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Ethidium homodimer 1 ethd 1

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Ethidium Homodimer-1 (EthD-1) is a fluorescent dye used to detect and quantify dead cells in a sample. It is a membrane-impermeable dye that only enters cells with compromised cell membranes, such as dead or dying cells. EthD-1 binds to nucleic acids, resulting in a bright red fluorescence that can be detected using appropriate fluorescence detection methods.

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23 protocols using ethidium homodimer 1 ethd 1

1

Spheroid Formation on Concave PDMS Microwells

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Spheroids were generated on PDMS-based concave microwells fabricated using soft lithography techniques and the meniscus of the PDMS prepolymer, as previously described46 (link). The concave micromolds consisted of 1 × 1 cm arrays of 500-μm diameter microwells, for a density of 100 wells per cm2. All substrates were coated with 3% (w/v) bovine serum albumin to prevent cell attachment. Trypsin-dispersed single PD-MSCs (200,000 cells per mold, passages 8–11) were seeded on top of the concave microwells, which allowed the cells to become trapped within the wells. At 5 min post-seeding, a flow of culture medium was gently applied to remove non-docked cells. The plated cells were cultured with medium containing FGF-4 (75 ng/ml) and heparin (3 μg/ml) (Peprotech). For measuring viability, spheroids were labeled with calcein-AM and ethidium homodimer-1 (EthD-1; Molecular Probes). Confocal microscope images were used for measuring diameters of spheriods and viability, and ImageJ software was used for quantification.
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2

Molecular Mechanisms of Cellular Stress Response

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Celastrol, cycloheximide (CHX), 3-methyladenine (3-MA), bafilomycin A1, chloroquine (CQ), ethylene glycol tetraacetic acid (EGTA), 1,2-bis(o-aminophenoxy) ethane-N,N,N'N'-tetraacetic acid (BAPTA), 1,2-bis(o-aminophenoxy)ethane-N,N,N'N'-tetraacetic acid acetoxymethyl ester (BAPTA-AM), ruthenium red, and MG132 were purchased from Sigma-Aldrich. Torin1 was purchased from Selleckchem. LysoTracker-Red, Rhod-2-AM, Fluo-3-AM, calcein- acetoxymethyl ester (calcein-AM), and ethidium homodimer-1 (EthD-1) were from Molecular Probes. 2-aminoethosxydiphenyl borate (2-APB), PD98059, SB203580, and SP600125 were obtained from Calbiochem. Dantrolene was obtained from Alexis Biochemicals. The following antibodies were used: anti-β-actin (Abcam); anti-ubiquitin, ATF4, and IP3R (Santa Cruz Biotechnologies); anti-caspase-8, caspase-3, and KDEL (Stressgen); anti-caspase-9 (Novus Biologicals); anti-p62 and anti-cathepsin L (BD Biosciences); anti-MCU (Sigma-Aldrich); anti-NBR1 (Abnova); anti-LC3B, CHOP, phospho-ERK1/2, total ERK1/2, phospho-JNK, total JNK, phospho-p38, and total p38 (Cell Signaling); HRP-conjugated anti-rabbit IgG and HRP-conjugated anti-mouse IgG (Molecular Probes).
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3

Assessing Cumulus Cell Viability

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At 44 h of culture, COCs were incubated with 2 μM Ethidium Homodimer-1 (EtHD-1; Invitrogen-Molecular Probes, Eugene, OR, USA) in OMM and cultured for another 4 h. COCs were washed 3 times in phosphate buffered saline (PBS) and fixed in 2% (w/v) formaldehyde. Subsequently, COCs were incubated for 5 min in 0.1 μg/mL 4,6-diamino-2-phenyl-indole (DAPI; Invitrogen-Molecular Probes, Landsmeer, the Netherlands), mounted under a coverslip with anti-fade mounting medium (Vectashield; Vectorlab, Burlingame, CA, USA), and imaged by confocal laser scanning microscopy (CLSM; Leica SPE-II, Heidelberg, Germany). Imaging was performed using a 368 and 543 nm laser to excite DAPI and EthD-1, respectively. Nuclei of cumulus cells were considered degenerated when stained for both DAPI and EthD-1, or when nuclei had a condensed or fragmented appearance. Viable oocytes containing a metaphase spindle together with a polar body were considered at the Metaphase II (M2) stage.
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4

Mitochondrial Calcium Regulation in Cell Stress

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The chemicals used in this study were cycloheximide (CHX), MG132, 1,2-bis (o-aminophenoxy) ethane-N,N,N′,N′-tetraacetic acid (BAPTA) and 1,2-bis (o-aminophenoxy) ethane-N,N,N′,N′-tetraacetic acid acetoxymethyl ester (BAPTA-AM) (Sigma-Aldrich, St Louis, MO, USA); Nutlin-3 (TOCRIS, Avonmouth, Bristol, UK); Rhod-2-acetoxymethyl ester (Rhod-2-AM), Fluo-3-acetoxymethyl ester (Fluo-3-AM), MitoTracker-Red (MTR), MitoTracker-Green (MTG), calcein-acetoxymethyl ester (calcein-AM), ethidium homodimer-1 (EthD-1), and 4′,6-diamidino-2-phenylindole (DAPI) (Molecular Probe, Eugene, OR, USA); Ru360 (Calbiochem, Darmstadt, Germany); bortezomib, and carfilzomib (Selleckchem, Houston, TX, USA). The antibodies used in this study were anti-β-actin, ubiquitin, ATF4, mitochondrial Ca2+ uniporter (MCU), HDM2 and p53 (Santa Cruz Biotechnology, Santa Cruz, CA, USA); CHOP/GADD153, GRP78, and mtHsp70 (Cell Signaling Technology, Danvers, MA, USA); cytochrome oxidase subunit II (COX II) (Invitrogen, Grand Island, NY, USA); protein disulfide isomerase (PDI) (Enzo Life Sciences, Farmingdale, NY, USA); rabbit IgG HRP, mouse IgG HRP and goat IgG HRP (Molecular Probe).
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5

