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104 protocols using filipin 3

1

Filipin III Labeling of CEMM

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Filipin III (Sigma, F4767) was used to label CEMM as reported previously.96 The cells seeded on coverglass slide changers were treated and fixed with 4% paraformaldehyde for 30 min and quenched in 50 mM NH4Cl3 for 10 min. Then the solution, which contained 0.2% BSA (Sigma, A7906), 0.2% fish skin gelatin (Sigma, G7041), and 50 μM of Filipin III was used to block, permeabilize, and stain the cells. After 20 min incubation at room temperature, PBS was used to wash the cells (3 times for 5 min). For combination with immunostaining, the Filipin-stained cells were followed by incubation of the indicated primary and secondary antibodies. Confocal microscopy was used to detect the signals.
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2

Cholesterol Colocalization with Mitochondria

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Cholesterol was stained by filipin III in cells fixed with paraformaldehyde. For the observation on colocalization of cholesterol and mitochondria, cells were incubated with mitotracker deep red (25 nM) for 30 min before fixation. Fixed cells were incubated with 50 μg/ml filipin III (SAE0088, Sigma, MO, USA) at room temperature for 1 h. The emission/excitation of filipin III were 340–380/385‐470 nm. Cells were screened with Perkin‐Elmer high‐content automatic imaging system (40× air or 63× water objective) in confocal mode, and the results were analyzed by Perkin‐Elmer Harmony image analysis software.
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3

Visualization of Lipid Droplets and Membrane Cholesterol

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Adherent mNSC cells plated on 35 mm glass bottom dishes (#D35-20-1.5-N; Cellvis) were fixed with 4% PFA for 10 min and washed three times with PBS. Fixed cells were stained with 1 µg/ml Nile Red (#N1142; Invitrogen) or 50 µg/ml Filipin III (#F4767; Sigma-Aldrich). Filipin III was reconstituted with anhydrous DMSO (#276855; Sigma-Aldrich) at 2 mg/ml and used either the same day or within 2 wk (stored immediately after DMSO reconstitution at −80°C). Since Filipin III is very unstable and bleaches rapidly, cells were stained one sample at a time with Filipin III freshly diluted to 50 µg/ml in PBS containing 500 nM nuclear counterstain siR-DNA (#CY-SC007; Cytoskeleton, Inc.) for 45 min in the dark at room temperature. Cells were washed once with 1.5 ml PBS and imaged immediately. Alternatively, fixed cells were stained with Nile Red (#N1142; Thermo Fisher Scientific) for 20 min at 37°C in PBS, nuclei counterstained with 6 μg/ml Hoechst-33342 (#H1399; Thermo Fisher Scientific), washed three times with PBS, and imaged in PBS.
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4

Lipid and Cholesterol Content Analysis

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To determine fatty acid uptake, cells were cultured in RPMI medium containing 0.5 μM of BODIPY 500/510 C12 (Life Technologies) at 37 °C for 15 min and then washed with FACS buffer for surface staining. For detection of lipid content and cholesterol content, after permeabilization and fixation, cells were stained using BODIPY 493/503 (Life Technologies) at a final concentration of 2 μM for measuring lipids or with Filipin III (Sigma) at a final concentration of 20μg/ml for measuring cholesterol content, together with other intracellular proteins.
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5

Quantifying Lipid Rafts in Cultured Cells

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A total of 3 × 104 cultured cells were preseeded in 24-well plates. Then, the cells were harvested, fixed with 4% paraformaldehyde and incubated with 0.05 mg/ml filipin III (Sigma, F4767) working solution for 2 h at room temperature. Then, the cells were sealed with SYTOX Deep Red stain (Invitrogen, P36990). This dye is excited by red light at 660 nm when bound to DNA and has an emission maximum at 682 nm; we detected these signals using a Cy5/deep red traditional filter. filipin III staining of cells was visualized with a Leica DMI6000 B microscope at excitation wavelengths of 340–380 nm and emission wavelengths of 385–470 nm. The quantification of Filipin staining was performed by ImageJ (v1.8.0).
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6

Immunostaining of LDLR in Cells

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Cells were transfected and cultured as described above then fixed with 3% paraformaldehyde (PFA) at room temperature for 20 min, washed with PBS, incubated with 30 mM glycine for 5 min and washed again with PBS. For LDLR staining cells were permeabilized with 0.05% Filipin III (Sigma #F4767) in 10% FCS for 30 min at room temperature. Primary antibody: rabbit monoclonal anti-LDLR (Fitzgerald #20R-LR002) was diluted 1:100 in 5% FCS overnight at 4 °C. Secondary antibody: goat polyclonal goat anti-rabbit IgG Alexa 568 (Invitrogen #A11011) was diluted 1:400 in 5% FCS. Fixed cells were imaged using a Zeiss LSM 780 confocal microscope using a 63×/1.4NA oil immersion objective. For plasma membrane LDLR staining, cells were not permeabilized, but directly stained for 1 hour at 4 °C with antibody recognising the extracellular part of LDLR, namely, mouse anti-LDLR-C7 antibody (Progen #61087) diluted 1:100 in PBS. As a secondary antibody, we used chicken anti-mouse IgG Alexa 488 (Invitrogen #A-21200) diluted 1:400. Cells were imaged on an Olympus FluoView 3000 confocal microscope using 60×1.3NA silicon oil immersion objective.
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7

