This work was supported by the Scientific Research Fund of Zhejiang Chinese Medicine University (2020ZG29), the Basic Public Welfare Research Project of Zhejiang Province (LGF19H150006, LTGY23B070001), the Project of Zhejiang Provincial Department of Education (Y202147028) and the Project of Experimental Technology of Zhejiang University Laboratory Department (SJS201712, SYB202130).

1. Cell culture
<ol>
	<li>Prepare a culture medium of Dulbecco&#39;s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS). Culture the human pancreatic cancer cell, PANC-1, in a 75 cm2 culture flask at a density of 1 x 106 cells/mL. Incubate the culture at 37 &#176;C with 5% CO2.</li>
	<li>Subculture the cells when cell density reaches 75%-80% under microscopic observation. Remove the medium, and rinse 2x with 3-5 mL of phosphate buffer saline (PBS; 0.01 M, pH 7.2-7.4).</li>
	<li>Discard the solution, add 1-2 mL of trypsin-EDTA solution, and let the cells detach until they become rounded and suspended in the medium under the microscope. Add fresh medium, aspirate, and disperse into 75 cm2 culture flasks with 15 mL culture medium. Use a sub-cultivation ratio of 1:2 to 1:4 (recommended). 
	&#8203;NOTE: All operations are performed in a biosafety cabinet to avoid cell contamination.</li>
</ol>
2. Culture medium collection
<ol>
	<li>Incubate the cells for 48 h at 37 &#176;C with 5% CO2. Collect cell supernatant (90 mL) in two 50 mL centrifuge tubes and centrifuge at 300 x g for 10 min at 4 &#176;C.</li>
	<li>Transfer the supernatant to new sterile tubes and centrifuge successively at 2,000 x g for 20 min, 10 000 x g for 30 min, and 12,000 x g for 70 min at 4 &#176;C.</li>
	<li>Remove the supernatant and rinse the pellet with 10 mL of PBS by pipetting gently. Centrifuge at 12,000 x g for 70 min at 4 &#176;C again and resuspend the pellet in 10 mL of PBS buffer to obtain a mixture of EVs.</li>
	<li>Perform nanoparticle tracking analysis (NTA) to quantify and size the EV mixture. Perform the NTA analysis according to the instrument operation reference manual and reference21.</li>
</ol>
3. Cell sorting
<ol>
	<li>Perform the standard startup procedure of the flow cell sorter. Turn ON the machine by pressing the Startup button. Click the Laser Power button on the laser control panel. Press the Change Tanks button in the smart sampler submenu to pressurize the fluidics. 
	NOTE: Ensure that the waste tank is empty, and the sheath tank is full before starting up.</li>
	<li>Use an ultrasonically cleaned 50 &#181;m jet-in-air nozzle and install it onto the nozzle assembly. Adjust the pressure to 80 psi for sheath fluid and 80.3 psi for sample flow on the pressure console.</li>
	<li>Press the Start Sheath Flow button to start the sheath stream flowing. Click the Bubble Button in the smart sampler submenu to automatically debubble for 10 min and then turn it off. 
	NOTE: For cell sorting, different sizes of air spray nozzles require different sheath fluid pressures to maintain liquid flow stability. In this method, a nozzle of 50 &#181;m was used, and only a sheath fluid pressure greater than or equal to 80 psi could generate stable side streams. The pressure difference between the sample flow and the sheath fluid determines the loading speed of sorting. Under the setting condition of the method (the pressure difference between the sample flow and the sheath fluid is 0.3-0.6 psi), the liquid flow was relatively stable, and the loading speed enabled the sorting efficiency to increase to 80% from 50% for pressure difference less than 0.3-0.6 psi.</li>
	<li>Align the stream and determine the laser spot. Turn ON the illumination chamber light to view the stream over the pinholes. Adjust the up-and-down, left-and-right, and front-and-back micrometers to center the stream on the pinhole and focus the stream.</li>
	<li>Select the Laser and Stream Intercept tab. Press the Green Arrow button continuously as prompted to complete the laser intercept and nozzle alignment calibration process.</li>
	<li>Access the fine laser alignment screen. Select 640-722/44 (H) channel as the X-axis parameter and 405-448/59 (H) channel as the Y-axis parameter. Press the Trigger Parameter Selector and choose the SSC Parameter of the 488 nm laser. Open all laser shutters. 
	NOTE: The X-axis and Y-axis parameters chosen depend on the laser configuration of the system. Other parameters are allowed if the system does not have a 640 nm or 405 nm laser. For best results, select lasers with the greatest spatial separation on the pinhole strip (not including the 355 nm laser).</li>
	<li>Dilute the rainbow fluorescent particles by adding one drop into 1 mL of double distilled water for a final concentration of 1 x 106 beads per mL. Open the door of the sample chamber and load a tube of the prepared rainbow fluorescent particles.</li>
	<li>Press the Start Sample button. Adjust up-and-down micrometers to optimize fluorescence intensity, making each signal as intense as possible. Press the Start Quality Control (QC) button on the touchscreen control panel to perform QC automatically.</li>
	<li>Perform drop delay. Access the sort setup screen and select the drop delay button. Press the IntelliSort Initialization button. The instrument automatically adjusts the frequency and amplitude of droplet oscillation to obtain the drop delay of 25 &#177; 5 and be able to visualize the break-off point of the drop clearly. Press the Maintain button.</li>
	<li>Select tube as the sort output type. Place a 15 mL tube holder in the sort chamber. Turn the plate voltage ON and set the plate voltage to approximately 4000 V.</li>
	<li>Turn on the test pattern by selecting the Stream Setup button. Adjust the charge phase slider and deflection slider to ensure that the image of the stream is lined up with the collection tube. Select the Check Mark button.</li>
	<li>Log in to the Summit workstation on the computer. Create a new protocol from the File main menu. Create a dot plot by selecting the Histogram tab in the Summit software control panel.</li>
	<li>Right-click the axes of the new dot plot in the workspace and choose FSC as the X-axis parameter and SSC as the Y-axis parameter. Present the FSC and SSC in logarithmic form.</li>
	<li>Select the Acquisition tab and locate the acquisition parameters panel. Enable all signals in the submenu of enabling parameters. Choose FSC as the trigger parameter and set the threshold of 0.01. Adjust the voltage and gain of FSC and SSC at 250 and 0.6 to ensure events within the FSC vs. SSC plot and populations are separated. 
	&#8203;NOTE: Threshold setting is equivalent to setting the particle size that can be detected by flow cytometry. The larger the threshold is, the larger the detected particles will be, and the small particles will be cut off by the threshold and cannot be detected. In this method, the threshold is set to 0.01, so all particles larger than electronic noise can be detected.</li>
</ol>
4. Isolation of sEV
<ol>
	<li>Dilute the fluorescent polystyrene microspheres to suspensions of 100 nm, 200 nm, and 300 nm. Add 1 &#181;L of microspheres to 1 mL of double distilled water.</li>
	<li>Load the microsphere suspension successively. Select Start under the acquisition menu of summit software and record 20,000 events. 
	NOTE: The number of events is optional. No less than 5,000 events are recommended to meet statistical significance.</li>
	<li>Right-click on the FSC vs. SSC dot plot to create rectangles and drag to resize and reposition the regions of electronic noise and 100 nm microsphere population. Right-click on the regions to rename them as R7 and R4, respectively. Repeat the above steps to frame the 200 nm and 300 nm microspheres with rectangles successively and rename them as R5 and R6, respectively.</li>
	<li>Finally, determine the 50-200 nm sorting region based on the electronic noise and the position of 200 nm particles defined as R8. 
	NOTE: The lower detection limit of 50 nm is placed just above the electronic noise of the flow cell sorter. The region between the noise and the 200 nm microsphere population can therefore be defined to be between 50-200 nm.</li>
	<li>Edit sort decisions in the sort logic and statistics panel. Double-click on the blank field of the left one (L1) stream. Select the region named R8 to create the sort logic. Choose the Abort mode of purity and select a droplet envelope of 1 drop for the L1 stream.</li>
	<li>Load 500 &#181;L sample of EVs mixture from step 2.3. Press the Start button under the acquisition menu in Summit to acquire data, and then press Start in the sort menu to collect 50-200 nm sEV into a 15 mL centrifuge tube. 
	NOTE: A sterile environment is necessary to minimize contamination during any procedure.</li>
	<li>Observe the presence of sEV by transmission electron microscopy (TEM) and verify the particle size of sEV using NTA. Perform western blot (WB) analysis to further confirm the expression of CD9, CD63, and CD81 markers18.</li>
</ol>

