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88 protocols using deltavision

1

Detailed Characterization of Yeast Meiotic Chromosome Pairing

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Immunostaining of chromosome spreads was performed as described previously (Shinohara et al, 2000 (link), 2003 (link)). Stained samples were observed using an epi-fluorescent microscope (BX51; Olympus) with a 100 X objective (NA1.3). Images were captured by CCD camera (Cool Snap; Roper) and, then processed using IP lab and/or iVision (Sillicon), and Photoshop (Adobe) software. For focus counting, more than 100 nuclei were counted at each time point. Zip1 PCs were defined as a relatively large Zip1 staining outside of the DAPI staining region.
High-resolution images were captured by a computer-assisted fluorescence microscope system (DeltaVision; Applied Precision). The objective lens was an oil-immersion lens (100X, NA = 1.35). Image deconvolution was carried out using an image workstation (SoftWorks; Applied Precision).
Pairing of chromosomes was analyzed in the whole yeast cells with two homologous LacI-GFP spots at CENX locus. Following fluorescence microscope imaging, the number of chromosomal locus-marked GFP foci in a single cell was counted manually.
The distance between two GFP foci on chromosome IV on a single focal plane in a intact yeast cell taken by the fluorescence microscope system (DeltaVision; Applied Precision) was measured by NIH image J program.
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2

Chromosome Spread Immunostaining and Microscopy

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Immunostaining of chromosome spreads was performed as described previously (Shinohara et al., 2000; Shinohara et al., 2003) . Stained samples were observed using an epi-fluorescent microscope (BX51; Olympus) with a 100 X objective (NA1.3). Images were captured by CCD camera (Cool Snap; Roper) and, then processed using IP lab and/or iVision (Sillicon), and Photoshop (Adobe) software.
For focus counting, more than 100 nuclei were counted at each time point.
High-resolution images were captured by a computer-assisted fluorescence microscope system (Delta vision, Applied Precision). The objective lens was an oil-immersion lens (100X, NA=1.35). Image deconvolution was carried out using an image workstation (SoftWorks; Applied Precision).
Pairing of chromosomes was analyzed in the whole yeast cells with two homologous LacI-GFP spots at CENX locus. Following fluorescence microscope imaging, the number of chromosomal locus-marked GFP foci in a single cell was counted manually.
The distance between two GFP foci on chromosome IV on a single focal plane in a intact yeast cell taken by the fluorescence microscope system (Delta vision, Applied Precision) was measured by NIH image J program.
Zip1 polycomplexes (PCs) were defined as a relatively large Zip1 staining outside of the DAPI staining region.
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3

Fluorescence Microscopy of Yeast Pexophagy

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For fluorescence microscopy, yeast cells were grown as described above to induce pexophagy. Samples were collected and then examined by microscopy (Delta Vision, Applied Precision) using a 100× objective, and pictures were captured with a CCD camera (CoolSnap HQ; Photometrics). Mitochondria were stained with MitoTracker Red CMXRos (Molecular Probes/Invitrogen, M7512).
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4

Macrophage Labeling and Quantification

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10,000 BMDM were seeded in 96-well plates, and subsequently treated with VT680-Macrin. For the saturation experiment (Fig. S4cd), 125,000 Raw macrophages were treated with 1 mL of culture media containing varying doses of Macrin (ranging from 1 to 100 nmol of VT680-Macrin). Given that total number of macrophages in mice (and even in the mouse liver alone) is estimated to be > 107,62 (link) our in vitro data (8×10−4 nmol VT680-Macrin (60 ng of Macrin) uptake per macrophage, without apparent saturation) predict that > 10× dose would be required for substantial saturation effects compared to the dose used for imaging. 24 hours after the treatment, the cells were carefully washed with PBS and fixed with 4% PFA. The cells were then stained with DAPI to label nuclei. Fluorescent images of VT680-Macrin inside the cells were then acquired using DeltaVision (Applied Precision) modified Olympus BX63 microscopy system with a Neo sCMOS monochrome camera (Andor) and an environmental chamber. Fluorescent intensities were quantified using Image J (NIH).
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5

Live-Cell Fluorescence Microscopy Imaging

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Fluorescence microscopy images were obtained by using the microscope system (DeltaVision; Applied Precision) comprising a wide-field inverted epifluorescence microscope (IX71; Olympus), a Plan Apochromat 60×, NA 1.4, oil immersion objective (Olympus). DeltaVision image acquisition software (softWoRx 3.3.0; Applied Precision) equipped with a charge-coupled device camera (CoolSNAP HQ; Photometrics) was used. Live cells were imaged in a glass-bottomed culture dish (MatTek Corporation) coated with soybean lectin and incubated at 27°C for most of the strains or at 36°C for the temperature-sensitive mutants. The latter were cultured in rich YE5S media until mid–log phase at 27°C and subsequently shifted to the restrictive temperature of 36°C before observation. To keep cultures at the proper temperature, a temperature-controlled chamber (Precision Control) was used. The sections of images at each time point were compressed into a 2D projection using the DeltaVision maximum intensity algorithm. Deconvolution was applied before the 2D projection. Images were taken as 10–14 sections along the z axis at 0.3-µm intervals; they were then deconvolved and merged into a single projection. Captured images were processed with Photoshop CS5 (version 12.0; Adobe).
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6

