This work was supported by a grant from the National Health Research Institutes (03-A1 BNMP11-014).

Note: The photomask designs for our microfluidic device fabrication were drawn by using a computer aided design (CAD) software. The designs were then utilized to fabricate chrome photomasks using a commercial service. The PDMS devices were made using soft lithography techniques.11
1. Fabrication of Master Molds by Lithography
<ol>
	<li>Before the photolithography process12, use the 4-inch silicon wafers as a substrate and dehydrate the wafers in a conventional oven at 1...

<ol>
	<li>Meacham, C. E., Morrison, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tumour+heterogeneity+and+cancer+cell+plasticity.">Tumour heterogeneity and cancer cell plasticity.</a> Nature. 501 (7467), 328-337 (2013).</li><li>Vermeulen, L., 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-cell+cloning+of+colon+cancer+stem+cells+reveals+a+multi-lineage+differentiation+capacity.">Single-cell cloning of colon cancer stem cells reveals a multi-lineage differentiation capacity.</a> P Natl Acad Sci USA. 105 (36), 13427-13432 (2008).</li><li>Shapiro, H. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Practical flow cytometry. , (2005).</li><li>Leong, K. G., Wang, B. E., Johnson, L., Gao, W. 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P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Integration+column:+microwell+arrays+for+mammalian+cell+culture.">Integration column: microwell arrays for mammalian cell culture.</a> Integr. Biol. 1 (11-12), 11-12 (2009).</li><li>Lindstrom, S., 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=High-density+microwell+chip+for+culture+and+analysis+of+stem+cells.">High-density microwell chip for culture and analysis of stem cells.</a> PloS one. 4 (9), e6997 (2009).</li><li>Lin, C. 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=A+microfluidic+dual-well+device+for+high-throughput+single-cell+capture+and+culture.">A microfluidic dual-well device for high-throughput single-cell capture and culture.</a> Lab Chip. 15 (14), 2928-2938 (2015).</li><li>Xia, Y. N., Whitesides, G. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Soft+lithography.">Soft lithography.</a> Angew Chem Int Edit. 37 (5), 550-575 (1998).</li><li>Shin, Y., 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=Microfluidic+assay+for+simultaneous+culture+of+multiple+cell+types+on+surfaces+or+within+hydrogels.">Microfluidic assay for simultaneous culture of multiple cell types on surfaces or within hydrogels.</a> Nat Protoc. 7 (7), 1247-1259 (2012).</li><li>Strober, W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Trypan+blue+exclusion+test+of+cell+viability.">Trypan blue exclusion test of cell viability.</a> Curr. Protoc. Immunol. Appendix 3 (Appendix 3B), (2001).</li><li>Lindstrom, S., Andersson-Svahn, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Miniaturization+of+biological+assays+-+Overview+on+microwell+devices+for+single-cell+analyses.">Miniaturization of biological assays - Overview on microwell devices for single-cell analyses.</a> Bba-Gen Subjects. 1810 (3), 308-316 (2011).</li><li>Lecault, V., 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=High-throughput+analysis+of+single+hematopoietic+stem+cell+proliferation+in+microfluidic+cell+culture+arrays.">High-throughput analysis of single hematopoietic stem cell proliferation in microfluidic cell culture arrays.</a> Nat Methods. 8 (7), 581-593 (2011).</li><li>Park, J. Y., 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+cell+trapping+in+larger+microwells+capable+of+supporting+cell+spreading+and+proliferation.">Single cell trapping in larger microwells capable of supporting cell spreading and proliferation.</a> Microfluid Nanofluid. 8 (2), 263-268 (2010).</li><li>Tirino, V., 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=Cancer+stem+cells+in+solid+tumors:+an+overview+and+new+approaches+for+their+isolation+and+characterization.">Cancer stem cells in solid tumors: an overview and new approaches for their isolation and characterization.</a> FASEB J. 27 (1), 13-24 (2013).</li><li>Chen, P. C., Huang, Y. Y., Juang, J. 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Microwell-based device systems6,14 have been utilized for single-cell manipulation and analysis, such as large-scale single cell trapping6 and single hematopoietic stem cell proliferation15. Although well size, number, and shape can be adjusted for specific applications, the single-cell isolation efficiency is always compromised when the size of the well is increased.9,15
To overcome this limitation, Park et al. reported a microfluidic chip ...