<ol>
	<li>Raposo, G., Stoorvogel, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Extracellular+vesicles:+exosomes,+microvesicles,+and+friends.">Extracellular vesicles: exosomes, microvesicles, and friends.</a> Journal of Cell Biology. 200 (4), 373-383 (2013).</li><li>Meldolesi, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Exosomes+and+ectosomes+in+intercellular+communication.">Exosomes and ectosomes in intercellular communication.</a> Current Biology. 28 (8), 435-444 (2018).</li><li>Andaloussi, S. E. L., M&#228;ger, I., Breakefield, X. O., Wood, M. J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Extracellular+vesicles:+biology+and+emerging+therapeutic+opportunities.">Extracellular vesicles: biology and emerging therapeutic opportunities.</a> Nature Reviews: Drug Discovery. 12 (5), 347-357 (2013).</li><li>Smith, Z. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single+exosome+study+reveals+subpopulations+distributed+among+cell+lines+with+variability+related+to+membrane+content.">Single exosome study reveals subpopulations distributed among cell lines with variability related to membrane content.</a> Journal of Extracellular Vesicles. 4, 28533 (2015).</li><li>Kalluri, R., LeBleu, V. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+biology,+function,+and+biomedical+applications+of+exosomes.">The biology, function, and biomedical applications of exosomes.</a> Science. 367 (6478), (2020).</li><li>Doyle, L. M., Wang, M. Z. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Overview+of+extracellular+vesicles,+their+origin,+composition,+purpose,+and+methods+for+exosome+isolation+and+analysis.">Overview of extracellular vesicles, their origin, composition, purpose, and methods for exosome isolation and analysis.</a> Cells. 8 (7), 727 (2019).</li><li>Cvjetkovic, A., L&#246;tvall, J., L&#228;sser, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+influence+of+rotor+type+and+centrifugation+time+on+the+yield+and+purity+of+extracellular+vesicles.">The influence of rotor type and centrifugation time on the yield and purity of extracellular vesicles.</a> Journal of Extracellular Vesicles. 3, 23111 (2014).</li><li>Zeringer, E., Barta, T., Li, M., Vlassov, A. V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Strategies+for+isolation+of+exosomes.">Strategies for isolation of exosomes.</a> Cold Spring Harbor Protocols. 2015 (4), 319-323 (2015).</li><li>Muller, L., Hong, C. S., Stolz, D. B., Watkins, S. C., Whiteside, T. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+biologically-active+exosomes+from+human+plasma.">Isolation of biologically-active exosomes from human plasma.</a> Journal of Immunological Methods. 411, 55-65 (2014).</li><li>Taylor, D. D., Shah, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Methods+of+isolating+extracellular+vesicles+impact+down-stream+analyses+of+their+cargoes.">Methods of isolating extracellular vesicles impact down-stream analyses of their cargoes.</a> Methods. 87, 3-10 (2015).</li><li>Coughlan, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Exosome+isolation+by+ultracentrifugation+and+precipitation+and+techniques+for+downstream+analyses.">Exosome isolation by ultracentrifugation and precipitation and techniques for downstream analyses.</a> Current Protocols in Cell Biology. 88 (1), 110 (2020).</li><li>Yang, D., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=and+perspective+on+exosome+isolation+-+efforts+for+efficient+exosome-based+theranostics.">and perspective on exosome isolation - efforts for efficient exosome-based theranostics.</a> Theranostics. 10 (8), 3684-3707 (2020).</li><li>Shao, H., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Chip-based+analysis+of+exosomal+mRNA+mediating+drug+resistance+in+glioblastoma.">Chip-based analysis of exosomal mRNA mediating drug resistance in glioblastoma.</a> Nature Communications. 6, 6999 (2015).</li><li>Zarovni, N., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Integrated+isolation+and+quantitative+analysis+of+exosome+shuttled+proteins+and+nucleic+acids+using+immunocapture+approaches.">Integrated isolation and quantitative analysis of exosome shuttled proteins and nucleic acids using immunocapture approaches.</a> Methods. 87, 46-58 (2015).</li><li>Sidhom, K., Obi, P. O., Saleem, A. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Review+of+exosomal+isolation+methods:+is+size+exclusion+chromatography+the+best+option.">Review of exosomal isolation methods: is size exclusion chromatography the best option.</a> International Journal of Molecular Sciences. 21 (18), 6466 (2020).</li><li>Konoshenko, M. Y., Lekchnov, E. A., Vlassov, A. V., Laktionov, P. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Isolation+of+extracellular+vesicles:+general+methodologies+and+latest+trends.">Isolation of extracellular vesicles: general methodologies and latest trends.</a> BioMed Research International. 2018, 8545347 (2018).</li><li>McKinnon, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Flow+cytometry:+an+overview.">Flow cytometry: an overview.</a> Current Protocols in Immunology. 120, 1-11 (2018).</li><li>Theodoraki, M. N., Hong, C. S., Donnenberg, V. S., Donnenberg, A. D., Whiteside, T. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Evaluation+of+exosome+proteins+by+on-bead+flow+cytometry.">Evaluation of exosome proteins by on-bead flow cytometry.</a> Cytometry A. 99 (4), 372-381 (2021).</li><li>Nolan, J. P., Duggan, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+individual+extracellular+vesicles+by+flow+cytometry.">Analysis of individual extracellular vesicles by flow cytometry.</a> Methods in Molecular Biology. 1678, 79-92 (2018).</li><li>Nolan, J. P., Jones, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Detection+of+platelet+vesicles+by+flow+cytometry.">Detection of platelet vesicles by flow cytometry.</a> Platelets. 28 (3), 256-262 (2017).</li><li>Dragovic, R. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sizing+and+phenotyping+of+cellular+vesicles+using+Nanoparticle+Tracking+Analysis.">Sizing and phenotyping of cellular vesicles using Nanoparticle Tracking Analysis.</a> Nanomedicine. 7 (6), 780-788 (2011).</li><li>Ramirez, M. I., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Technical+challenges+of+working+with+extracellular+vesicles.">Technical challenges of working with extracellular vesicles.</a> Nanoscale. 10 (3), 881-906 (2018).</li><li>Song, X., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Improved+strategy+for+jet-in-air+cell+sorting+with+high+purity,+yield,+viability,+and+genome+stability.">Improved strategy for jet-in-air cell sorting with high purity, yield, viability, and genome stability.</a> FEBS Open Bio. 11 (9), 2453-2467 (2021).</li><li>Zucker, R. M., Elstein, K. H., Gershey, E. L., Massaro, E. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Increasing+sensitivity+of+the+Ortho+analytical+cytofluorograph+by+modifying+the+fluid+system.">Increasing sensitivity of the Ortho analytical cytofluorograph by modifying the fluid system.</a> Cytometry. 11 (7), 848-851 (1990).</li></ol>

