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Ethidium homodimer

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Ethidium homodimer is a fluorescent dye used in molecular biology applications. It is a membrane-impermeable dye that binds to nucleic acids, primarily double-stranded DNA, and emits a red fluorescent signal upon binding. Ethidium homodimer is commonly used for the detection and quantification of DNA in various laboratory techniques, such as gel electrophoresis and fluorescence-based assays.

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87 protocols using ethidium homodimer

1

Cell Viability Quantification Methods

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Cell death was determined by trypan blue and ethidium homodimer staining. For trypan blue staining, an aliquot of the cell suspension was incubated with an equal volume of 0.4% trypan blue and the percentage of dead cells (identified by blue staining) was calculated relative to the total cell numbers in 4 independent fields using a hemacytometer. For ethidium homodimer staining, cells were incubated with ethidium homodimer (Life Technologies) for 30 min at room temperature according to the manufacturer’s instructions, mounted in Vectashield with DAPI (Vector,Burlingame, CA, USA) and visualized with an Olympus BX50 fluorescent microscope (Center Valley, PA, USA). Staining cells were counted in four randomly selected fields, for a total of at least 250 cells. Propidium iodide staining was also used for cell death confirmation, as described in Supplemental data (SD) (Fig. S3).
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2

Cell Viability Assessment Using LIVE/DEAD Assay

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A two-colour fluorescence assay (LIVE/DEAD Assay; Molecular Probes, consisting of calcein as a marker of viable cells and ethidium homodimer as a marker of dead cells; Invitrogen) was employed to determine the cell viability in the constructs. Each sample was washed in PBS 3 times before staining. The samples were stained for 15 min in the dark and washed 3 times in PBS after staining. A confocal microscope (Xcellence; Olympus) was used for image acquisition. Three different fields were counted for each sample. Cell viability was calculated as (number of green stained cells/number of total cells) ×100%.
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3

Live/Dead Cytotoxicity Assay for Aggregates

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MP cytotoxicity was assessed by the live/dead assay. After 14 days of culture, the aggregates were stained with a solution that contained 1 μM calcein AM and 2 μM ethidium homodimer (Invitrogen) at room temperature for 30 min. Then, the solution was removed, and the aggregates were washed with PBS and imaged using a fluorescent microscope (IX71 Olympus).
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4

Vitrification of Human Oocytes

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For human oocytes vitrification, they were used in Gardner’s (G1; Vitrolife) medium20 that consists of 20% knockout serum replacement (KSR, Gibco) and buffered by HEPES at pH 7.2. We followed the same experimental procedures for human oocyte vitrification like mouse oocyte vitrification steps that used DMSO-based CPA and ectoine-based bio-inspired CPA. To check the viability of mouse and human oocytes after the vitrification procedure, the recovered oocytes were cultured at 37 °C for 10 min following the manufacture instructions and literatures (Choi, et al., 2015a (link), Choi, et al., 2015b (link)) in FHM20 medium and G120 with 2μM calcein AM and 4 μM ethidium homodimer (Invitrogen)/propidium iodide (PI; 10μg/ml) for live (green) and dead (read) staining, respectively.
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5

Fibrin Membrane-Mediated hBM-dMSC Adhesion

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The freshly isolated fibrin membranes were placed onto ultra-low attachment 24-well plates in 2 mL of stem cell medium, and 25,000 hBM-dMSCs (5 passages) were seeded onto the membranes and cultured on them for 6 days. The medium was refreshed every 2 days. On the 7th day live-dead staining was performed to visualize attaching cells. The membranes were washed 3 times with PBS (phosphate-buffered saline) and stained in PBS containing 1 mM Calcein-AM (Invitrogen, Carlsbad, CA, USA), 4 mg/mL ethidium homodimer (Invitrogen), and 20 mg/mL Hoechst (Invitrogen, Carlsbad, CA, USA) for 30 min. The gels were washed again 3 times for 10 min with FluoroBrite DMEM (Gibco, Paisley, Scotland), and images were taken by an inverse fluorescent Nikon Eclipse Ti2 microscope (Tokyo, Japan).
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6

