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21 protocols using silicone insert

1

Wound Healing Assay for Migratory Capacity

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To determine the migratory capacity of the treated cells, wound healing assays were performed49 (link) after treatment with IC50 concentrations alone with or without EP. After treatment, 4 × 104 cells were plated on a 24-well plate with a silicone insert (Ibidi) that formed a 500-μm ± 50 μm cell-free gap after removal. Cells were incubated overnight at 5% CO2 and 37 °C until a confluent cell monolayer was formed, then the silicone inserts were removed. Images of the wounds were captured with DP72 CCD camera connected to Olympus IX-70 inverted microscope at 0 h (when culture inserts were removed) and then every 2–4 hours (depending on the cell line used and optimized in preliminary tests), until the wounds of the control group were completely sealed (for HUVEC 12 h, CHO 24 h, FaDu 26 h). At each time point, the cell-free area was quantified using FIJI image analysis software50 (link) and a kinetic analysis was made from the obtained values. The cell migration rate of each experimental group was normalized to the migration rate of untreated cells. The assay was not performed in B16F1 cells because these cells have very limited migratory potential.
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2

Wound Closure Kinetics Assay

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For wound migration assay, 7.5 × 104 cells were seeded on each of the two compartments (growth area: 0.22 cm2/compartment) of silicone culture inserts (Ibidi GmbH), grown for 5 days, and starved for 16 h. At the onset of the experiment, the silicone insert was removed leaving a gap free of cells of 500  ± 100 μm width (according to manufacturer). Cells were gently washed with serum-free media to remove cell debris and treated as indicated. Digital images were obtained with an Olympus CellR microscope and area measurements were performed using ImageJ software. The rate of wound closure was measured by subtracting the area of the wound at 24 h from the area at 0 h.
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3

Wound Healing Assay for Anti-Migration Potential

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The anti-migration potential of L. plantarum L125 CFCS was examined using the wound healing assay. To this end, HT-29 cells were seeded in polymer coverslip inserts in 35 mm µ-Dishes at a density of 80,000 cells per silicone insert (Ibidi, Gräfelfing, Germany) and were incubated in standard conditions overnight. The next day, the inserts were removed to reveal a 500 µm cell-free gap. Then, the cells were treated with undiluted CFCS from L. plantarum L125 or L. rhamnosus GG. Untreated cells (control) were maintained in the cell culture medium, as mentioned above. Photographs were taken with a ZEISS Primovert light microscope (Zeiss, Göttingen, Germany) equipped with a digital camera (Axiocam ERc 5 s) at 0, 24 and 48 h post-treatment.
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4

Optimized In Vitro Wound Healing Assay

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The in vitro wound healing migration assay was optimized according to Ho et al. [28 ]. Wound healing and migration assays were done by seeding the 786-O cells (3.5 × 104/well) into the Ibidi-silicone insert (Ibidi; Cat. #81176, Germany) and incubated for attachment. This insert allows the formation of a well‐defined edge without physically scratching or wounding the cell monolayer after removal of the inserts. In order to monitor cell movement within the wounded area following their incubation with diverse concentrations of cisplatin combined with HWG or RA, three wounds were photographed immediately after picking up the insert (T0) and after 6 h. The endpoint of the assay was measured by calculating the reduction in the width of the wound after 6 h and comparing it to T0 with the non-treatment control group set at 100%.
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5

Wound Healing Assay with Inhibition

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RT4 cells were first seeded at a concentration of 4 × 104 cells/100 μl in both chambers of an Ibidi-silicone insert (Ibidi, Martinsried, Germany). This insert allows for the formation of a well-defined edge without physically scratching or wounding the cell monolayer. Cells were cultured for 24 h in DMEM containing 10% FBS to form a confluent monolayer. Then, cells were grown in serum-free DMEM and Mitomycin C (5 μg/ml, Sigma #M4287) to inhibit cell proliferation for 12 h prior to careful removal of the insert. Cells were incubated in the CM from HFs, HFs + TGFß or iCAFs for 24 h in presence or absence of an anti-IL-6 antibody (1 μg/mL). The migration was visualized at the indicated times (0, 6, and 12 h) under an inverted microscope (TE2000, Nikon). Migration distances were measured using the ImageJ analysis software (National Institutes of Health, Bethesda, MD).
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6

