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122 protocols using stage top incubator

1

Bioluminescent Circadian Rhythms Imaging

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PER2::LUC is a luciferase fusion protein that reports its expression bioluminescently. Time-dependent changes in PER2::LUC expression were measured in real-time via a cooled-CCD camera (imaging) or a photomultiplier (luminometry). Bioluminescence imaging was performed in a previously described custom-made, light-sealed inverted microscope system [26 (link)], which has a simplified optical path optimized for low-light imaging, with a 4× objective lens and a 0.35× relay lens (Olympus). The cultured sample was maintained at 37 °C in a stage-top incubator (Tokai HIT, Shizuoka, Japan), and time-lapse imaged with an Orca R2 cooled-CCD camera (Hamamatsu Photonics, Hamamatsu, Japan) with external water-cooling (20 °C; TGV-10, Taipei, Taiwan). Images were taken under 1 h exposure at 4×4 binning, at a sampling interval of 1 h. For luminometry, an equal number of control and test samples were measured on the same 8-dish wheel in Kronos Dio (ATTO, Tokyo, Japan); light from each dish was measured under 1 min exposure at sampling interval of 10 min, with the nominal temperature of 37 °C and actual temperature maintained between 37.6–37.7 °C, measured with iButton datalogger in the dish (DS1921L, Maxim Integrated, San Jose, CA, USA). Bioluminescence traces were detrended using the HP filter as described previously [23 (link)].
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2

Visualizing Acidic Compartments in 661W Cells

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In order to visualize acidic compartments, live cell imaging was performed for 661W cells stained with AO (R&D systems). 661W cells were plated in a multi-well glass bottom dish (Matsunami Glass Industry) at a density of 10,000 cells per well and incubated overnight at 37 °C. The medium was replaced with DMEM containing 1% FBS, and the cells were incubated with either 10 µg/mL MBE, 10 µM D3S5G or 10 µM D3G5G for 1 h at 37 °C, followed by exposure to blue light for 8 h. AO was added to a final concentration of 1 mg/mL, and the cells were incubated for 20 min at 37 °C. Finally, the medium was changed to prewarmed Live Cell Imaging Solution (LCIS, Thermo Fisher Scientific) containing 5.5 mM glucose and 1% FBS, and cells were subjected to live cell imaging using a 40× oil lens on an FV3000 microscope (Olympus Co.) equipped with a stage top incubator (Tokai Hit Co., Shizuoka, Japan). AO green and red fluorescence intensities were measured using ImageJ Ver. 1.53c (National Institutes of Health) for 24 cells each in four independent experiments to obtain the intensity ratio of green vs. red.
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3

Dynamic Live-Cell Imaging of MSCs

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Twelve h after co-culturing PTECs with MtDsRed2-MSCs or the addition of DsRed2-Mt, time-lapse observations and imaging of phase contrast and fluorescence were commenced with Axio Observer Z1 (Carl Zeiss) at 37 °C in 5% CO2 using a stage top incubator (Tokai Hit, Fujinomiya, Japan).
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4

Time-lapse Microscopy of NHEK Cultures

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NHEKs were seeded confluently in two-well culture inserts (ibidi) on glass-bottom dishes (Matsunami). Culture inserts were removed after overnight incubation, followed by washing with PBS. Cells were then cultured in Humedia-KG2, MCDB153 medium, or low chloride MCDB153 medium. After 12 or 24 h of cultivation, calcein-AM (Dojindo) was added to the culture medium to visualize the cells. ImageJ software was used for data analysis. For time-lapse analysis, cells were cultured in a Stage Top Incubator (TOKAI HIT) on a confocal laser scanning microscope (IX83 Olympus) and images were captured every 10 min.
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5

Mitochondrial and ER Morphometric Analysis

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In mitochondrial morphological analysis, 5-10 z-stack images (1-μm steps) of pMT-mKO1 plasmid-transfected cells were acquired using the confocal microscopy system (FV3000, Olympus). Deconvolution was applied to maximum projection images to clarify the mitochondrial contours. Mitochondrial length was defined as the longitudinal axial length of each mitochondrial fragment, which were traced with cellSens life science imaging software (Olympus). Mitochondrial length was calculated as the mean length of mitochondria within a single cell.
In ER morphological analysis, mCherry-Sec61B-expressing cells were kept in a humidified atmosphere at 37°C using a Stage Top incubator (Tokai-hit). Live cell images were acquired using the confocal microscopy system (FV3000, Olympus). The standard deviation (SD) and mean of the fluorescence intensity were obtained using line-scan analysis by the FV31S-SW (Olympus) in a randomly selected cell region. The ER morphology was defined as reticular when the coefficient of variation (CV) scores (SD/mean) were >0.2.
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Quantifying Kinetics of Sensor Activation

