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12 protocols using nanoparticle tracking analyzer

1

Isolation and Characterization of sEVs from MSCs

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The isolation of sEVs from MSCs was performed by ultracentrifugation as described previously [22 (link)]. Briefly, after 2–3 passages, when the cell reached 70% confluence, the complete culture medium of MSCs was replaced with DMEM/F12 containing 10% sEV-depleted FBS (SBI, USA). Forty-eight hours later, the culture medium was collected, centrifuged at 2000×g for 10 min and 10,000×g for 30 min at 4 °C to remove dead cells, cellular debris and apoptotic bodies. Then the supernatants were passed through a 0.22 μm membrane filters (Millipore, SLGP033RB) and centrifuged at 100,000×g for 75 min. Subsequently, the supernatants were discarded, and the pellet was resuspended in phosphate-buffered saline (PBS). The resuspensions were centrifuged again at 100,000×g for 75 min, and the deposition was resuspended with PBS for following application or stored at −80 °C.
Nanoparticle tracking analyzer (NTA) (Particle Metrix GmbH, Germany) and transmission electron microscope (TEM) (Hitachi, Japan) were used to measure the particle size and concentration of sEVs. Expression of the sEVs markers was determined by Western blot, including CD63, CD9, tumor susceptibility gene 101 (TSG101) and Calnexin.
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2

Characterization of Purified Small Extracellular Vesicles

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Well-established markers of purified sEVs were verified by western blot analysis. The following antibodies were used: anti-CD63 (1:1000 dilution, Cat No. 25682-1-AP, Proteintech), CD9 (1:2000 dilution, Cat No. 20597-1-AP, Proteintech), TSG101 (1:10,000 dilution, Cat No. 28283-1-AP, Proteintech), Alix (1:20,000 dilution, Cat No. 12422-1-AP, Proteintech), Calnexin (1:10,000 dilution, Cat No. 66903-1-Ig, Proteintech). The morphology of sEVs was examined by transmission electron microscope (TEM, H-7650C, Hitachi, Japan). Briefly, the purified sEVs were fixed in 4% paraformaldehyde (PFA), 10 µl of sEVs solution was dropped on the copper grid, incubated at room temperature for 10 min. After washing three times with sterile distilled water, 10 µl of 2% uranyl acetate was dropped on the copper grid for negative staining for 1 min, the floating liquid was absorbed by filter paper, and dried under an incandescent lamp for 2 min. Finally, the particle morphology was visualized by TEM at 80 kV. The size distribution and concentration of sEVs were measured using Nanoparticle tracking analyzer (NTA, Particle Metrix, Germany).
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3

Isolation and Characterization of Extracellular Vesicles from Fibroblasts

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Fibroblasts were derived from human foreskin explants and cultured in Dulbecco's Modified Eagle's Medium (DMEM, Gibco, USA, 11885092), The concentration of glucose in the culture medium was 5.5 mmol/L in normal glucose (NG) group, and 30 mmol/L in high glucose (HG) group. After 5 days, the cultured medium was collected every 48 h from passage 3 to passage 7. The supernatants of these cells were mixed together. EVs were collected from supernatant by a series of ultra-high-speed centrifugation procedures according to the steps reported in literatures (13 (link)).
The morphology of NG-EVs and HG-EVs was observed by transmission electron microscope (TEM) (Hitachi, Japan) and the particle size was measured by nanoparticle tracking analyzer (Particle Metrix GmbH, Germany). Expressions of EV positive markers CD63 (abcam, ab68418), TSG101 (abcam, ab133586), and negtive marker calnexin (abcam, ab133615) were analyzed by Western blot. A brief step of uptake assay is as follows. The membrane of EVs was labeled with PKH67 (green). HUVECs were counterstained by actin (cytoskeleton, red) and DAPI (cell nucleus, blue). The internalization process was observed under confocal microscope (Leica, Germany).
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4