In Vitro Wound Healing Migration Assay

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The in vitro wound healing migration assay was optimized according to Ho et al. [28] . Wound healing and migration assays were done by seeding the 786-O cells (3.5x10 4 /well) into the Ibidi-silicone insert (Ibidi; Cat. #81176, Germany) and incubated for attachment. This insert allows the formation of a well-de ned edge without physically scratching or wounding the cell monolayer after removal of the inserts. In order to monitor cell movement within the wounded area following their incubation with diverse concentrations of cisplatin combined with HWG or RA, three wounds were photographed immediately after picking up the insert (T 0 ) and after 6 h. The endpoint of the assay was measured by calculating the reduction in the width of the wound after 6 h and comparing it to T 0 with the non-treatment control group set at 100%.
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7

In Vitro Wound Healing Assay

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The in vitro wound healing migration assay was optimized according to Ho et al. [28] . Wound healing and migration assays were done by seeding the 786-O cells (3.5 × 10 4 /well) into the Ibidi-silicone insert (Ibidi; Cat. #81176, Germany) and incubated for attachment. This insert allows the formation of a well-de ned edge without physically scratching or wounding the cell monolayer after removal of the inserts. In order to monitor cell movement within the wounded area following their incubation with diverse concentrations of cisplatin combined with HWG or RA, three wounds were photographed immediately after picking up the insert (T 0 ) and after 6 h. The endpoint of the assay was measured by calculating the reduction in the width of the wound after 6 h and comparing it to T 0 with the non-treatment control group set at 100%.
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8

Cell Migration and Invasion Assays

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To assess cell migration, cells were seeded at a density of 3×10 5 cells/mL in both chambers of an Ibidi-silicone insert (Ibidi, Germany). This insert allows for the formation of a well-defined "edge" without physically scratching or wounding the cell monolayer. Cells were cultured for 12 h to form a confluent monolayer before careful removal of the insert, and images were acquired after 24 h (Nikon Eclipse TE2000-U, Japan).
For the invasion assays, cells cultured on substrates of different stiffness for 48 h were removed by trypsinization and then seeded into the upper compartment (3×10 4 cells/well) of a transwell chamber (Corning, USA). After incubation for 12 h, cells that did not invade in the upper wells were removed with cotton swabs. Cells that had passed through the membrane on the lower surface of the insets were fixed with 4% paraformaldehyde and stained using crystal violet. These data were quantified using ImageJ software.
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9

Wound Healing Assay of Endothelial Cells

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Differentiated iBMECs were purified on CN IV-FN and subsequently subcultured onto 2-well plates with silicone inserts (ibidi) designed for the wound healing assay. The wells were pre-coated with LN 511-E8 or CN IV-FN. The next day, the inserts were removed and the medium was changed to endothelial cell medium without bFGF and retinoic acid. Using an EVOS FL Auto microscope, phase contrast images were taken every 3 h from the same spot, and the area void of cells in each image was calculated using ImageJ. Three independent replicates per condition were evaluated for this experiment.
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10

Cardiac Fibroblast Wound Healing Assay

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P0 rat cardiac fibroblasts were used for cell scratch/wound healing assays. Silicone inserts (Ibidi, Martinsried, Germany) were placed in a 6-well culture dish and a cell suspension of 2.85 × 109 cells/mL was prepared. 70 μL of this cell suspension (approximately 2.5 × 105 cells) was added to each chamber of the silicone insert separated by the silicone divider of the insert. The area surrounding the insert was covered with 1.5 mL DMEM-F12 media to prevent drying out of cells. Cells were allowed to adhere and grow overnight in complete growth media (10% FBS DMEM-F12). The next day, the media was changed to a 2% FBS DMEM-F12 solution and cells were incubated in low serum for an additional 24 hours. Cells were then treated with Baf-A1 (7.5 nM) or CQ (35 μM) for 48 hours. After 48 hours, inserts were removed and light microscopy images acquired every 6 hours until the untreated control cells reached 100% confluency (i.e. cell migration was complete). Data were analyzed by comparing the difference between the scratch area percentage at 0, 12 and 24 hours in Baf-A1 and CQ treated cells versus controls using Wimasis Image Analysis software (Wimasis Image Analysis, Munich, Germany).
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