The authors declare no conflicts of interest.

This protocol outlines an optimized method to isolate and purify sEV with the specified particle size of 50-200 nm using a flow cell sorter, which was validated by NTA. The method solved the bottleneck problem of obtaining sEV with uniform particle size and high purity, avoiding interference from unrelated biological molecules wrapped in large-sized EVs22. Fast, high-throughput analyses are possible with flow cytometry, which can capture 100,000 particles per second and make 70,000 sorting decisions per second17, greatly reducing the time and reflecting the heterogeneity of sEV particles. Moreover, this flow cytometry-based protocol can be customized based on individual interests in subpopulations of EVs of specific sizes. Alternative gate ranges can be used to identify and isolate the populations of interest with the same instrument parameters set as the above, such as air spray nozzle, sheath fluid pressure, sample flow pressure, and triggering threshold parameter. 
The technical difficulty of this method lies in the separation of populations with different size ranges, particularly distinguishing from background noise. We identified a panel of critical sort settings. First, the size of the nozzle affects the sorting rate. In order to improve the concentration of sEV obtained by sorting, a 50 &#181;m nozzle is used in this method, and 80 psi of sheath fluid pressure is required to stabilize the side stream. With higher sheath fluid pressure, drop frequencies increase, resulting in higher event rates and shorter sorting time23. However, increasing sheath fluid pressure attenuates the sensitivity of FSC and fluorescence signals due to the reduced time it takes to pass through the laser and the number of photons reaching the detector24. Notably, it is difficult to maintain the stability of the side stream under this pressure, which requires high cleanliness of the nozzle and pipeline. Second, ultrasonic cleaning of the nozzle and flushing of flow cytometry pipes are strongly recommended to increase the likelihood of experimental success. Lastly, voltage and gain are critical for population separation, especially for small size particles. Here, a voltage of 250 V and gain of 0.6 can effectively separate the sEV at 50-200 nm with FSC triggering and plot in logarithmic form.
One caveat of the approach is that in some cases, the concentration of the sEV is too high, or the sEV aggregate, during the sorting process, making it difficult to achieve a single-particle suspension. The aggregated sEV will be discarded due to the over-amplified signal. 
Collectively, with the advantages of high-throughput analysis of flow cytometry, this method optimized nozzle size, sheath fluid pressure, sample flow pressure, and triggering threshold parameter leading to successful isolation of 50-200 nm sEV. Besides, not only does this method allow for the separation of specific size particles, but it also allows for synchronous classification or proteome analysis of sEV based on antigen expression, opening up numerous downstream research applications.

