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26 protocols using flotillin 1

1

Lipid Raft Isolation from Brain and Cells

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For lipid raft isolation [32 (link)], cerebral cortex, cerebellum, N2a cells were homogenized in lysis buffer (25 mM Tris-HCl pH 8, 140 mM NaCl, 1% Triton X-100, 1 mM EDTA (EDS, Sigma-Aldrich), supplemented with 1 mM PMSF (Sigma-Aldrich), 1 mM Na3VO2, 10 mM NaF, and 1X Protease Inhibitor Cocktail. Lysates were homogenized through a 22G needle. Samples were adjusted to 40% Optiprep (Sigma-Aldrich) and loaded at the bottom of tubes (Quick-Seal® Polypropylene Tube, Beckman Coulter Inc., Brea, CA). A discontinuous gradient was layered on the top (30% and 5% Optiprep in lysis buffer). Samples were centrifuged at 400,000g/4h, 4μC, VTi 65.2 rotor. Fractions of 500 μl (8-9 fractions) were analyzed for lipid-raft microdomains by immunobloting for flotillin-1 (1:1000, Cell Signaling Technology, Danvers, MA) and caveolin-1 (1:1000, BD Bioscience, San Jose, CA) [33 (link)] (Supplementary Material Figure 3).
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2

Exosomal Surface Marker Expression

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Expression of exosomal surface markers on the ExoQuick-isolated exosomes was detected by western blotting, in triplicate. Serum samples were used as a negative control. Exosome samples from the blood of CLP and sham mice were lysed, and the total proteins were separated by polyacrylamide gel electrophoresis (PAGE) and electrotransferred to polyvinylidene fluoride (PVDF) membranes (Millipore, Billerica, MA, USA). The membranes were blocked with 5% skim milk in PBS/Tween-20 and incubated with primary antibodies against CD9 (cat # ab92726, 1:1000; Abcam, Cambridge, MA, USA), TSG101 (cat # ab30871, 1:1000; Abcam), Flotillin-1 (cat # 18634, 1:1000; Cell Signaling Technology, Danvers, MA, USA), CD81 (cat # ab109201, 1:1000; Abcam), and Calnexin (cat # ab22595, 1:1000; Abcam) at 4°C overnight. The PVDF membranes were washed with 0.1% TBS/Tween 20 for 10 min, three times at room temperature and incubated with horseradish peroxidase (HRP)-conjugated secondary antibodies (cat # NA931; GE Healthcare Amersham, Piscataway, NJ, USA) for 2 h at room temperature, and the detected proteins were quantified using a FluorChem SP imaging system (Alpha Innotech, San Leandro, CA, USA).
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3

EV Protein Characterization by Western Blot

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Protein lysates obtained from EVs isolated by UCF, scUCF, Vn96, ME buffer and Scr peptide (from Fig. 1a, Step 6ii) were separated by sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE) and analyzed by Western blotting using the BioRad mini-gel system for canonical EV protein markers as well as Calnexin, an endoplasmic reticulum protein that is not localized in EVs. All antibodies were supplied by Santa Cruz Biotechnology (Dallas, TX) except for antibodies to Flotillin-1 (Cell Signaling Technologies; cat # 18634S) and Calnexin (Abcam, cat # 22,595). Santa Cruz antibodies included CD63 (sc-5275), CD9 (sc-59140), and HSC70 (sc-7298). All primary antibodies were incubated overnight at 4 °C in 5% milk/PBS at a dilution of 1:1,000, with the exception of HSC70 which was used at a dilution of 1:500. Goat anti-rabbit and goat anti-mouse secondary antibodies were purchased from Jackson ImmunoResearch Inc. and used at 1:10,000. Clarity Western ECL blotting substrate (Bio-Rad, Hercules, CA) was used for Western blot detection.
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4

Investigating Mitochondrial and Cell Signaling

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PKH67 was purchased from Sigma, MitoTracker deep red and CellLight™ Mitochondria-RFP, BacMam 2.0 were obtained from ThermoFisher. Growth Factor Reduced Matrigel was obtained from BD Biosciences (BD No. 354230). Antibodies to Ser616-phosphohry lated Drp1, Drp1, MFN1, MFN2, Ser473-phosphorylated AKT, Thr308-phosphorylated Akt, Akt, EGFR, MMP9, ILK, HIF1α, Calnexin, VDAC, Flotillin 1, E-cadherin, Vimentin, SNAIL, Ki67, cleaved-Caspase 3, phosphorylated Ezrin-Radixin-Moesin (pERM) complex were obtained from Cell Signaling. An antibody to hDlg was from Santa Cruz. An antibody to Tsg101 was from ProteinTech. Antibodies to CD63 and CD9 was from Abcam. An antibody to β-actin was from Sigma. The Akt inhibitor MK2206 (1 μM) was purchased from Selleck Chemicals and ILK inhibitor Cpd22 (600 nM) was purchased from Sigma.
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5

