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12 protocols using vybrant dil

1

Cell Separation via Aptamer-Conjugated SAMs

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Hep G2 cells and RFP-HNDFCs were mixed at 1.0 × 105 cells per cell type in 2 mL of culture medium. Aptamer-conjugated oligopeptide SAMs were prepared using mixtures of peptide-N3 and peptide-COOH at 0.1%, 1%, and 10% peptide-N3. The cell mixture was poured on the aptamer-conjugated SAMs. After 3 h of culture, non-attached cells were washed twice with PBS and the number of each type of cells was counted on microscopic images using ImageJ software. SAMs without conjugation of aptamers and bare gold surfaces were used as controls. To obtain a separation curve through multistep enrichment of target cells, separation with the oligopeptide SAM was examined using cell suspensions at various ratios of Hep G2 cells to RFP-HNDFCs or normal human hepatocytes. In both cases, the cell density was 2.0 × 105 cells/2 mL/well. To distinguish Hep G2 cells from normal human hepatocytes, Hep G2 cells were previously stained with Vybrant-Dil (Thermo Fisher, Japan) in DMEM without serum for 15 min at 37 °C, followed by washing thrice with DMEM supplemented with 10% FBS. The number of fluorescently labeled and non-labeled cells was counted on microscopic images.
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2

HUVEC Spheroid Angiogenesis Assay

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150,000 Human Umbilical Vein Endothelial Cells (HUVECs)/plug (Lonza, Basel, Switzerland) were stained with Vybrant Dil (1:200 in 1 mL Basal Medium (EBM); Thermo Fischer #V-22885). After incubation (45 min at 37°C, 5 min at 4°C) cells were washed with EBM (Lonza, Basel, Switzerland), resuspended (25 mL EGM containing 20% methocel; Sigma-Aldrich, Taufkirchen, Germany) and cultured in hanging drops (25 µL/drop). Harvesting of spheroids and injection of matrigel containing spheroids into SCID-mice (Harlan Winkelmann, Borchen, Germany) were performed as described in 28 (link). At day 26 after injection, the matrigels were analyzed as described below.
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3

Melanoma Spheroid Invasion Assay

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The melanoma cells were stained with Vybrant DiL (Thermo Scientific, Dreieich, Germany) for 15 min at 37 °C before spheroid formation was initiated as described above. Plasma treatment was performed on day four, followed by incubation for 4 h. Spheroids (with residual amounts of original medium) were transferred to a fresh round-bottom multiwell plate without adding new culture medium and overlaid with 50 µL of matrigel (Corning, Wiesbaden, Germany). Plates were centrifuged at 500× g for 5 min in a precooled centrifuge (4 °C). matrigel was allowed to polymerize for 1 h at 37 °C, and 100 µL of culture medium was added. Spheroids and outgrowths of single melanoma cells were visualized in real-time using high-content imaging for 72 h. Fresh culture medium (50 µL) per well was added on day 2.
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4

Visualizing OMVs Uptake in Cells

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Isolated OMVs were labeled by incubating with 1% (v/v) Vybrant Dil (Thermo Fisher Scientific) at 37°C for 30 min. Unbound dyes were removed by ultracentrifugation and PBS washing three times. PBS was also incubated with dye in the same way as the OMVs and used for negative control. After treating with labeled OMVs, cells were fixed with 4% para-formaldehyde. Fixed cells on coverslip were mounted using ProLong Gold reagent with DAPI. The cells were then examined using confocal microscopy (LSM700, Carl Zeiss, Oberkochen, Germany).
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5

Cell Labeling with CellTracker and Vybrant

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A 10 mM solution of CellTracker™ Red and Green (ThermoFischer) was prepared in sterile DMSO (PAN Biotech). H4-II-EC3 cells were incubated for 30 min in culture medium with 10 μM of CellTracker™ in the culture flask, before PBS washing and exposition to the TrypLE™ express enzyme. Alternatively, Jurkat and hMSCs were stained for Vybrant™ Dil (red) and PC-3 were labeled with Vybrant™ Dio (green), following the manufacturer instructions (ThermoFisher).
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6

