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Nile red

Manufactured by Santa Cruz Biotechnology
Sourced in United States

Nile Red is a fluorescent dye that is commonly used in biological research for the detection and quantification of lipids and lipid-containing structures. It exhibits strong fluorescence when bound to neutral lipids, making it a useful tool for the visualization and analysis of lipid droplets and other lipid-rich organelles.

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7 protocols using nile red

1

Quantitative Lipid Droplet Analysis

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Lipid droplet quantification by Nile Red staining was performed after incubation of cells with serum free medium for 5 days. Nile Red (15 μg/μL) (Santa Cruz Biotechnology, Dallas, United States) was added to the cell medium for 20 min at 37°C. Nile Red fluorescence was analyzed at 580 nm using an EnSpire Mulitmode plate reader (PerkinElmer, Waltham, United States). For normalization cell vitality was assessed using the alamarBlue assay (ThermoFisher, Waltham, United States) according to the manufacturer’s instructions.
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2

Glucose Uptake and Adipogenesis Assays

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3T3-L1 pre-adipocytes were grown and differentiated in 96-well plates (Greiner Bio-One) as previously described.22 The surrounding empty wells were filled with sterile 1X PBS to mitigate evaporation. After reaching 50% confluency, the cells were transfected with CD24 siRNA as described above. To measure glucose uptake, cells were washed with 40 µl of glucose-free serum-free (GS free media) DMEM followed by incubation with 100 μg/ml 2-(N-(7-Nitrobenz-2-oxa-1, 3-diazol-4-yl) Amino)-2-deoxyglucose (2-NBDG) (Cayman Chemical), a fluorescent glucose analog, in GS free media for 45 minutes at 37°C. Following 2-NBDG incubation, the wells were washed seven times with 1X PBS to remove excess 2-NBDG. Fluorescence was measured immediately using a Synergy Mx fluorescence plate reader (Biotek) at excitation and emission wavelengths of 480 and 550 nm, respectively. After obtaining 2-NBDG fluorescence, mature adipocytes (5 d post insulin treatment), were stained with 10 μg/ml Nile red (Santa Cruz Biotechnology Inc.) and fluorescence was measured on a Synergy Mx fluorescence plate reader at excitation and emission wavelengths of 520 and 580 nm, respectively.
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3

Quantifying Lipid Droplet Dynamics

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Cells were grown on glass coverslips, treated as required and fixed with 4% paraformaldehyde. Lipid droplets were visualized by staining with 0.1 μg/mL Nile Red (Santa Cruz) or HCS LipidTox green (1:200, Invitrogen H34475). For co-staining, cells were fixed with 4% paraformaldehyde, blocked for 1h in IF solution (PBS, 2% BSA, 0.1% Triton-X100), and incubated overnight with mouse a-myc (1:250, Cell Signaling 2276S), followed by donkey anti-mouse Alexa Fluor 594 secondary (1:400, Invitrogen R37115), donkey anti-rabbit Alexa Fluor 488 (1:400, Invitrogen A21206) and LipidTox green (1:200, Invitrogen H34475) for 1 hour at room temperature. Finally, cells were incubated with Hoechst 33342 nuclear stain for 5 minutes, and mounted with SlowFade Diamond antifade mounting media (Life Technology S36968). Slides were imaged on an Olympus FV3000 confocal microscope or a Zeiss Axioskope wide field microscope. Lipid droplet numbers and sizes were quantified with ImageJ and the particle counting plugin.
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4

Antifungal Activity Assay Protocol

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Pluronic F-127, RPMI-1640 medium with the addition of l-glutamine and without
sodium bicarbonate, PBS (phosphate-buffered saline), propidium iodide, and amphotericin B
were purchased from Sigma-Aldrich (USA). Nile red was obtained from Santa Cruz
Biotechnology (USA). Fluconazole and verapamil hydrochloride were obtained from Pol-Aura
(Poland). Sterile, purified water was purchased from Polpharma (Poland).
3-morpholinopropanesulfonic acid (MOPS) was purchased from J&K Scientific (China).
Mueller Hinton LAB-AGAR with glucose and methylene blue were both purchased from Biomaxima
(Poland). Sabouraud dextrose agar with chloramphenicol was purchased from Liofilchem
(Italy). Sabouraud dextrose liquid medium was purchased from Oxoid (Great Britain).
Tryptic soy broth was bought from Biomaxima (Poland). Zymo Research—YeaStar RNA Kit
was obtained from TK Biotech (Poland). The primers were ordered from Genomed (Poland). The
TranScriba Kit and the RT HS-PCR Mix Probe were supplied by A&A Biotechnology
(Poland).
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5