Tamoxifen Metabolites Antimicrobial Evaluation

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Bacterial suspensions (adjusted to optical density at 600 nm = 0.2) of MDR A. baumannii Ab186 and MDR E. coli EcMCR+ strains were placed on a 96-well plate, incubated with 2 and 16 mg/L of tamoxifen metabolites mixture, respectively, and mixed in a solution of phosphate buffered saline containing Ethidium Homodimer-1 (EthD-1) (1:500) (Invitrogen, Carlsbad, CA, USA). After 10 min of incubation, fluorescence was monitored during 160 min using a Typhoon FLA 9000 laser scanner (GE Healthcare Life Sciences, Marlborough, MA, USA) and quantified with ImageQuant TL software (GE Healthcare Life Sciences, USA). Bacterial counts were obtained at the beginning and end of the experiment to ensure that the metabolite mixture did not present bactericidal activity against A. baumannii and E. coli strains.
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6

Cell Viability Assay Reagents

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All chemicals were purchased from Sigma-Aldrich Chemical Co. and used without further purification. Calcium acetoxymethyl ester (calcein AM), and ethidium homodimer 1 (EthD-1) were obtained from Invitrogen Corp. (Carlsbad, CA). All chemicals and reagents were of analytical grade. Water was purified with a Milli-Q plus system (Millipore Co., Bedford, MA).
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7

Cytotoxicity Assay Protocol

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High-glucose Dulbecco's Modified Eagle's Medium (DMEM), phosphate buffered saline (PBS), penicillin–streptomycin, and trypsin were purchased from Caisson (Smithfield, VA, USA). Hoechst 33342, calcein AM, ethidium homodimer-1 (EthD-1), and paraformaldehyde were purchased from Invitrogen (Carlsbad, CA, USA). paraformaldehyde was purchased from Alfa Aesar (Haverhill, MA, USA).
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8

Viability Assay for Microtissues

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The live/dead® viability kit for mamalian cells (Invitrogen, Paisley, UK) was used to stain the live and dead cells of the microtissues formed in the calcium alginate microcapsules. The live/dead® cell viability kit can differentiate live cells from the dead cells by double staining of both the HaCaT and ORL-48 cells in the microtissues with green-fluorescent Calcein-Acetoxymethyl (AM, Invitrogen, Paisley, UK), which indicates intracellular esterase activity, and red-fluorescent Ethidium homodimer-1 (EthD-1) (Invitrogen, Paisley, UK), which indicates the loss of plasma membrane integrity. After 16 days of culture, the HaCaT and ORL-48 microtissues formed in the calcium alginate microcapsules were incubated in 2 μM of Calcein-AM and 4 μM of EthD-1 stain solutions for 20 min in the dark. Subsequently, the stain solutions were removed and the microtissues were washed three times in HBSS solution. The stained microtissues were captured using a BX53 fluorescence microscope (Olympus, Tokyo, Japan) mounted with a DP73 digital camera.
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9

Assessing Drug-Induced Spheroid Cell Death

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For drug treatment, lung cancer cells (NCI-H460, A549, and SK-MES-1) and stromal cells (WI38 and HUVEC) were seeded at a density of 6 × 103 cells/well in 96-well round-bottomed ultra-low attachment microplates. After 1 day, 10 or 20 μM of Gefitinib and Cisplatin (all from Sigma-Aldrich, St. Louis, MO, USA) were added to the spheroids for 2 days, and then spheroid cell death was detected using the cell-impermeant viability indicator ethidium homodimer-1 (EthD-1; Invitrogen Life Technologies, Grand Island, NY, USA). EthD-1 is a high-affinity nucleic acid stain that fluoresces weakly until bound to DNA, whereupon it emits red fluorescence (excitation/emission maxima ~ 528/617 nm). Spheroids were incubated in 4 μM EthD-1 in complete medium for 30 min in a 37 °C incubator, and images were obtained and the intensity of EthD-1 fluorescence measured using the Operetta® High Content Screening System (Perkin Elmer).
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10

Fabrication of PDMS Array Chips for DCST

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For the fabrication of array chips for DCST, poly(dimethylsiloxane) (PDMS) monomers and curing agents were purchased from Dow Corning (Midland, MI, USA). Poly(methyl methacrylate) (PMMA, 3 mm thickness) plates were purchased from YM Tech (Daejeon, Korea). Phosphate-buffered saline (PBS), Dulbecco’s modified Eagle’s medium (DMEM), fetal bovine serum (FBS), penicillin/streptomycin (P/S) were purchased from Corning (Corning, NY, USA). Rat tail collagen type I was purchased from Corning. Calcein-AM and ethidium homodimer-1 (EthD-1) and Hoechst 33342 solution were purchased from Invitrogen (Carlsbad, CA, USA). CellTrackerTM Green CMFDA and CellTrackerTM Red CMTPX dyes for cell tracking were purchased from Thermo Fisher Scientific (Waltham, MA, USA). Doxorubicin hydrochloride for drug treatment was purchased from Sigma-Aldrich (St. Louis, MO, USA). Other chemicals and reagents were purchased from Sigma-Aldrich unless otherwise stated.
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