A cell releases extracellular vesicles (EVs) of varying sizes that result in signaling molecules and membrane inclusions, which are important for intercellular communication1. EVs of different sizes also play different biological roles, with 50-200 nm sEV being able to precisely distribute RNA, DNA, and proteins to the correct extracellular location. The sEV also helps determine their secretion mechanisms, involving not only the regulation of normal physiological processes such as immune surveillance, stem cell maintenance, blood coagulation, and tissue repair but also the pathology underlying several diseases such as tumor progression and metastasis2,3. Effective isolation and analysis of sEV are critical for identifying biomarkers and designing future drug interventions.
With continuous research on the clinical application of sEV, the isolation methods of sEV have put forward higher requirements. Due to the heterogeneity of sEV in size, source, and contents, as well as their similarity with other EVs in physicochemical and biochemical properties, there is no standard method for sEV isolation4,5. Currently, ultracentrifugation, size exclusion chromatography (SEC), polymer precipitation, and immunoaffinity capture are the most common sEV isolation methods6. Ultracentrifugation is still the gold standard for sEV isolation in research, despite being time-consuming, resulting in low purity with a wide size distribution of 40-500 nm and significant mechanical damage to the sEV after long-term centrifugation7,8,9. Polymer precipitation, which usually uses polyethylene glycol (PEG), suffers from unacceptable purity for subsequent functional analysis with concomitant precipitation of extracellular protein aggregates and polymer contamination10,11. Immunoaffinity capture-based methods require high-cost antibodies with varying specificity, as well as have problems with low processing volume and yields12,13,14. Particle size is one of the main indicators to evaluate the purity of isolated sEV. Although sEV purity remains an unattainable goal, SEC removes a considerable quantity of medium components, and the sEV particles extracted by the SEC method are mainly in the range of 50-200 nm15. The existing techniques have a few disadvantages, including but not limited to being time-consuming, low purity, low yield, poor reproducibility, low throughput of samples, and potential damage of sEV, which makes it incompatible with clinical utilization16. Thus, a rapid, inexpensive, and size-specified sEV isolation method applicable to diverse biofluids is an essential need in several research and clinical situations.
In flow cytometry, single particles are analyzed in a high-throughput, multiparametric manner, and subsets are sorted out17. Due to the heterogeneity of EVs, a single-particle flow cytometric measurement would be ideal, which has been used to investigate EVs following the paradigms of cell analysis, with light scatter and fluorescence labels being used to identify physiology-related features and protein components18,19,20. Nevertheless, conventional flow cytometry is challenged by the small size of sEV and low abundance of surface biomarkers. The sensitivity of flow cytometry could be improved by optimizing detection parameters to distinguish background noise and sEV regardless of using forward scatter (FSC), side scatter (SSC), or fluorescence threshold triggering parameter19.
With the present protocol, high-resolution flow cytometric sort settings were optimized using fluorescent beads as standard. By selecting the proper nozzle size, sheath fluid pressure, threshold triggering parameter, and voltages controlling scattered light intensities, we were able to isolate a specific subset of sEV from a complex mixture.

<table><tbody><tr><td>Centrifuge tube</td><td>Beckman Coulter</td><td>344058</td><td></td></tr><tr><td>Culture flasks</td><td>Corning&amp;nbsp;</td><td>430641</td><td></td></tr><tr><td>Dulbecco&amp;rsquo;s modified eagle medium</td><td>Corning Cellgro</td><td>10-013-CV</td><td></td></tr><tr><td>Fetal bovine serum</td><td>SUER</td><td>SUER050QY</td><td></td></tr><tr><td>Flow cell sorter</td><td>Beckman Coulter</td><td>Moflo Astrios EQ</td><td></td></tr><tr><td>Human pancreatic cancer cell, PANC-1</td><td>NA</td><td>NA</td><td>PANC-1 cells were donated by Professor Weijun Yang, College of Life Sciences, Zhejiang University</td></tr><tr><td>Laser particle size and zeta potential analyzer&amp;nbsp;</td><td>Malvern</td><td>Zetasizer Nano ZS 90</td><td></td></tr><tr><td>Phosphate buffer saline</td><td>Gibco</td><td>C20012500BT</td><td></td></tr><tr><td>Polystyrene fluorescent microspheres</td><td>Beckman Coulter</td><td>6602336</td><td></td></tr><tr><td>Transmission electron microscopy</td><td>JEOL</td><td>JEM-1200EX</td><td></td></tr><tr><td>Trypsin-EDTA solution</td><td>Gibco</td><td>1713949</td><td></td></tr><tr><td>Ultra rainbow fluorescent particles</td><td>Beckman Coulter</td><td>B28479</td><td></td></tr><tr><td>Ultracentrifuge</td><td>Beckman Coulter</td><td>Optima-L80XP</td><td></td></tr><tr><td>Ultracentrifuge rotor</td><td>Beckman Coulter</td><td>SW32TI</td><td></td></tr></tbody></table>

optimization of flow cytometric sorting parameters for high-throughput isolation and purification of small extracellular vesicles