Nile Red Staining of P1-Treated Bacterial Cells

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Nile Red (Santa Cruz Biotechnology Inc., Dallas, TX) as a lipophilic stain was used to stain untreated and P1-treated cells according to the literature.77 ,78 (link) Briefly, cells (OD600 ~ 0.2) were treated with 0–100 μM of P1 in a shaker-incubator (1h, 37 °C, 250 rpm). The cell suspension was centrifuged (4700 rpm, 15 min) and the pellet was resuspended in 1 mL of 5 mM PBS buffer. A stock solution of 25 mM Nile Red in dimethylsulfoxide (DMSO; Alfa Aesar, Haverhill, MA) was prepared first, and 2 μL of this stock dye solution were added to the bacterial suspensions (untreated and P1-treated) to yield the final concentration of Nile Red as 50 μM in the suspension. The cells were incubated in the dye for 3 h, after which the cells were centrifuged, washed twice with 5 mM PBS and resuspended in the same buffer. For CLSM imaging, 10 μL of these cells were added to glass slides (Home Science Tools, Billings, MT) and covered with coverslips. A Nikon A1R-Ti2 confocal laser scanning microscope (Center for Biotechnology, Beadle center, UNL) with a 60x objective lens was used to image the samples. The Nile Red was excited with a 560 nm laser line and emission was collected from 570–620 nm.
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6

Quantifying Lipid Accumulation in Cells

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Lipid accumulation was determined by Nile Red (Santa Cruz biotechnology sc-203747). Cells (3 × 105 cells/well) were seeded in 6-well plate and treated with 0.5 mM FFA for 24 h. Cells were harvested and diluted 1 × 106 cells/ml. The diluted cells were stained with 0.125 μg/ml of Nile Red for 10 min at a 37℃ incubator. The stained cells were analyzed by BD Acuri C6 Plus (USA San Jose, CA, USA).
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7

Thyroid Cancer Cell Line Characterization

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The human TC cell lines TPC1 and 8505C, derived from PTC and ATC, respectively, were cultured with RPMI-1640 (Gibco, Thermo Scientific, MA, USA) medium containing 10% fetal bovine serum (FBS) (Gibco, Thermo Scientific, MA, USA) and 1% penicillin at 37 °C with 5% CO2. LY294002 (Biogems International, CA, USA), Lipofectamine 2000 (Invitrogen, CA, USA), Nile red (Santa Cruz Biotechnology, Texas, USA), G418 (GenePharma, Shanghai, China), puromycin (Gibco, Thermo Scientific, MA, USA), and polybrene (GenePharma, Shanghai, China) were also used in this study. The antibodies used were anti-PC (Santa Cruz Biotechnology, TX, USA), anti-SREBP1c (Affinity Biosciences, OH, USA), anti-FASN (Abcepta, CA, USA), anti-phospho-mTOR (Santa Cruz Biotechnology, TX, USA), anti-mTOR (Proteintech Group, IL, USA), and anti-phospho-Akt (Cell Signaling Technology, MA, USA). Antibodies against ACC1 (Proteintech Group, IL, USA), ACLY (Epigentek, NY, USA), E-cadherin (Affinity Biosciences, OH, USA), Vimentin (Affinity Biosciences, OH, USA), snail1 (Proteintech Group, IL, USA), ZEB2 (Proteintech Group, IL, USA), GAPDH (Beyotime Biotechnology, Shanghai, China), and α-Tubulin (Beyotime Biotechnology, Shanghai, China) were also used in this study.
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