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57 protocols using phase contrast microscopy

1

Scratch Assay for Cell Migration Analysis

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According to our previous study, we conducted the scratch assay (Shen et al., 2022 (link)). Briefly, 2 × 105 cells/mL were added to plates containing a septum in the middle, which underwent incubation at 37°C. Each septum was removed after the cells reached confluence. SCs underwent an additional 9-h incubation and were visualized by phase-contrast microscopy (Leica Microsystems). Migration rates for SCs were obtained by measuring the remaining septal area with Image-Pro Plus (Media Cybernetics).
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2

Evaluating Cell Toxicity via Microscopy and NRU Assay

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After 24 h of treatment with toxins, cell morphological changes were observed by phase contrast microscopy (Leica Microsystems, Wetzlar, Germany), and the neutral red uptake (NRU) assay was performed as previously described [22 (link)]. Absorbance was measured at 540 nm with a microplate reading spectrofluorometer (Fluostar OPTIMA, BMG Labtech, Champigny sur Marne, France). Three independent experiments were performed, and for each experiment, the median of the three technical replicates was expressed relative to that of the vehicle control. When possible, the IC50 was determined using GraphPad Prism Software (La Jolla, CA, USA).
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3

Tube Formation Assay for Angiogenesis

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For tube formation assays, 96‐well plates were precoated with 50 μl of growth factor‐reduced Matrigel (BD Biosciences) for 30 minutes at 37°C. HUVECs were seeded at a density of 20,000 cells per well and incubated with conditioned medium at 37°C. After 4–6 hours, capillary network structures were imaged by phase‐contrast microscopy (Leica Microsystems) and the total number of interconnecting branches in each group counted using Image‐Pro software (Media Cybernetics, Rockville, MD,
http://www.mediacy.com).
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4

Podocyte Migration Assay Protocol

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Transwell cell culture inserts (pore size 8 μm; Corning Co-Star Corp., Cambridge, MA, USA) were placed in RPMI 1640 medium supplemented with 15% foetal bovine serum in the lower compartment. Podocytes with different pretreatments were harvested with trypsin and resuspended in serum-free medium. The upper chambers were seeded with 1 × 105 cells/ml, which were allowed to attach at 37°C for 12 h. Non-migratory cells were then removed from the upper surface of the chambers, and migrated cells on the lower membrane surface were fixed with 4% paraformaldehyde and stained with haematoxylin. The number of migrated cells was counted in 3 separate fields per membrane at 200× using phase-contrast microscopy (Leica Microsystems, GmbH). The data are presented as the mean ± S.D.
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5

Transwell Assay for Cell Migration

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Transwell cell‐culture inserts (pore size 8 μm; Corning Costar Corp., Cambridge, MA, USA) were rinsed once with PBS and placed in RPMI1640 with 10% foetal bovine serum in the lower compartment. The heights of the medium in the upper and lower compartments were maintained at similar levels; thus, bulk flow was not because of a hydrostatic pressure gradient. Podocytes pre‐treated with different conditions were harvested with trypsin and re‐suspended in serum‐free RPMI1640 medium. The upper chambers were seeded with 1 × 104/ml cells, which were then allowed to attach at 37°C for 6 or 12 hrs, respectively. Next, non‐migratory cells were removed from the upper surface of the membrane, and migrated cells were fixed with 4% paraformaldehyde and stained with haematoxylin. The number of migrated cells in the centre of a membrane (one field) was counted using phase contrast microscopy (Leica Microsystems GmbH). The data presented denote the mean ± S.D. of 6 independent experiments.
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6

Transwell-Based Invasion and Migration Assay

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For invasion assays, MCF7 or SKBR3 cancer cells (1 × 105) were loaded in the upper well of a Transwell chamber (8-μm pore size; Corning Glass, Seoul, Korea) that was precoated with 10 mg/mL growth factor-reduced Matrigel (BD Biosciences, Seoul, Korea) on the upper side of the chamber with the lower well filled with 0.8 mL growth medium. After incubation for 48 h, non-invaded cells on the upper surface of the filter were removed with a cotton swab, and cells that had migrated onto the lower surface of the filter were fixed and stained with a Diff-Quick kit (Fisher, Pittsburgh, PA, USA) and photographed (magnification, ×20). Invasiveness was determined by counting cells in five microscopic fields per well, and the extent of invasion was expressed as an average number of cells per microscopic field. Cells were imaged by phase contrast microscopy (Leica Microsystems, Bannockburn, IL, USA). For the migration assay, we used the Transwell chambers with inserts that contained the same type of membrane but without the Matrigel coating.
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7

In Vitro Tube Formation Assay

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Matrigel matrix (Becton-Dickson) was liquefied overnight on ice at 4°C. 50 µl of the matrix was aliquoted in 96-well plates and incubated at 37°C for 30–60 min prior to plating 5×104 cells per well. Cells were cultured for 24 hrs and tube formation monitored by inspection by phase contrast microscopy (Leica Microsystems). At the end of the 24 hr incubation, cells were labeled with 1 µM Calcein AM (Trevigen) and cell viability assessed using a fluorescent inverted microscope with a 485 nm excitation filter.
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8

Breast Cancer Cell Invasion and Migration Assay

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For invasion assay, breast cancer cells were loaded in Transwells with 8 μm pore size filter inserts (Corning Glass, Seoul, Korea) that were precoated with 10 mg/mL growth factor-reduced matrigel (BD Biosciences, Seoul, Korea) on the upper side of the chamber with the lower well filled with 0.8 ml of growth medium. After incubation for 48 h at 37 °C, and For migration assay, we used Transwells with inserts that contained the same type of membrane but without the matrigel coating. After incubation for 24 h at 37 °C. Non-invaded cells on the upper surface of the filter were removed with a cotton swab and migrated cells on the lower surface of the filter were fixed and stained with the Diff-Quick kit (Fisher, Pittsburgh, PA, USA) and photographed (magnification ×20). Invasiveness and motility were determined by counting cells in four microscopic fields per well, and the extent of invasion was expressed as an average number of cells per microscopic field. Cells were imaged by phase-contrast microscopy (Leica Microsystems, Bannockburn, IL). All experiments were repeated three times.
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9

Cell Migration Wound Healing Assay

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Wound healing assay was conducted to examine the capacity of cell migration. Briefly, a wound was generated when the cells reached 80–90% confluency in a 6-well plate by scratching the surface with a 1,000-µl pipette tip. The cells were then incubated in 1% FBS for 24 h, and then photographed using phase contrast microscopy (Leica Microsystems). The distance between the wound edges of the scratch area was analyzed using Adobe Photoshop 7.0. All experiments were performed in triplicate.
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10

Transwell Invasion Assay for Cancer Cells

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For the invasion assay, the cells (2.5 × 104 cells in serum-free medium) were seeded in the upper well of the Transwell chamber (8-mm pore size; Corning Glass, Corning, New York, NY, USA) that was precoated with 10 mg/mL growth factor-reduced Matrigel (BD Biosciences, Franklin Lakes, NJ, USA). The lower well was filled with 0.8 mL of growth medium containing 10% fetal bovine serum as a chemoattractant. After incubation for 48 h at 37 °C, non-invaded cells on the upper surface of the filter were removed with a cotton swab, and migrated cells on the lower surface of the filter were fixed and stained with a Diff-Quick kit (Fisher, Waltham, MA, USA). Cells were imaged by phase contrast microscopy (Leica Microsystems, Wetzlar, Germany; magnification 10×). Invasiveness is determined by counting cells in five microscopic fields per well, and the extent of invasion is expressed as an average number of cells per microscopic field.
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