Currently placing single cells individually in a culture space is commonly achieved by using limiting dilution or fluorescence-activated cell sorting (FACS). For many laboratories, limiting dilution is a convenient method, as it only requires a pipette and tissue culture plates, which are readily available. In this case, a cell suspension is serially diluted to an appropriate cell density, and then placed into culture wells by using a manual pipette. These compartmented single cells are then used for cell analysis, such as genetic heterogeneity screening1 and colony formation2. However, this method is low-throughput and labor-intensive, without utilizing a robotic arm for assistance, because the Poisson distribution nature of the limiting dilution method restricts single-cell events to a maximum probability of 37%3. FACS machines with an integrated robotic arm can overcome the limitation of Poisson distribution by accurately placing one single-cell in a culture well at a time4. However, the high mechanical shear stress (thus, lowered cell viability)5 and machine purchase and operational costs have limited its usage in many laboratories.
To overcome the above limitations, microscale devices have been developed to highly efficiently load single cells into microwells6. However, the microwells do not provide adequate space for the loaded cells to proliferate, due to the need of making the size of each microwell close to that of a single cell to maximize the single-cell loading probability. As culture assays are required in many cell-based applications (e.g., clonogenic assay7), larger microwells (from 90 - 650 &#181;m in diameter or in side length) have also been utilized to allow for extended cell cultures. However, like the limiting dilution method, they also possess low single cell loading efficiencies, ranging from 10 - 30%.8,9
Previously, we have developed a high-throughput microfluidic platform to isolate single cells in individual microwells and demonstrate its application in clonogenic assay of the isolated cells.10 The device was made with poly-dimethylsiloxane (PDMS), and comprises two sets of microwell arrays with different microwell sizes, which can largely improve the efficiency in loading a single cell in a microwell whose size is significantly larger than the cell. Notably, this &#34;dual-well&#34; concept allows the size of the culture area to be flexibly adjusted without affecting the single-cell capture efficiency, making it straightforward to adjust the design of the device to suit different cell types and applications. This high-efficiency method should be useful for long-term cell culture experiments for cell heterogeneity studies and monoclonal cell line establishment.