Small extracellular vesicles (sEV) can be released from all cell types and carry protein, DNA, and RNA. Signaling molecules serve as indicators of the physiological and pathological state of a cell. However, there is no standard method for sEV isolation, which prevents downstream biomarker identification and drug intervention studies. In this article, we provide a detailed protocol for the isolation and purification of 50-200 nm sEV by a flow cell sorter. For this, a 50 &#181;m nozzle and 80 psi sheath fluid pressure were selected to obtain a good sorting rate and stable side stream. Standard sized polystyrene microspheres were used to locate populations of 100, 200, and 300 nm particles. With additional optimization of the voltage, gain, and forward scatter (FSC) triggering threshold, the sEV signal could be separated from the background noise. These optimizations provide a panel of critical sort settings that enables one to obtain a representative population of sEV using FSC vs. side scatter (SSC) only. The flow cytometry-based isolation method not only allows for high-throughput analysis but also allows for synchronous classification or proteome analysis of sEV based on the biomarker expression, opening numerous downstream research applications.

The flow chart diagram for the experimental protocol is shown in Figure 1. In this method, standard sized polystyrene microspheres were used as reference standards for particle size distribution. Under the specific instrumental parameter condition, the particle signal could be clearly distinguished from the background noise in the FSC vs. SSC plot using the logarithmic form. Gating strategies are shown in Figure 2. R4, R5, and R6 refer to the positions of 100 nm, 200 nm, and 300 nm microspheres, respectively. R7 is the detection limit of electronic noise below 50 nm, and R8 is the position range of 50-200 nm particles.
The particle size distribution of the EVs mixture derived from PANC-1 cells was in the wide range of 40-400 nm after ultracentrifugation (Figure 3). To isolate and purify the 50-200 nm sEV, flow cytometric sorting was performed to obtain the specific size sEV according to the location of standard microspheres (Figure 4). The quality of isolation was verified by NTA, and it was found that the particle size range of sEV after sorting was between 50-200 nm (as shown in Figure 5). The presence of sEV was further observed by TEM, indicated by red arrows in Figure 6A, and the isolated sEVs were confirmed to contain markers of CD9, CD63, and CD81 by WB analysis (Figure 6B).
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/64360/64360fig01v2.jpg" /> 
Figure 1. Flow chart diagram for the experimental protocol. PANC-1 cell culture medium was collected and ultracentrifuged to obtain the EVs mixture. Sorting parameters were optimized for isolation and purification of 50-200 nm sEV which was verified by NTA. <a href="https://www.jove.com/files/ftp_upload/64360/64360fig01largev2.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 2" class="xfigimg" src="/files/ftp_upload/64360/64360fig02.jpg" /> 
Figure 2. Flow cytometry analysis of standard-sized polystyrene microspheres to locate the 50-200 nm size range in the FSC vs. SSC plot. Diluted suspensions of 100 nm, 200 nm, and 300 nm microspheres were loaded and analyzed by a flow cytometer as shown in the FSC vs. SSC dot plot. R4, R5, and R6 refer to the positions of 100 nm, 200 nm, and 300 nm particles, respectively. R7 is the electronic noise as the detection limit for 50 nm particles, and R8 represents the position range of 50-200 nm particles. <a href="https://www.jove.com/files/ftp_upload/64360/64360fig02large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 3" class="xfigimg" src="/files/ftp_upload/64360/64360fig03.jpg" /> 
Figure 3. NTA analysis of particle size distribution of EVs obtained by ultracentrifugation. The frequency distribution of different particle sizes is represented by the data as particle percentage vs. size. <a href="https://www.jove.com/files/ftp_upload/64360/64360fig03large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 4" class="xfigimg" src="/files/ftp_upload/64360/64360fig04.jpg" /> 
Figure 4. Flow cytometry analysis of the collected EV sample. The FSC vs. SSC dot plot shows a sample of the collected EV mixture loaded and analyzed by a flow cytometer. The sEV in the size range of 50-200 nm within the R8 region were sorted. <a href="https://www.jove.com/files/ftp_upload/64360/64360fig04large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 5" class="xfigimg" src="/files/ftp_upload/64360/64360fig05.jpg" /> 
Figure 5. Verification of particle size distribution of sEV after sorting using NTA. Representative particle percentage vs. size histogram shows the size distribution of the sorted sEV. <a href="https://www.jove.com/files/ftp_upload/64360/64360fig05large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 6" class="xfigimg" src="/files/ftp_upload/64360/64360fig06.jpg" /> 
Figure 6. Characterization of sEV isolated by sorting. (A) A representative TEM image of sorted sEV (indicated by red arrows). Scale bar = 200 nm. (B) Western blot analysis of CD9, CD81, and CD63 markers in the sorted sEV. <a href="https://www.jove.com/files/ftp_upload/64360/64360fig06large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>

Watch this Scientific Journal Video about Optimization of Flow Cytometric Sorting Parameters for High-Throughput Isolation and Purification of Small Extracellular Vesicles at JoVE.com

Optimization of Flow Cytometric Sorting Parameters for High-Throughput Isolation and Purification of Small Extracellular Vesicles

This protocol provides a rapid and size-specific isolation method for small extracellular vesicles by optimizing the size of the air spray nozzle, sheath fluid pressure, sample flow pressure, voltage, gain, and triggering threshold parameters.