Evaluating EGFR Signaling Dynamics

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Gefitinib (AstraZeneca), Phenylarsine Oxide (PAO) (Sigma‐Aldrich), Filipin III (Sigma‐Aldrich), anti‐EGFR (sc‐373746), anti‐EGFR (4267, Cell signaling), anti‐p‐EGFR (2234, Cell signaling), anti‐STAT3 (sc‐8019), anti‐p‐STAT3 (sc‐8059), anti‐ERK (9102, Cell signaling), anti‐p‐ERK (9101, Cell signaling), anti‐EEA1 (610457, BD Biosciences), anti‐PARP (9542, Cell signaling), anti‐c‐Myc (9402, Cell signaling), anti‐β‐actin (A5316), Goat anti‐mouse IgG (H + L)‐HRP conjugate (1706516, Bio‐Rad), Goat anti‐rabbit IgG polyclonal HRP conjugated (ADI‐SAB‐300, Enzo), Alexa Fluor 488 goat anti‐rabbit antibody (A32731, Thermo Fisher Scientific), and Alexa Fluor 594 goat anti‐mouse antibody (A32742, Thermo Fisher Scientific).
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8

Cholesterol Trafficking Inhibition Assay

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Cell culture media and reagents were purchased from Thermo Fisher Scientific (Waltham, MA, USA). These include Dulbecco’s modified Eagle’s medium (DMEM), fetal bovine serum (FBS), and penicillin/streptomycin. A CellTiter 96 Aqueous One Solution Cell Proliferation Assay System was purchased from Promega (Madison, WI, USA). U18666A, Filipin III, 2-hydroxypropyl-β-cyclodextrin (HPβCD) and 2-hydroxypropyl-γ-cyclodextrin (HPγCD) were obtained from Sigma-Aldrich (St. Louis, MO, USA). Primary antibodies used in this study are as follows: rabbit polyclonal antibody for mCherry (Abcam ab183628); rabbit monoclonal antibody for GAPDH (Cell Signaling #5174).
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9

Fatostatin Modulates Lipid Metabolism

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Fatostatin (4-[4-(4-methylphenyl)-1,3-thiazol-2-yl]-2-propylpyridine hydrobromide) was purchased from Chembridge Corporation and its chemical structure was described in Supplementary Fig. S1. Ribonuclease A, propidium iodide (PI), Oil Red O and Filipin III were purchased from Sigma-Aldrich. Annexin V-fluorescein isothiocyanate (FITC) Apoptosis Detection Kit I and Matrigel Basement Membrane Matrix were purchased from BD Bioscience. The Free Fatty Acid Quantification Kit and Cholesterol/Cholesterol Ester Detection Kit were obtained from Abcam. pHMGCoASyn-Luc construct was obtained from Dr. Hitoshi Shimano of Tsukuba University. pFASN-700-Luc and pFASN-700-mutSRE-Luc constructs were obtained from Dr. Timothy F. Osborne of Sanford-Burnham Medical Research Institute. pLDLR-Luc and pLDLR-mutSRE constructs were obtained from Addgene (Cambridge, MA).
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10

Curcumin-Loaded PLGA Nanoparticle Synthesis

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Curcumin (95% purity) was obtained from Alfa Aesar (Ward Hill, MA, USA); PLGA (Resomer RG 503 H) was supplied by Evonik (Essen, Germany); poly(vinyl alcohol) (PVA, Mowiol 4-88) was purchased from Kuraray (Hattersheim, Germany); polysorbate 80 (Tween 80), 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), 2’,7’-dichlorofluorescin diacetate (DCFDA) and tert-butyl hydroperoxide (TBHP) were obtained from Sigma-Aldrich Chemie (Taufkirchen, Germany). Inhibitors of cellular uptake, viz. Filipin III, chlorpromazine and dynasore were also obtained from Sigma Aldrich. Ultrapure water, generated by a PURELAB flex 4 device (ELGA LabWater, High Wycombe, UK) was used for all experiments. For cell culture studies, ultrapure water was additionally autoclaved and filter-sterilised using 0.2 μm polyethersulphone membrane filters (Sarstedt, Nümbrecht, Germany) prior to use. HPLC-grade ethyl acetate (VWR, Darmstadt, Germany) was used to prepare the organic phases. All other chemicals used were of analytical grade. All buffers used in this study were prepared in the laboratory, unless stated otherwise.
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