<table border="0" cellpadding="0" cellspacing="0" width="1323">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:401px;">AutoCAD software</td>
			<td style="width:225px;">Autodesk</td>
			<td style="width:235px;">AutoCAD LT 2011</td>
			<td style="width:463px;">Part No. 057C1-74A111-1001</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Silicon wafer&#160;</td>
			<td>Eltech corperation</td>
			<td style="width:235px;">SPE0039</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Conventional oven</td>
			<td>YEONG-SHIN company</td>
			<td style="width:235px;">ovp45</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Plasma cleaner</td>
			<td>Nordson</td>
			<td style="width:235px;">AP-300</td>
			<td>Bench-Top Plasma Treatment System</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">SU-8 50 negative photoresist</td>
			<td>MicroChem</td>
			<td>Y131269</td>
			<td style="width:463px;"></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">SU-8 100 negative photoresist</td>
			<td>MicroChem</td>
			<td>Y131273</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Spin coater</td>
			<td>Synrex Co., Ltd.</td>
			<td>SC-HMI 2&#34; ~ 6&#34;</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Hotplate</td>
			<td>YOTEC company</td>
			<td>YS-300S</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Msak aligner</td>
			<td>Deya Optronic CO.</td>
			<td>A1K-5-MDA</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">SU-8 developer</td>
			<td>Grand Chemical Companies</td>
			<td>GP5002-000000-72GC</td>
			<td>Propylene glycol monomethyl ether acetate</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Scanning laser profilometer</td>
			<td>KEYENCE</td>
			<td>VK-X 100</td>
			<td></td>
		</tr>
		<tr height="40">
			<td height="40" style="height:40px;">Trichlorosilane</td>
			<td>Gelest, Inc</td>
			<td>SIT8174.0</td>
			<td style="width:463px;">TRIDECAFLUORO-1,1,2,2-TETRAHYDROOCTYL.&#160; Hazardous. Corrosive to the respiratory tract., reacts violently with water.</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Desiccator</td>
			<td>Bel-Art Products&#160;</td>
			<td>F42020-0000</td>
			<td>SPACE SAVER VACUUM DESICCATOR 190MM WHITE BASE</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Polydimethylsiloxane (PDMS) kit</td>
			<td>Dow corning</td>
			<td>Sylgard 184</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Harris Uni-Core puncher</td>
			<td>Ted Pella Inc.</td>
			<td>15072</td>
			<td>with 0.75 mm inner-diameter</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Removable tape</td>
			<td>3M Company</td>
			<td>Scotch Removable Tape 811</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Stereomicroscope</td>
			<td>Leica Microsystems</td>
			<td>Leica E24</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Bovine serum albumin (BSA)</td>
			<td>Bersing Technology</td>
			<td>ALB001.500</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">DMEM basal medium</td>
			<td>Gibco</td>
			<td style="width:235px;">12800-017</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Fetal bovine serum</td>
			<td>Thermo Hyclone</td>
			<td>SH30071.03HI</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Antibiotics</td>
			<td>Biowest</td>
			<td>L0014-100</td>
			<td>Glutamine-Penicillin-Streptomycin</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Recombinant enzyme mixture</td>
			<td>Innovative cell technology</td>
			<td style="width:235px;">AM-105</td>
			<td>Accumax</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">DiIC12(3) cell membrane dye</td>
			<td>BD Biosciences</td>
			<td style="width:235px;">354218</td>
			<td>Used as a cell tracker</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Syringe pump</td>
			<td>Harvard Apparatus</td>
			<td style="width:235px;">703007</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Plastic syringe (1 mL)</td>
			<td>BD Biosciences</td>
			<td style="width:235px;">309659</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:401px;">23 gauge blunt needles</td>
			<td>Ever Sharp Technology, Inc.</td>
			<td style="width:235px;">TD21</td>
			<td></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;">Poly-tetrafluoroethene (PTFE) tubing</td>
			<td>Ever Sharp Technology, Inc.</td>
			<td style="width:235px;">TFT-23T</td>
			<td>&#160;inner diameter, 0.51 mm; outer diameter, 0.82 mm</td>
		</tr>
	</tbody>
</table>

a microfluidic platform for high-throughput single-cell isolation and culture

Studying the heterogeneity of single cells is crucial for many biological questions, but is technically difficult. Thus, there is a need for a simple, yet high-throughput, method to perform single-cell culture experiments. Here, we report a microfluidic chip-based strategy for high-efficiency single-cell isolation (~77%) and demonstrate its capability of performing long-term single-cell culture (up to 7 d) and cellular heterogeneity analysis using clonogenic assay. These applications were demonstrated with KT98 mouse neural stem cells, and A549 and MDA-MB-435 human cancer cells. High single-cell isolation efficiency and long-term culture capability are achieved by using different sizes of microwells on the top and bottom of the microfluidic channel. The small microwell array is designed for precisely isolating single-cells, and the large microwell array is used for single-cell clonal culture in the microfluidic chip. This microfluidic platform constitutes an attractive approach for single-cell culture applications, due to its flexibility of adjustable cell culture spaces for different culture strategies, without decreasing isolation efficiency.

The microfluidic platform for single-cell isolation and culture comprises a microchannel (200 &#181;m in height) with two sets of microwell arrays (Figure 2A). The two sets of microwell arrays are termed as capture-well (25 &#181;m in diameter and 27 &#181;m in depth) and culture-well (285 &#181;m in diameter and 300 &#181;m in depth) for single-cell isolation and culture, respectively, and each capture-well is positioned at the center of a culture-well when seen from the...

Watch this Scientific Journal Video about A Microfluidic Platform for High-throughput Single-cell Isolation and Culture at JoVE.com

A Microfluidic Platform for High-throughput Single-cell Isolation and Culture

Here, we present a protocol for isolating and culturing single cells with a microfluidic platform, which utilizes a new microwell design concept to allow for high-efficiency single cell isolation and long-term clonal culture.