Small extracellular vesicles (sEV) can be released from all cell types and carry protein, DNA, and RNA. Signaling molecules serve as indicators of the ...

optimization-flow-cytometric-sorting-parameters-for-high-throughput

Nanyang Technological University

Research

JoVE Journal

Biochemistry

2.1K Views.  Zhejiang University School of Medicine. This protocol provides a rapid and size-specific isolation method for small extracellular vesicles by optimizing the size of the air spray nozzle, sheath fluid pressure, sample flow pressure, voltage, gain, and triggering threshold parameters.

Video: Optimization of Flow Cytometric Sorting Parameters for High-Throughput Isolation and Purification of Small Extracellular Vesicles

Flow Cytometric Isolation of Primary Murine Type II Alveolar Epithelial Cells for Functional and Molecular Studies

Throughout the last years, the contribution of alveolar type II epithelial cells (AECII) to various aspects of immune regulation in the lung has been increasingly recognized. AECII have been shown to participate in cytokine production in inflamed airways and to even act as antigen-presenting cells in both infection and T-cell mediated autoimmunity 1-8. Therefore, they are especially interesting also in clinical contexts such as airway hyper-reactivity to foreign and self-antigens as well as infections that directly or indirectly target AECII. However, our understanding of the detailed immunologic functions served by alveolar type II epithelial cells in the healthy lung as well as in inflammation remains fragmentary. Many studies regarding AECII function are performed using mouse or human alveolar epithelial cell lines 9-12. Working with cell lines certainly offers a range of benefits, such as the availability of large numbers of cells for extensive analyses. However, we believe the use of primary murine AECII allows a better understanding of the role of this cell type in complex processes like infection or autoimmune inflammation. Primary murine AECII can be isolated directly from animals suffering from such respiratory conditions, meaning they have been subject to all additional extrinsic factors playing a role in the analyzed setting. As an example, viable AECII can be isolated from mice intranasally infected with influenza A virus, which primarily targets these cells for replication 13. Importantly, through ex vivo infection of AECII isolated from healthy mice, studies of the cellular responses mounted upon infection can be further extended.
Our protocol for the isolation of primary murine AECII is based on enzymatic digestion of the mouse lung followed by labeling of the resulting cell suspension with antibodies specific for CD11c, CD11b, F4/80, CD19, CD45 and CD16/CD32. Granular AECII are then identified as the unlabeled and sideward scatter high (SSChigh) cell population and are separated by fluorescence activated cell sorting 3.
In comparison to alternative methods of isolating primary epithelial cells from mouse lungs, our protocol for flow cytometric isolation of AECII by negative selection yields untouched, highly viable and pure AECII in relatively short time. Additionally, and in contrast to conventional methods of isolation by panning and depletion of lymphocytes via binding of antibody-coupled magnetic beads 14, 15, flow cytometric cell-sorting allows discrimination by means of cell size and granularity. Given that instrumentation for flow cytometric cell sorting is available, the described procedure can be applied at relatively low costs. Next to standard antibodies and enzymes for lung disintegration, no additional reagents such as magnetic beads are required. The isolated cells are suitable for a wide range of functional and molecular studies, which include in vitro culture and T-cell stimulation assays as well as transcriptome, proteome or secretome analyses 3, 4.

We describe the rapid isolation of primary murine type II alveolar epithelial cells (AECII) by flow cytometric negative selection. These AECII show high viability and purity and are suitable for a wide range of functional and molecular studies regarding their role in respiratory conditions such as autoimmune or infectious diseases.

Throughout  the last years, the contribution of alveolar type II epithelial cells (AECII)  to various aspects of immune regulation in the lung has been ...

Immunology and Infection

Purification of High Yield Extracellular Vesicle Preparations Away from Virus

One of the major hurdles in the field of extracellular vesicle (EV) research today is the ability to achieve purified EV preparations in a viral infection setting. The presented method is meant to isolate EVs away from virions (i.e., HIV-1), allowing for a higher efficiency and yield compared to conventional ultracentrifugation methods. Our protocol contains three steps: EV precipitation, density gradient separation, and particle capture. Downstream assays (i.e., Western blot, and PCR) can be run directly following particle capture. This method is advantageous over other isolation methods (i.e., ultracentrifugation) as it allows for the use of minimal starting volumes. Furthermore, it is more user friendly than alternative EV isolation methods requiring multiple ultracentrifugation steps. However, the presented method is limited in its scope of functional EV assays as it is difficult to elute intact EVs from our particles. Furthermore, this method is tailored towards a strictly research-based setting and would not be commercially viable.

This protocol isolates extracellular vesicles (EVs) away from virions with high efficiency and yield by incorporating EV precipitation, density gradient ultracentrifugation, and particle capture to allow for a streamlined workflow and a reduction of starting volume requirements, resulting in reproducible preparations for use in all EV research.

One of the major hurdles in the field of extracellular vesicle (EV) research today is the ability to achieve purified EV preparations in a viral infection ...

Microfluidic Device for Continuous Extracellular Vesicle Isolation from Human Urine

Single Step Isolation of Extracellular Vesicles from Large-Volume Samples with a Bifurcated A4F Microfluidic Device

Extracellular vesicles (EVs) hold immense potential for various biomedical applications, including diagnostics, drug delivery, and regenerative medicine. Nevertheless, the current methodologies for isolating EVs present significant challenges, such as complexity, time consumption, and the need for bulky equipment, which hinders their clinical translation. To address these limitations, we aimed to develop an innovative microfluidic system based on cyclic olefin copolymer-off-stoichiometry thiol-ene (COC-OSTE) for the efficient isolation of EVs from large-volume samples in a continuous manner. By utilizing size and buoyancy-based separation, the technology used in this study achieved a significantly narrower size distribution compared to existing approaches from urine and cell media samples, enabling the targeting of specific EV size fractions in future applications. Our innovative COC-OSTE microfluidic device design, utilizing bifurcated asymmetric flow field-flow fractionation technology, offers a straightforward and continuous EV isolation approach for large-volume samples. Furthermore, the potential for mass manufacturing of this microfluidic device offers scalability and consistency, making it feasible to integrate EV isolation into routine clinical diagnostics and industrial processes, where high consistency and throughput are essential requirements.