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To obtain the time constant for sensor activation, red fluorescent dye Antonia Red-Dextran (3000 M.W., Sigma-Aldrich) and N/OFQ (MedChem Express) were simultaneously applied in bolus to sensor-expressing HEK293T cells at 37°C with a stage top incubator (Tokai Hit). Fluorescent signals were excited at 488 nm (NOPLight) and 561 nm (Red-Dextran dye) and recorded using the high-speed line-scan function (Zeiss LSM 800) at 800Hz. The onset latency of each experiment was first determined by calculating the time for the red-dextran fluorescent signal to reach 85% percent of maximal value at the plateau. Only experiments with an onset latency smaller than 50 ms were considered in subsequent analysis to minimize the contribution of N/OFQ peptide diffusion to the temporal profile of sensor response. Membrane-corresponding pixels were first selected by thresholding pixel-wise ΔF/F0 at 65% criteria. Fluorescent signal change of each membrane pixel was then normalized and fitted by a mono-exponential association model using custom-written MATLAB script to derive the time constant τ.
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7

Live-Cell Imaging Protocols for Fluorescence Microscopy

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Live-cell imaging. Confocal fluorescence imaging was performed on an IX83/FV3000 confocal laser-scanning microscope (Olympus) equipped with a PlanApo N 60×/1.42 NA oil objective (Olympus), a Z drift compensator system (IX3-ZDC2, Olympus) and stage top incubator (Tokai Hit). Lasers used for excitation were: 405 nm for mTagBFP2; 488 nm for Azami-Green and EGFP; 561 nm for mCherry and Monti-Red; and 640 nm for tdiRFP670 and miRFP670. Live-cell imaging was performed at 37 °C under a humidified preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission.
The copyright holder for this this version posted November 10, 2020. ; https://doi.org/10.1101/2020.11.09.375766 doi: bioRxiv preprint 14 5% CO2 atmosphere. Fluorescence and differential interference contrast (DIC) images were analyzed using the Fiji distribution of ImageJ 65 .
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8

Live Cell Imaging of Adhered Cells

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Cells were plated in a 4 well glass bottom chamber slide (Cellvis; Mountain View, CA, USA) pre-coated with 1 µg/mL fibronectin, at a density of 10,000 cells/well. After 2 h of equilibration, the chamber was placed on the Olympus IX83 microscope in a stable environment at 37 °C, 90% humidity and 5% CO2 using the STXG Stage top Incubator (Tokai Hit Stage top Incubator) connected to an INU incubation system controller (Tokai Hit; Shizuoka-ken, Japan) and imaged for 20 min to 5 h, depending on the experiment. Cells were imaged every 15 s to 5 min, again depending on the experiment, using relief contrast or DIC and/or LED-based fluorescence (X-cite 120 LED Boost, Excilitas Technologies, Waltham, MA, USA with a dry 20×, 40×- or 100× oil immersion objectives.
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9

Measuring Mitochondrial ROS in Alveolar Macrophages

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Cells were seeded on 35-mm glass bottom dishes (MatTek Corporation, Ashland, MA) and incubated with the superoxide indicator MitoSOX™ Red (5 μM, Invitrogen, Eugene, OR) for 15 min at 37 °C. Cells were washed with PBS, the media was replaced with exposure media, and the dish was inserted into a closed, thermo-controlled (37 °C) stage top incubator (Tokai Hit Co., Shizuoka-ken, Japan) atop the motorized stage of an inverted Nikon TiE fluorescent microscope (Nikon Inc., Melville, NY) equipped with a 60X oil immersion optic (Nikon, CFI PlanFluor, NA 1.43) and NIS Elements Software. MitoSOX™ Red was excited using a Lumencor diode-pumped light engine (SpectraX, Lumencor Inc., Beaverton OR) and detected using a DsRed longpass filter set (Chroma Technology Corp) and ORCA-Flash4.0 sCMOS camera (HAMAMATSU Corporation, Bridgewater, NJ). Data was collected on approximately 80 to 100 cells per stage position, with eight to ten stage positions in each of the separate experiments for 180 min. Data were analyzed using NIS Elements (Nikon Inc., Melville, NY). Data from three independent analyses for each particle size were used in the statistical calculations. Stage positions in which the particles did not result in alveolar macrophage (AM) generation of ROS were not used in the statistical analysis.
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10

Localization of GFP-ESCO1 in HeLa Cells

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Stable HeLa cells that had been induced to express GFP-tagged ESCO1 transgenes for 24 hours were incubated with 250nM SIR-DNA (Cytoskeleton Inc.) and 2μg/ml doxycycline in Opti-MEM (Gibco) and kept in a 37 °C and 5% CO2 environment with a stage-top incubator (Tokai Hit). Images were collected with a 60x oil objective lens on a Nikon N2 Confocal microscope and analyzed using FIJI.
For localization measurements, a region of interest (ROI) was selected for a spot identified by SiRDNA as being within the nucleus in an interphase cell or chromosomes in a mitotic cell. An ROI of the same size was placed within the cell’s cytoplasm (identified by GFP and transmitted light) and mean intensities of GFP from both regions were collected. Local background was measured by a larger ROI and subtracted. Statistical analysis was performed by Kruskal-Wallis test with Dunn’s multiple comparisons test as follow-up.
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