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46 protocols using primovert inverted microscope

1

Endothelial Tube Formation Assay

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Prior to seeding, 96-well plates were coated with 50 μL/well of Matrigel (Corning) and incubated at 37 °C for 30 min. PAECs were then seeded at 20,000 cells/well in the growth medium and further incubated at 37 °C for 6–8 h. Images were taken for each well every 1 h after 4 h using a Zeiss Primovert Inverted Microscope (Zeiss) attached to a Zeiss Axiocam ERc 5 s (Zeiss), to determine the optimal time point for the quantitative analysis. Images in low magnification (×4) were captured for each well. Each image was divided into 16 rectangles, and 10 rectangles were randomly chosen. The lengths of tubes between the branching junctions were measured and summed in each single rectangle, and then values obtained from 10 rectangles were averaged. A measurement example is shown in Supplementary Fig. 9. We performed experiments 3 independent times using 1–2 wells for each group.
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2

Quantifying Endothelial Cell Migration Dynamics

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For endothelial cell migration analysis (44 (link), 45 (link)), EA.hy926 cells were plated in 24-well plates at a density of 8 × 104 cells/well. When cells reached 90% confluency, they were synchronized in DMEM/antibiotics medium for 16 h and then cell monolayers were scratched using a pipette tip (200 μl). Wounded cells were rinsed with warm DPBS to remove nonadherent cells and then EA.hy926 cells were incubated with 0.35 μM (at apoA-I concentration) human HDL (apoB-depleted plasma), for 1 h at 37°C with or without 2.5 μg/ml of blocking antibody for PCSK9, in DMEM/antibiotics medium for 24 h. At the end of the incubation period, cells were fixed with ice-cold methanol for 15 min, permeabilized in 0.1% Triton X-100/DPBS for 15 min, and stained with hematoxylin (Sigma Aldrich) for 5 min. Cells were photographed on marked positions at 0 and 24 h, using the 10x objective lens of a Zeiss Primovert Inverted microscope (Zeiss, Germany). Wound healing was quantified, following analysis of images with ImageJ analysis software (NIH, Bethesda, MD) (46 ), by measuring the number of cells that migrated.
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3

Morphological Changes in HeLa and Hep-G2 Cells

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Morphological changes in HeLa and Hep-G2 cells were observed after treatment with the aqueous FPB extract for 24 hrs. Briefly, HeLa (5x10 3 /well) and Hep-G2 (8x10 3 /well) cells were seeded into a 24-well plate (in triplicates) and incubated for 24 hrs to attach. Thereafter, HeLa and Hep-G2 cells were treated with the previously determined IC 50 concentrations of 0.5 and 1.3 mg/mL respectively for 24 hrs, and washed once with PBS, cells morphologies were viewed under the ZEISS Primo Vert inverted microscope (ZEISS, Germany) and images captured at x200 magnification.
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4

Phase Contrast Imaging of Cell Suspensions

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The same cell suspensions prepared for the inoculation of the corneal tissue were used to generate the phase contrast images. Samples of each morphology were placed onto microscope slides and overlaid with a glass coverslip. The cells were then viewed on a Zeiss Primovert inverted microscope (Zeiss, Cambridge, UK) at a magnification of x400 and the images were acquired on a Canon EOS M50 digital camera using a Zeiss P95-T2 DSLR 1.6x trinocular microscope adapter.
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5

Giemsa Staining of EHEC-Infected HCMs

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Giemsa staining of HCMs and bacteria was performed according to methods described previously by Rajan et al. (85 (link)) and Tatsuno et al. (86 (link)). HCMs were infected with EHEC strains as described above. Bacteria and infected cells were imaged under a Zeiss Primovert inverted microscope at a ×40 magnification. Bacterial clusters on HCMs containing >8 bacteria were considered MCs (86 (link)). The number of MCs was scored as the sum from 20 random microscopic fields. A technician counted the MCs in a blind manner to ensure objectivity.
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6