Author Spotlight: Asymmetric Field Flow Fractionation for Bioreactor Integration

Extracellular vesicles hold immense promise for biomedical applications, but current isolation methods are time-consuming and impractical for clinical use. In this study, we present a microfluidic device that enables the direct isolation of extracellular vesicles from large volumes of biofluids in a continuous manner with minimal steps.

Extracellular vesicles (EVs) hold immense potential for various biomedical applications, including diagnostics, drug delivery, and regenerative medicine. ...

Bioengineering

Size Exclusion Chromatography for Separating Extracellular Vesicles from Conditioned Cell Culture Media

Extracellular vesicles (EVs) are nano-sized lipid-membrane bound structures that are released from all cells, are present in all biofluids, and contain proteins, nucleic acids, and lipids that are reflective of the parent cell from which they are derived. Proper separation of EVs from other components in a sample allows for characterization of their associated cargo and lends insight into their potential as intercellular communicators and non-invasive biomarkers for numerous diseases. In the current study, oligodendrocyte derived EVs were isolated from cell culture media using a combination of state-of-the-art techniques, including ultrafiltration and size exclusion chromatography (SEC) to separate EVs from other extracellular proteins and protein complexes. Using commercially available SEC columns, EVs were separated from extracellular proteins released from human oligodendroglioma cells under both control and endoplasmic reticulum (ER) stress conditions. The canonical EV markers CD9, CD63, and CD81 were observed in fractions 1-4, but not in fractions 5-8. GM130, a protein of the Golgi apparatus, and calnexin, an integral protein of the ER, were used as negative EV markers, and were not observed in any fraction. Further, when pooling and concentrating fractions 1-4 as the EV fraction, and fractions 5-8 as the protein fraction, expression of CD63, CD81, and CD9 in the EV fraction was observed. The expression of GM130 or calnexin was not observed in either of the fraction types. The pooled fractions from both control and ER stress conditions were visualized with transmission electron microscopy and vesicles were observed in the EV fractions, but not in the protein fractions. Particles in the EV and protein fractions from both conditions were also quantified with nanoparticle tracking analysis. Together, these data demonstrate that SEC is an effective method for separating EVs from conditioned cell culture media.

The protocol here demonstrates that extracellular vesicles can be adequately separated from conditioned cell culture media using size exclusion chromatography.

Extracellular vesicles (EVs) are nano-sized lipid-membrane bound structures that are released from all cells, are present in all biofluids, and contain ...

Neuroscience

Techniques for the Analysis of Extracellular Vesicles Using Flow Cytometry

Extracellular Vesicles (EVs) are small, membrane-derived vesicles found in bodily fluids that are highly involved in cell-cell communication and help regulate a diverse range of biological processes. Analysis of EVs using flow cytometry (FCM) has been notoriously difficult due to their small size and lack of discrete populations positive for markers of interest. Methods for EV analysis, while considerably improved over the last decade, are still a work in progress. Unfortunately, there is no one-size-fits-all protocol, and several aspects must be considered when determining the most appropriate method to use. Presented here are several different techniques for processing EVs and two protocols for analyzing EVs using either individual detection or a bead-based approach. The methods described here will assist with eliminating the antibody aggregates commonly found in commercial preparations, increasing signal&#8211;to-noise ratio, and setting gates in a rational fashion that minimizes detection of background fluorescence. The first protocol uses an individual detection method that is especially well suited for analyzing a high volume of clinical samples, while the second protocol uses a bead-based approach to capture and detect smaller EVs and exosomes.

Many different methods exist for the measurement of extracellular vesicles (EVs) using flow cytometry (FCM). Several aspects should be considered when determining the most appropriate method to use. Two protocols for measuring EVs are presented, using either individual detection or a bead-based approach.

Extracellular Vesicles (EVs) are small, membrane-derived vesicles found in bodily fluids that are highly involved in cell-cell communication and help ...

Biology

Flow Cytometric Analysis of Extracellular Vesicles from Cell-conditioned Media

Flow cytometry (FC) is the method of choice for semi-quantitative measurement of cell-surface antigen markers. Recently, this technique has been used for phenotypic analyses of extracellular vesicles (EV) including exosomes (Exo) in the peripheral blood and other body fluids. The small size of EV mandates the use of dedicated instruments having a detection threshold around 50-100 nm. Alternatively, EV can be bound to latex microbeads that can be detected by FC. Microbeads, conjugated with antibodies that recognize EV-associated markers/Cluster of Differentiation CD63, CD9, and CD81 can be used for EV capture. Exo isolated from CM can be analyzed with or without pre-enrichment by ultracentrifugation. This approach is suitable for EV analyses using conventional FC instruments. Our results demonstrate a linear correlation between Mean Fluorescence Intensity (MFI) values and EV concentration. Disrupting EV through sonication dramatically decreased MFI, indicating that the method does not detect membrane debris. We report an accurate and reliable method for the analysis of EV surface antigens, which can be easily implemented in any laboratory.

