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150 protocols using cell f software

1

Intracellular ROS Quantification via H2DCF-DA

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To measure intracellular ROS production, the cells growing on coverslips were loaded with 5 μM dihydrofluorescein diacetate (H2DCF-AC; 20 min, 37°C), thoroughly rinsed with Hank’s Balanced Salt Solution, and mounted on slides. Live cells were examined with the Olympus IX71 fluorescence microscope equipped with the Cell^F software (Olympus). The fluorescence of the dye was excited at 488 nm for 500 ms. the corrected total cell fluorescence (CTCF) of individual cells was calculated using the Cell^F software (Olympus), and presented in percentage frequency (“cumulative distribution”) graph. The experiments were repeated three times with similar results and representative data from one experiment is shown in Figure 4. Collected data was analyzed as described above (“Immunocytochemistry”).
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2

Stem Cell Growth on Nanoparticles

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The growth curve of stem cells on NPs and on CTR was measured at 3, 7, 14, and 21 Days (D). To count the cell nuclei, at each time point, cultures were harvested and fixed in 4% paraformaldehyde and rinsed with PBS, and coverslips were mounted and nuclei were counterstained with Vectashield Antifade Mounting Medium with 4′,6-diamidino-2-phenylindole (DAPI) (Vector Laboratories Inc., Burlingame, CA, USA). The quantification of the number of cells on NPs and CTR was carried out considering 10 different photos (10× magnification) to cover the total NP deposition area, and the DAPI-stained nuclei were counted by using the Cellf software (Soft Imaging System, Olympus, Münster, Germany, version 2.5, Accessed in 2006). Images were acquired using a fluorescence microscope (Eclipse-TE2000-S, Nikon, Tokyo, Japan) equipped with the F-ViewII FireWire camera and Cellf software (Soft Imaging System, Olympus, Münster, Germany, version 2.5, Accessed in 2006). The stem cell proliferation is expressed as a mean of 3 independent experiments ± SEM.
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Intracellular ROS and Calcium Imaging

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To measure intracellular ROS production the cells growing on coverslips were loaded with 5 μM dihydrofluorescein diacetate (H2DCF-AC, Sigma; 20 min, 37 °C), thoroughly rinsed with Hank’s Balanced Salt Solution, and mounted on slides. Live cells were examined with the Olympus IX71 fluorescence microscope equipped with the Cell^F software (Olympus). The fluorescence of the dye was excited at 488 nm for 500 ms58 (link).
The Ca2+-sensitive fluorescent dye Fluo-3-AM was used to detect the relative change of the Ca2+-dependent fluorescence in cells. Cells were loaded for 30 min with 5 µM dye in amino-acids- and serum-free medium, washed twice and incubated for 15 min in full culture medium (de-esterification of the dye). The fluorescence was measured with the FV-1000 confocal microscope (Olympus) using excitation and emission wavelengths of 488 and 525 nm, respectively. The measurements were taken from at least 70 cells (usually over 100 cells) from randomly selected areas. All cells observed in the areas were used for measurements. The corrected total cell fluorescence (CTCF) of individual cells was calculated using the Cell^F software (Olympus) and presented in percentage frequency graphs (“cumulative distribution”) graphs. The experiments were performed in triplicate, with similar results.
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4

BAC-FISH Protocol for Chromosomal Analysis

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DNA was isolated from single Escherichia coli colonies (QIAprep Spin Miniprep Kit; Qiagen) (Farrar and Donnison 2007 (link)), labeled with digoxygenin-11-dUTP and/or tetramethylrhodamine-5-dUTP (Roche Diagnostics) by nick translation, and used as molecular probes for BAC-FISH. In some cases, two or three BAC clones were simultaneously analyzed in various combinations (multi-BAC-FISH). These studies were carried out on mitotic metaphase chromosomes. Cytological preparations were made from root meristematic tissues, as previously described (Lesniewska et al. 2011 (link)). Slide quality was controlled by observation under a phase-contrast microscope (BX41; Olympus). FISH was performed according to the protocol previously adapted for use in L. angustifolius (Lesniewska et al. 2011 (link); Książkiewicz et al. 2013 (link)). Digoxygenated DNA probes were detected with FITC-conjugated antidigoxigenin primary antibodies (Roche Diagnostics). Chromosomes were counterstained with 2 μg/ml 4',6-diamidino-2-phenylindole (DAPI) (Sigma) in Vectashield antifade mounting medium (Vector Laboratories, Burlingame, CA). Preparations were examined under a BX 60 microscope (Olympus) using the Cell_F software (Olympus). The images were captured using a CCD monochromatic camera and superimposed using Micrografx Picture Publisher 8 software (Corel).
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5