Dental Pulp Stem Cell CFU-F Assay

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Isolated cells (10 × 103) from the deciduous dental pulp tissue were seeded into a 100-mm culture dish (Corning) and were cultured in 10 mL of XFM (Biological Industries) for 14 days. The culture dish was treated with 3 mL of 4% paraformaldehyde (Merck, Darmstadt, Germany) and 0.1% toluidine blue (Merck) in PBS (pH 7.4; Nacalai Tesque) for 18 h. After washing five times with 1 mL of PBS, the dish was air-dried and was imaged with a GT-X980 scanner (Epson, Suwa, Nagano). Numbers of CFU-F, which contained > 50 cells, were counted using a Primovert inverted microscope (Carl Zeiss Microscopy).
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7

TRAP Staining and Microscopic Analysis of Osteoclasts

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OCs were stained for tartrate-resistant acid phosphatase (TRAP) and were analyzed using light microscopy. OC groups (n=4) were prepared based on a modified manufacture’s protocol (Sigma-Aldrich). Briefly, OCs were rinsed three times with 1x PBS, fixed in a fixative solution comprising of 25mL citrate solution, 65mL acetone, and 8mL of 37% formaldehyde for 15min. Followed by 3 rinses in deionized water. Staining solution consisting of 45mL of deionized water at 37°C, 1mL diazotized Fast Garnet GBC solution, 0.5mL Naphthol AS-BI Phosphate Solution, 2mL Acetate solution, and 1mL Tartrate solution was prepared and 200μL of staining solution was added to each well and allowed to incubate for 1hr at 37°C. Samples were counterstained with 200μL hematoxylin solution for 2min and rinsed in deionized water prior to imaging with a Carl Zeiss Primo Vert™ Inverted Microscope (Zeiss, Oberkochen, Germany). Representative images were selected from 18 images per well and n=4 per group.
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8

Scratch Wound Healing Assay

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When cells had spread to 6‐well plates, cell surfaces were scratched with a 200‐μL pipette tip. Cells were washed with sterile PBS and cultured with compounds in 1% FBS medium. The scratch widths were observed under a Zeiss Primovert inverted microscope and quantified using ImageJ software after 0, 24, and 48 h.
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9

Cell Proliferation Assay with Crystal Violet

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The cell proliferation assay was performed by using crystal violet staining method. A density of 5 × 104 AGS cells were seeded for each well in six-well plates, the cells were treated with 18.5 μM STO-609, and DMSO was taken as the control. We also knockdown CAMKK2 by using CAMKK2 siRNA and studied the effect of CAMKK2 knockdown on cellular proliferation. The cells were transfected with CAMKK2 siRNA and scrambled siRNA (transfection described under siRNA transfection). They were allowed to grow for 72 h and were washed with PBS, fixed with methanol, and stained with 3% crystal violet. The live cells were stained with crystal violet, while dead cells were washed away as they did not remain adherent. Images were taken with a Primovert inverted microscope (Carl Zeiss, Germany). Each measurement was performed in duplicate, and the experiments were repeated thrice.
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10

Colony-Forming Ability of Cancer Cells

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Cancer cell colony-forming ability was determined as previously described [24 (link)]. The bottom of a 6-well plate was first pretreated with poly-D-lysine hydrobromide for 4 hours and then washed once with deionized water. Afterwards, LA-N-1 cells were seeded in each well (400 cells/well) and allowed to settle overnight. On the following day, cells were treated with either solvent control (0.5% ethanol) or various concentrations of DHA or EPA for 24 hours. Subsequently, the wells were washed and replaced with fresh RPMI medium. The medium was changed every 3 days. After 6 days, colonies were fixed with 100% ice-cold methanol and stained with Hemacolor staining solutions (Merck Millipore, Darmstadt, Germany). The colonies were counted under a light microscope (Carl Zeiss™ Primo Vert™ Inverted Microscope; Carl Zeiss, Oberkochen, Germany) and the percentage (%) of colonies formed was calculated as follows:
% of colonies formed = Number of colonies of n-3 PUFAs-treated cellsNumber of colonies of the controlcells without n-3 PUFAs treatment
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