Probing RhoA/ROCK Pathway Inhibitors on Sep15 Deficient Cell Morphology

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To examine the effect of the inhibitors of proteins that participate in RhoA/ROCK pathway on the morphology of Sep15 deficient cells, blebbistatin (10 µM), Y27632 (5 µM) or C3 transferase (2.5 µg/ml) was added to the medium after mounting the cells on the stage of a time-lapse microscope (Deltavision, Applied Precision). Cells were incubated at 37°C with 5% CO2 and images acquired with 10 sec time intervals for initial 2 hours and then 1 min intervals up to 12 hours.
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7

Fluorescent Protein Localization Protocol

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To analyze fluorescently tagged proteins, cells were washed once with PBS, settled onto glass slides, and fixed with 4% paraformaldehyde in PBS for 5 min (Nerusheva and Akiyoshi, 2016 (link); Ishii and Akiyoshi, 2020 (link)). Cells were then permeabilized with 0.1% NP-40 in PBS for 5 min and embedded in mounting media (1% wt/vol 1,4-diazabicyclo[2.2.2]octane, 90% glycerol, 50 mM sodium phosphate, pH 8.0) containing 100 ng/ml DAPI. Images were captured on a DeltaVision fluorescence microscope (Applied Precision) with softWoRx (version 5.5) housed in Micron Oxford. Fluorescent images were captured at RT with a CoolSNAP HQ camera using a 60× objective lens (1.42 NA) or 100× objective lens (1.4 NA) and processed in Fiji software (Schneider et al., 2012 (link)). Typically, 25 optical slices spaced 0.2-µm apart were collected. Maximum intensity projection images were generated by Fiji. Kinetochore localization of endogenously tagged kinetochore proteins or ectopically expressed KKT2/3 fragments were examined manually by quantifying the number of cells that clearly had detectable kinetochore-like dots at indicated cell cycle stages.
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8

Imaging Membrane Protein Localization

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Parental HT-1080, HT-BFP, HT-HER2-GFP, and SKBR3 cells were plated overnight at 50% confluency on 96-well plates (Ibidi). Tzm-A647 was incubated with the cells for 30 minutes at 5% CO2 and 37 °C at 5 μg/mL. The cells were then washed 5 times with PBS, and fixed with 4% PFA (EMS). The cells were imaged with a DeltaVision (Applied Precision) modified BX63 microscope (Olympus) fitted with a camera (Andor).
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9

Immunofluorescence Imaging of Spermatocytes

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Cells were cultured on coverslips in the presence or absence of 100 nM camptothecin for 22 h. Cells were permeabilized with CSK buffer (10 mM PIPES at pH 6.8, 100 mM NaCl, 300 mM Sucrose, 3 mM MgCl2, 1 mM EGTA, 0.5% Triton X-100, 1× protease inhibitor cocktail, 1× phosphatase inhibitor) for 5 min on ice and fixed with 2% PFA (Sigma) for 15 min at room temperature. The coverslips were blocked in TBST containing 3% BSA. Subsequently, coverslips were incubated with primary antibodies in TBST containing 3% BSA for overnight, washed 3 times with TBST and secondary antibodies for 1 h. After washing with TBST, the coverslips were mounted with Vectashield media (Vector Laboratories).
Stained spreads were observed using an epi-fluorescence microscope (BX51; Olympus) with a 60 × objective (NA1.3). Images were captured by CCD camera (CoolSNAP; Roper). Mouse spermatocyte spreads were observed using a computer-assisted fluorescence microscope system (DeltaVision; Applied Precision). The objective lens was an oil immersion lens (100×; NA, 1.35). Image deconvolution was performed using an image workstation (SoftWorks; Applied Precision), and afterwards processed using iVision (Sillicon), and Photoshop (Adobe) software tools.
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10

Fluorescence Microscopy Imaging of Mouse Spermatocytes

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Images of mouse spermatocyte spreads and testicular cell squashes were acquired using a computer-assisted fluorescence microscope system (DeltaVision; Applied Precision) with a 60× NA 1.4 oil immersion objective. Image deconvolution was performed using an image workstation (softWoRx version 6.5.2; Applied Precision) and afterward processed using Imaris (version 9.2.1; Oxford Instruments, UK) and Photoshop (version 23.2.2; Adobe, USA) software tools. Images in each figure are matched exposure.
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