Images were processed with Fiji [36 (link)]. OSER assay analysis was conducted as previously described [19 (link)].
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5

Imaging and Quantifying Protein Foci

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All image acquisition was performed on the PICT-IBiSA Orsay Imaging facility of Institut Curie. Cells were grown in filtered supplemented EMM-glutamate. Exponentially growing cultures were centrifuged and resuspended in 50 µL of fresh medium. Two µL from this concentrated solution was dropped onto a Thermo Scientific slide (ER-201B-CE24) covered with a thin layer of 1.4% agarose in filtered EMMg. 13 z-stack pictures (each z step of 300 nm) were captured using a Spinning Disk Nikon inverted microscope equipped with the Perfect Focus System, Yokogawa CSUX1 confocal unit, Photometrics Evolve512 EM-CCD camera, 100 X/1.45-NA PlanApo oil immersion objective and a laser bench (Errol) with 491 (GFP) and 561 (MmCherry) nm diode lasers, 100 mX (Cobolt). Pictures were collected with METAMORPH software and analyzed with ImageJ. For Pcf2-GFP and Rad52-GFP foci, a threshold (using the find maxima tool, >400 for Pcf2-GFP foci and >100 for Rad52-GFP) was setup at the same level for each genetic background analyzed within the same experiment. Images from Figure 6C were deconvolved using the Huygens remote manager software.
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