BAC-FISH for Metaphase Chromosome Localization

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Localization of BAC clones in metaphase mitotic chromosomes was performed with the use of fluorescent in situ hybridization (BAC-FISH). BAC probe labelling, chromosome squash preparation, and the FISH procedure was done according to the protocol [34 (link)]. The quality of chromosome slides was checked under a phase-contrast microscope BX41 (Olympus, Tokyo, Japan). After FISH, slides were examined with an epifluorescence microscope BX60 (Olympus) using the Cell_F software (Olympus). Images were captured using a CCD monochromatic camera and superimposed using Micrografx Picture Publisher 8 (Corel, Ottawa, ON, Canada).
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6

Apoptotic Nuclear Morphology Assay

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The effects of the combination treatments of antimetabolite agents and polyphenols were further investigated on the apoptotic nuclear morphological changes following Hoechst 33342 and propidium iodide staining and fluorescence microscopy (Sigma). Cells were at 0.5 × 106 cells seeded in 12-well plates per ml and treated for 24 hrs with each antimetabolite and polyphenol alone and in combination at their LSD. A 0.1% (v/v) ethanol and a 10 μM NaOH vehicle control were also included. Following 24 hrs of treatments, 100 μl of cells were transferred to a 96-well plate, 10 μl of 2μg/ml Hoechst 33342 dye was added to each well and incubated for 5 min in the dark. A further 10 μl of 2μg/ml propidium iodide dye was added and incubated for 15 min in the dark. Plates were examined using inverted fluorescence microscope. Two hundred cells (live and apoptotic) were counted and apoptotic nuclei determined for each sample and expressed as a percentage. The Cell-F software (Olympus) was used to capture fluorescent microscope images.
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7

Spheroid Growth Assay Protocol

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For this assay 50,000 cells were plated in 100 µl of solution (35% methylcellulose solution and 65% culture medium DMEM) as a drop on petri dishes and reversely cultured under standard humidi ed conditions. After 24h the spheroid was carfully washed with PBS and transferred into 48-well-plates with 200 µl including the different treatment. The size of the spheroid was monitored after 24h, 48h, 72h and 96h with Olympus x71 and cell-F-Software (Olympus, Tokyo, Japan). The distance between cell package at time 0h and the respective time was measured by Image J software.
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8

Cell Death Analysis via PI and Annexin V

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Cells were seeded the same way as for the cell viability assay. After 72 hours of treatment cells were stained with propidium iodide staining (PI) (Invitrogen, Darmstadt, Germany) for 20 minutes [1 µg/ml]. Pictures were taken with Olympus x71 and cell-F-Software (Olympus, Tokyo, Japan). The area of uorescent cells was measured with Image J software.
Further 100,000 or 200,000 cells/well were plated into 6-well-plates and again treated after 2h with 1 µM. After 24 or 72h medium and cells were collected, washed with PBS and stained with 0,1% Annexin V and 0,1% 7-ADD (Biolegend, San Diego, USA). Results were obtained by Flow Cytometer BD FACSCanto II (BD Bioscience, Heidelberg, Germany) and analyzed with WinList 3D 8.0 software.
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9

Cytoskeleton Staining and Cell Migration Assay

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For the staining of cytoskeleton 50,000 cells were seeded/well on glass cover slides in a 12-well plate. Treatment followed after 5 hours. 24 h after treatment cells were xated with PFA 4% and stained with Phalloidin 488 (1:50) and Hoechst (1:10 000). Pictures were taken by Axio Observer with Zen Software (Zeiss, Oberkochen, Germany).
Cell migration assay 100,000 cells/well were plated into 12-well plate. A sratch was made with a sterile pipette tip right through the layer of cells. Images were taken (0h) and cells were treated with different concentrations (0,5 µM and 5 µM) of the compounds. Pictures were taken by Olympus x71 and cell-F-Software (Olympus, Tokyo, Japan) at various times. To analyze the data the distance between cells was measured using Image J software.
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10

Methanol-Induced GFP Expression Analysis

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Strain GFP‐PTS1/WT was precultured in the YPD medium at 28°C and 180 rpm overnight, then collected by centrifugation at 10 000 × g for 5 min at 4°C and washed three times using sterilized ultrapure water. The cell pellets were then induced in the L‐MeOH/YNB and H‐MeOH/YNB media at an optical density (OD660) of 0.5, followed by incubation at 28°C and 180 rpm for 16 h. After cultivation, the strain induced under L‐MeOH or H‐MeOH conditions was centrifuged at 10 000 × g for 5 min at 4°C. The cell pellets were diluted with sterilized ultrapure water at the concentration of OD660 of 0.5 and immediately underwent fluorescence microscopy (OLYMPUS BX53, Olympus, Tokyo, Japan). The objective used was an oil‐immersion lens (UPLSAPO 100XO, 1.4 NA, Olympus). GFP was imaged with 488 nm wavelength laser excitation and a 520 nm emission filter, and was captured by cell f software (Olympus).
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