Extracellular Vesicle Protein Analysis

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The extracellular vesicles were lysed with RIPA lysis and extraction buffer (Thermo Fisher Scientific, Waltham, MA, USA), 1X protease cocktails, and phenylmethylsulfonyl fluoride (Sigma-Aldrich, Burlington, MA, USA). Denatured proteins were mixed with NuPAGE LDS Sample Buffer (Invitrogen, Waltham, MA, USA) and β-mercaptoethanol, and then heated at 95°C for 5 min. Proteins were electrophoresed on Bolt Bis-Tris Plus gels (Invitrogen) and electroblotted onto polyvinylidene difluoride (PVDF) membranes. The membranes were blocked and incubated overnight at 4°C with the following primary antibodies: flotillin-1, CD9 (Cell Signaling Technology, Danvers, MA, USA), CD81 (Novus Biologicals, Centennial, CO, USA), and β-actin (Santa Cruz Biotechnology, Dallas, TX, USA). The membranes were then washed four times with PBS-T. Immunoblots were visualized using SuperSignal West Femto Maximum Sensitivity Substrate (Thermo Fisher Scientific) and ImageQuant LAS4000 mini (GE Healthcare, Chicago, IL, USA).
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6

Exosome Protein Profiling by Western Blot

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Cells and exosomes were lysed with radioimmunoprecipitation assay (RIPA) buffer (Beyotime) containing phenylmethylsulfonyl fluoride. The protein concentration was determined using the BCA Protein Assay Kit (Pierce) following the manufacturer's instructions. The samples were analyzed by sodium dodecyl sulfate (SDS)-PAGE, transferred to polyvinylidene fluoride membranes (Millipore, Billerica, MA, USA), and incubated first with primary antibodies targeting Hes1, CD9, Alix, flotillin-1 (Cell Signaling Technology), HEY1, β-actin (Proteintech, Wuhan, China), and VDAC1 (Abcam, Cambridge, UK) and then with HRP-conjugated goat anti-mouse or anti-rabbit IgG secondary antibodies (Zhuangzhi Bio, Xi'an, China).
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7

Western Blot Analysis of Proteins

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Culture supernatants and cell lysates were analyzed by western blotting. Proteins in these samples were separated by SDS-PAGE (under reducing and non-reducing conditions) and then transferred to polyvinylidene difluoride membranes. Antibodies to the following proteins were used as primary antibody to detect them: HRF (anti-TPT1 mAb clone 2C4, Catalog #, H00007178-M03) from Abnova was used unless otherwise depicted), Flotillin-1, CD9, Annexin, and CD54 (Cell Signaling Technology). Horseradish peroxidase-linked anti-mouse IgG Ab and Horseradish peroxidase-linked anti-rabbit IgG Ab were used as secondary antibody.
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8

Exosome Protein Quantification and Analysis

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The BCA method was used to quantify exosome protein, and the concentration of the exosome protein was adjusted according to the quantitative results. Diluted exosomes were added to sodium dodecyl sulfate buffer and boiled for western blot analysis. In this study, 10% separating gel was used. The gel and electrodes were assembled in the SDS-PAGE chamber. Next, 20 µl sample per well was loaded onto a 10% acrylamide gel for electrophoresis running at 120 V until the bromophenol blue front ran out of the gel. Proteins on the gels were transferred to nitrocellulose or polyvinylidene fluoride membranes and detected by immunoblotting. Primary antibodies against CD54, HSP70, Flotillin-1, and GM130 were obtained from Cell Signaling Technology (Danvers, Massachusetts, USA). Secondary antibodies were rabbit-anti-mouse (Dako, Carpinteria, CA, USA) or HRP-conjugated goat anti-rabbit (Santa Cruz) antibodies.
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9

Western Blot Analysis of Cell Signaling Proteins

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Western blot was performed as we recently described [21 (link), 26 ]. Primary antibodies raised against SRSF1 (Santa Cruz, sc-33,652), EIF3B (Santa Cruz, sc-137,214), TIA1 (Santa Cruz, sc-166,247), beta-actin (A5441), and Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) (Santa Cruz, sc-47,724) were used for detection. Nuclear and cytoplasmic protein extraction was extracted following ROCKLAND Nuclear & Cytoplasmic Extract Protocol [34 (link)], and verified by Histone-H3 (CST, 4499S) and GAPDH (Santa Cruz, sc-47,724) detection. Antibodies used for exosome marker detection include: CD63, CD81 (Santa Cruz Bio Technology Inc., CA, USA), Flotillin-1 and Calnexin (Cell Signaling Technology, Inc., MA, USA).
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10

Exosome Purity and Protein Contamination Analysis

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Exosome purity and protein contamination were determined by Western blot for exosome-specific proteins Flotillin-1 and CD9 and plasma protein stain Ponceau S. Briefly, Western blots were conducted by taking an aliquot of fractions 4 to 12 of the final density gradient; 37.5 μL of each fraction was mixed with 4 × Laemmli buffer containing 2-mercaptoethanol. The sample was boiled at 95°C for 5 minutes and resolved by sodium dodecyl sulfate-polyacrylamide gel electrophoresis on a 10% gel. The gel was transferred onto a polyvinylidene difluoride membrane using a standard tank protocol. The membrane was stained with 0.1% w/v Ponceau S to visualize total protein, followed by a 1-hour block in 5% nonfat milk. The membrane was probed with CD9 (Abcam, Cambridge, Mass) and Flotillin-1 (Cell Signaling Technology, Danvers, Mass) in 1% nonfat milk. The primary antibodies were used at a dilution of 1:500. The membrane was washed with 0.1% PBS-T detergent and probed with an anti-rabbit horseradish peroxidase antibody (1:1000 dilution; ThermoFisher Scientific, Waltham, Mass). Subsequently, the membrane was rewashed with 0.1% PBS-T and visualized using enhanced chemiluminescence on an ImageQuant LAS 4000 (GE Healthcare Life Sciences, Marlborough, Mass).
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