The protocol describes a reproducible method designed for use with cell culture supernatants to detect surface epitopes on small extracellular vesicles (EV). It utilizes specific EV immunoprecipitation using beads coupled with antibodies that recognize surface antigen CD9, CD63, and CD81. The method is optimized for downstream flow cytometry analysis.

Flow cytometry (FC) is the method of choice for semi-quantitative measurement of cell-surface antigen markers. Recently, this technique has been used for ...

Size Determination and Phenotypic Analysis of Urinary Extracellular Vesicles using Flow Cytometry

Extracellular vesicles, EVs, are a heterogeneous complex of lipidic membranes, secreted by any cell type, in any fluid such as urine. EVs can be of different sizes ranging from 40-100 nm in diameter such as in exosomes to 100-1000 nm in microvesicles. They can also contain different molecules that can be used as biomarkers for the prognosis and diagnosis of many diseases. Many techniques have been developed to characterize these vesicles. One of these is flow cytometry. However, there are no existing reports to show how to quantify the concentration of EVs and differentiate them by size, along with biomarker detection. This work aims to describe a procedure for the isolation, quantification, and phenotypification of urinary extracellular vesicles, uEVs, using a conventional cytometer for the analysis without any modification to its configuration. The method&#39;s limitations include staining a maximum of four different biomarkers per sample. The method is also limited by the amount of EVs available in the sample. Despite these limitations, with this protocol and its subsequent analysis, we can obtain more information on the enrichment of EVs markers and the abundance of these vesicles present in urine samples, in diseases involving kidney and brain damage.

This protocol describes a method for the isolation of urinary extracellular vesicles, uEVs, from healthy human donors and their phenotypic characterization by the size and surface marker expression using flow cytometry.

Extracellular vesicles, EVs, are a heterogeneous complex of lipidic membranes, secreted by any cell type, in any fluid such as urine. EVs can be of ...

Fluorescence-Based Sorting of Adipose-Derived Extracellular Vesicles

Setting a Successful Sorting for Extracellular Vesicle Isolation

Extracellular vesicles (EVs) released by mesenchymal stromal cells (MSCs) contain a set of microRNAs with regenerative and anti-inflammatory roles. Therefore, purified MSC-EVs are envisioned as a next-generation therapeutic option for a wide array of diseases. In this protocol, we report the strategy for successfully sorting EVs from the supernatant of adipose-derived MSCs (ASCs), often used in orthopedics regenerative medicine applications.
First, we described the sample preparation, focusing on EV isolation and labeling steps with carboxyfluorescein succinimidyl ester (CFSE) for fluorescence detection; subsequently, we detailed the sorting process, which constitutes the main part of the protocol. 
In addition to the rules defined by MISEV 2023 and MIFlowCyt EV guidelines, we applied specific experimental conditions concerning nozzle size, frequency, and sheath pressure. Morphological parameters are established using beads of diameters selected to cover the theoretical range of EV size. After ASC-EVs sorting, we performed a purity check of the sorted fraction by re-analyzing it with the sorter and verifying the EV size distribution with the nanoparticle tracking analysis technique.
Due to the increasing importance of EVs, having a pure population to study and characterize is becoming crucial. Here, we demonstrate a winner strategy to set up sorting to achieve this goal.

This protocol provides a detailed description of sorting extracellular vesicles (EVs) released by mesenchymal stromal cells. In particular, it focuses on the instrument setting and the optimization of the sorting conditions. The goal is to sort extracellular vesicles while preserving their characteristics.

Extracellular vesicles (EVs) released by mesenchymal stromal cells (MSCs) contain a set of microRNAs with regenerative and anti-inflammatory roles. ...

Characterizing Extracellular Vesicles from Biological Fluids

Extracellular vesicles (EVs) are structures that are produced from cells and participate in intercellular communication by transporting biomolecules from one cell to another. EVs have been shown to travel short and far distances in the body and are tissue-specific. EVs are not only found in tissues, but they can also be found in practically all bodily fluids, such as tears, saliva, cerebral spinal fluid, blood, etc. Even though EVs can be collected non-invasively from tears and saliva, only small volumes can be collected at a time, which can cause issues in obtaining enough EVs to analyze proteins. The scanner discussed in this paper is a nanoparticle analyzer that provides a solution to&#160;this problem, allowing us to characterize and study the phenotype, size, and total particle count of EVs from as little as 1 &#181;L of biological fluid. This protocol will expand the knowledge of EVs from small volumes of samples that are difficult to extract from patients. This could enhance patient comfort and potentially identify new therapeutic targets for a range of diseases and disorders.

Here, we demonstrate the characterization method for extracellular vesicles (EVs) collected from biological fluids, such as tears and saliva, of human subjects. The scanner used in this method is capable of detecting the phenotype, size, and total particle count of EVs from 1 &#181;L of the sample.

Extracellular vesicles (EVs) are structures that are produced from cells and participate in intercellular communication by transporting biomolecules from ...

Flow Cytometry-Based Cell Sorting for Different Circulatory B Cell Populations

Source: Tzeng, S. J. <a href="https://app.jove.com/v/54582">The Isolation, Differentiation, and Quantification of Human Antibody-secreting B Cells from Blood: ELISpot as a Functional Readout of Humoral Immunity.</a> J. Vis. Exp. (2016).
In this video, we describe a protocol for the flow cytometry-based sorting of na&#239;ve B cell, memory B cell, and plasmablast plasma cell subpopulations from human peripheral blood B cells. The different B cell subpopulations can be distinguished based on fluorophore-based antibody binding to the CD19, CD27, and CD38 receptors expressed on the B cell surfaces, followed by cell sorting.

Source: Tzeng, S. J. The Isolation, Differentiation, and Quantification of Human Antibody-secreting B Cells from Blood: ELISpot as a Functional Readout of ...