Isolation and Characterization of Exosomes

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Exosomal fetal bovine serum (FBS) was generated by centrifuging FBS at 100,000 × g for 16 h, as described previously [42 (link)]. Exosomes were obtained from the supernatant of hAMSCs or SCLCs at ~80% confluence after replacing the complete medium with exosomal FBS for 24 h. The supernatants were then centrifuged at 300 × g for 10 min, 2000 × g for 10 min and 10,000 × g for 30 min. Subsequently, exosomes were collected by ultracentrifugation at 100,000 × g for 70 min, resuspended in phosphate-buffered saline (PBS) and stored at −80°C. Exosome morphology and size were examined using a transmission electron microscope and a nanoparticle tracking analyzer (ZetaView_Particle Metrix, Germany), respectively. Expression of exosome protein markers was determined via WB analysis using antibodies against CD9, CD63 and TSG101 (Abcam, USA).
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5

Exosome Diameter Measurement Protocol

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Exosome suspensions were collected after adding 10 μL of 10% glycine to 10 μL vesicles in 90 μL buffer, diluted with PBS to a final ratio of 1:200, and lysed with mammalian protein extraction reagent (Millipore, Billerica, MA, USA). Exosome diameters (nm) were calculated using a Nano Particle tracking analyzer (ZetaVIEW S/N 17-310, Particle Metrix, Germany).
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6

Nanoparticle Tracking Analysis of EVs

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The particle size and concentration were measured using a ZetaView® (Particle Metrix) Nanoparticle Tracking Analyzer following the manufacturer's instruction. EVs were diluted in PBS between 100- and 1000-fold to obtain a concentration within the recommended measurement range (0.5X105 to 1010 cm-3).
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7

Exosome Size and Zeta-Potential Analysis

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The size and zeta-potential of exosomes were examined by the Nanoparticle Tracking Analyzer (Particle Metrix GmbH, Germany) with the corresponding ZetaView® software [13 (link)]. This instrument tracked the Brownian motion of particles over time and subsequently calculated particle sizes.
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8

Isolation and Characterization of Gram-Negative OMVs

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After culturing bacteria for 16–18 h at 37°C, bacteria were removed by centrifugation (8000 g, 10 min, 4°C), and the supernatant was filtered with a 0.22-μm filter (Merck Millipore, Darmstadt) to remove the remaining bacteria. OMVs were harvested by ultracentrifugation (150,000 g, 1.5 h, 4°C) and suspended in PBS for storage at -80°C until used. OMV size was measured by capturing images at 11 positions by a Nanoparticle Tracking Analyzer (Particle Metrix GmbH, Meerbusch) and analyzed using the ZetaView 8.02.31 software. OMV morphology was observed through a transmission electron microscope (Hitachi H-7500, Tokyo). A limulus amebocyte lysate chromogenic endotoxin quantitation kit (Thermofisher, Waltham) was used to check the LPS content present in Gram-negative OMVs.
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9

Isolation and Characterization of Renal Cancer Stem Cells and Small Extracellular Vesicles

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Human RCC cell lines A498, 786-O, OS-RC-2, ACHN, and SW839, and the human renal tubular epithelial cell line HK2 were obtained and cultured according to the instructions and previous research (30 (link)). RCSCs were isolated as described earlier (31 (link)), and their morphology was observed. A single sp was transplanted to a new T25 flask and proliferated stably. Then, RCSCs were identified by Western blot (WB) and real-time quantitative polymerase chain reaction (RT-qPCR). sEVs were isolated as previously reported, including in our earlier study (32 (link)-34 (link)). Details of the operations are described in the Appendix 1. The obtained sEVs were placed under a transmission electron microscope (TEM, Hitachi H-7650) to morphological observation and evaluation. A Nanoparticle Tracking Analyzer (Particle Metrix, Germany) was used to determine the size and distribution of the sEVs. WB was applied to detect the sEVs marker proteins.
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10

Nanoparticle Tracking Analysis of EVs

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The particle size and concentration were measured using a ZetaView® (Particle Metrix) Nanoparticle Tracking Analyzer following the manufacturer’s instruction. The following parameters were used for measurement: (Post Acquisition parameters (Min brightness: 22, Max area: 800, Min area: 10, Tracelength: 12, nm/Class: 30, and Classes/Decade: 64)) and Camera control (Sensitivity: 85, Shutter: 250, and Frame Rate: 30)). EVs were diluted in PBS between 20- and 200-fold to obtain a concentration within the recommended measurement range (0.5 × 105 to 1010 cm−3).
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