Evaluating Marine EVs' Effects on Cell Proliferation

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The effect of marine EVs on proliferation in normal or inflammatory environments was evaluated using the water-soluble tetrazolium salt (WST) assay (EZ-cytox, DoGenBio, Seoul, Korea). Briefly, based on the protein concentration measured by the Bradford assay, mEVs were diluted to 5, 10, 15, and 20 μg/mL in FBS-free RPMI-1640 medium and treated onto RAW 264.7 cells for 24 h. In the inflammatory environment, the same concentration of LPS (50 ng/mL) was used. The WST assay was performed according to the manufacturer’s instructions.
To check the cell viability, highest concentration marine EVs (20 μg/mL) in FBS-free medium were treated on RAW-264.7 for 24 h. Then, the medium was changed using the live and dead assay kit containing calcein-AM and ethidium homodimer (Invitrogen) in Hanks’ balanced salt solution (HBSS, Welgene, Gyeongsan, Korea) for 1 h. After 1 h, live and dead cells were observed using a fluorescence microscope (Carl Zeiss).
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7

Hydrogel Encapsulation of Human Cardiac Stem Cells

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Briefly, thin hydrogels encapsulating hCSCs (2 × 106 cells/mL) were prepared by placing a drop of hydrogel formulation (12 µL) at the center of a sterile coverslip. Then, another coverslip was placed immediately on top of the drop to yield a hydrogel sandwiched between the coverslips. The sandwiched hydrogel was then placed in culture media for a few minutes and then the top coverslip was gently released and pushed aside using a pair of sharp pointed forceps without damaging the underlying hydrogel. The hydrogels were cultured for a period of 5 days, following which they were incubated in calcein acetoxymethyl (calcein-AM, 0.2 µg/mL) and ethidium homodimer (2.5 µg/mL) (Invitrogen, Paisley, UK) for 15 min in supplemented DMEM at 37 °C to stain for live cells and dead cells. Live cells were visualized as green and dead cells as red under a fluorescence microscope (EVOS FL Auto2, Thermo Fisher Scientific, Waltham, MA, USA).
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8

Cartilage Viability Assay Protocol

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Twenty-four hours after trauma or IL-1β treatment, engineered cartilage constructs were bisected transversely and stained with Calcein AM (Invitrogen, Cat# L3224A) and ethidium homodimer (Invitrogen, Cat# L3224B) for 45 min in a 37 °C incubator. Images of the cut, transverse plane through the center of the construct were taken using a confocal microscope (Olympus FluoView FV1200) set for red (527ex nm/624em nm) or green (488ex nm/520em nm) detection. 40 × and 100 × magnification were used to take pictures. Ten stacks for each construct were taken with a z-stack density of 10 um. Fiji ImageJ software was used to process images and quantify live and dead cells.
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9

Live/Dead Staining of Bone Marrow Explants

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After incubation of BMEs in different media, bone chips were washed three times with PBS and stained in PBS containing 1 μM Calcein-AM (Invitrogen, Carlsbad, CA, USA), 5 μg/mL ethidium homodimer (Invitrogen, Carlsbad, CA, USA), and 5 μg/mL Hoechst 33342 (Invitrogen, Carlsbad, CA, USA) for 40 minutes. The experiments were performed in case of two patients' four-four BMEs (8 replica) after 5 days' incubation in FCS, HAS, or serum-free media, in total 3 different media. The samples were washed three times with PBS and imaged immediately with a Nikon A1R confocal microscope (Nikon-KOKI Imaging Center, Budapest).
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10

Evaluating cell viability in hybrid constructs

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A two-color fluorescence assay (LIVE/DEAD Assay, Molecular Probes, consisting of calcein, as a marker of viable cells, and ethidium homodimer, as a marker of dead cells, Invitrogen) was employed to determine HKs viability within the hybrid constructs immediately after the hybrid construct was produced, and to determine the HCECs viability after the cells incubating on the surface of the construct for 24 h. Each sample was washed in PBS 3 times before staining. Samples were stained for 15 min while avoiding light and washed 3 times in PBS after staining. A confocal microscope (Xcellence, Olympus) was used for image acquisition. Three different fields were counted for each sample.
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