Cytotoxicity Evaluation of Au-NPs

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Chemicals including HPLC grade methanol (34860-2.5L-R), acetic acid (45754-500ML-F), HPLC grade water (270733-2.5L), acetyl salicylic acid (A5376-100G), egg yolk L-α-phosphotidycholine, lypophilised powder (P3556-1G), and Tween-80 viscous liquid (P1754-500ML) were supplied by Sigma Aldrich, Gillingham, UK. Dialysis sack (MW cut of 12000) (D9777-100FT) was obtained from Sigma Aldrich, Gillingham, UK. DMEM-F12 (31331-028) foetal bovine serum (10100147-500ML), penicillin–streptomycin (15070063, 100ML), 1.5 Mm glutamine (A2916801-200ML), phosphate-buffered saline (PBS) (10010-500ML), MEM phenol-free (51200038-500ML), and 1 mM cell-labelling solution Vybrant Dil (V22885) were supplied by Thermo Fisher Scientific, Waltham, MA, USA. AlamarBlue (BUF012B) was obtained from Bio-Rad, Hercules, CA, USA. Human skin fibroblasts (primary cells originated from a patient) were kindly supplied by the Department of Medicine at Swansea University. Au nanoparticles (Au-NPs) were provided by the School of Engineering at Swansea University.
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7

Tumor Cell Lysis Evaluation

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Following KDM1A inhibitor pretreatment (or control condition without treatment), SH-SY5Y tumor cells were labeled with Vybrant™ Dil and DiO Cell-Labeling Solution (Thermo Fischer Scientific, Waltham, MA, USA) according to the manufacturer’s instructions, mixed in a 50:50 ratio with each other, and seeded at 5 × 105 tumor cells/well of a 12-well plate. Stimulated untransduced T cells were added (E:T ratio of 1:1) after tumor cells had settled 3 h. The ratio of living KDM1A-treated to untreated tumor cells remaining in each well was flow cytometrically determined after 24 h. Specific lysis was calculated using the formula, [1 − (Ratio untreated:treated tumor cells cocultured with unstimulated T cells/Ratio untreated:treated tumor cells cocultured with stimulated T cells)] × 100.
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8

Quantifying Cell Aggregate Morphology

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MDA-MB-231 cells were co-stained with Hoechst33342 and Vybrant Dil stains (Thermo Fisher Scientific, Waltham, Massachusetts) for covisualization of the nucleus and the cell membrane, respectively. Images were captured using an Olympus FV3000 confocal microscope (Olympus, Center Valley, Pennsylvania). The morphology of individual cells was assessed using FIJI ImageJ circularity analysis (National Institutes of Health).
The size of cellular aggregates was assessed using ImageJ. Average cellular aggregate sizes were recorded by taking an average of the size of every cellular aggregate consisting of 3 or more cells. Multiple interrogation regions were examined per sample. Average size distribution histograms were also created to account for the relative proportion of singlet ( ∼10-15 μm), doublet ( ∼15-20 μm), small (20-30 μm), medium (30-100 μm), large (100-200 μm) and extra-large (200-400 μm) cellular clumps per interrogation area.
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9

Visualization of Nuclear Envelope Formation

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CSF extracts were depleted of XendoU or control IgG, and Cy5-dCTP (GE Healthcare) was added to extracts at a concentration of 1 µM. Samples were extracted every 10 min and examined by squash using the Olympus microscope setup described for visualization of ER networks. Nuclear intensity of Cy5-dCTP was calculated at each time point using MetaMorph. To monitor nuclear envelope formation in depleted extracts, Vybrant DiL (Invitrogen) was diluted 1:500 in extract that contained sperm nuclei and GFP Histone H1. Aliquots were monitored by squash every 10 min with 10–15 random fields imaged live.
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10

Monocyte Adhesion to Inflamed Aortic Vessels

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Aortic vessels were isolated from C57BL/6 mice and stimulated in Krebs buffer with bovine serum albumin (BSA) (1:1,000 w/v) and TNF-α for 4 h at 37°C. TNF-α activated vessels were mounted onto the cannulas and Krebs solution warmed at 37°C was used to flood the vessel chamber to mimic in-vivo conditions. Monocytes were re-suspended in 6 ml of RPMI at the concentration of 1 × 106 cells/ml. 1 mM of Vybrant Dil (Invitrogen) was added for 10 min in dark conditions, to fluorescently label the cells. Cell solutions were transferred into a terafusion syringe pump (Teruma) which was used to direct the movement of the cells through the aortic vessel at a rate of 7.1 ml per hour. Images of adhered monocytes were taken using the Zesiss Discover V.20 Fluorescence Microscope (Carl Zeiss MicroImaging) mounted on a Hammastsu HD Camera (Hamamatsu®) at 0, 2.5, 5, 7.5, and 10 min. Data was then quantified by calculating the number of stationary fluorescent dots per field of view (FOV).
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