Studying the heterogeneity of single cells is crucial for many biological questions, but is technically difficult. Thus, there is a need for a simple, yet ...

The overall goal of this protocol is to demonstrate the fabrication and operation of a microfluidic chip, which allows for high-efficiency single-cell isolation and culture. This method provides a useful tool for any area that would benefit from single-cell isolation and culture. The main advantage of this technique is that it is highly efficient at loading single cells into large microwell arrays.Additionally, only gentle flow and the gravitational force are used to operate the device, which minimizes the cell damage. The implication of this technique is turned towards the end diagnosis of human disease such as cancer, in which cellular heterogeneity affects the response of cell, so We came up with the idea of developing this method when we were establishing microwell cell line, because limit dilution method was very time-consuming and inefficient. Now this method can provide insight into individual cell analysis.It can also be applied to other applications such as the establishment of and time-ness of observation of individual cell course and behavior. To begin, fabricate silanized master molds for both the single cell isolation layer and the microwell culture layer, using standard photolithography as described in the accompanying text protocol. For each master mold, combine 16 grams of PDMS base with 1.6 grams of a curing agent in a disposable cup, and stir the mixtures until combined.Then, place the master molds into 150 millimeter petri dishes, and pour the PDMS on top of the molds. Place the petri dishes into a desiccator and apply a vacuum for one hour to remove air bubbles from the PDMS. After one hour, remove the dishes from the desiccator and place them in a conventional oven at 65 degrees Celsius for three to six hours to cure the PDMS.Then, remove the dishes from the oven and let them cool down to room temperature. Once cool, peel the cured PDMS capture-well array and microwell culture array from the master molds and cut out the devices using a razor blade. Next, use a 0.75 millimeter punch to create one hole at each end of the microchannel on the capture-well array layer.Use tape to clean what will become the inner surface of the device, and then place the individual layers with the inner surfaces facing up into a plasma cleaner for a brief oxygen plasma treatment. When finished, remove the PDMS layers from the plasma cleaner and use a stereo microscope to align and connect the top and bottom layers of the device. Place the aligned device in an oven at 65 degrees Celsius for 24 hours to create a permanent bond between the PDMS layers.Next, place the bonded PDMS device in deionized water and place the container in a desiccator under vacuum for 15 minutes, in order to remove the air from the microchannel of the device. With all of the air now removed from the device, place the PDMS device in a tissue culture hood and use UV light to sterilize the surface of the device for 30 minutes. Next, replace the deionized water in the device with 5%bovine serum albumin in PBS and incubate the device at 37 degrees Celsius for 30 minutes.This will block the surface and improve the transfer efficiency of isolated cells from capture-wells to the culture-wells. After 30 minutes, replace the blocking solution in the device with sterile PBS. Prepare a single-cell suspension with 2.5 million cells per milliliter and load a pipette with 50 microliters of the suspension.Then, transfer the cells into the device through the device's outlet hole. Load another 50 microliters of the cell suspension and transfer it into the device through the inlet hole to evenly fill up the entire microchannel with cells. Once loaded, use a sterile plug made from one millimeter diameter nylon fishing line to seal the outlet hole of the device.Then, fill a one milliliter sterile syringe with culture medium, eject any residual air bubbles, and set it into the syringe pump. Connect a 23 gauge blunt needle to the syringe and use polytetrafluoroethylene tubing to connect the needle to the inlet of the device. After connecting the tube, remove the plug from the outlet hole and wait two minutes while the cells settle into the single cell capture-wells by gravitational force.Next, set the syringe pump to 600 microliters per minute. Remove the outlet plug and wash away the uncaptured cells for 30 seconds. Wait two minutes for the pressure to stabilize.Then remove the tube from the inlet of the device and seal both the inlet and outlet holes with plugs to form a closed culture system. Now flip the device by hand to transfer the captured single cells to the culture microwells on the other side of the device. Then, place the device in a 100 millimeter tissue culture dish, add 10 milliliters of sterilized PBS around the device, and place the dish into an incubator.To replace the culture medium, first place two droplets of culture medium on top of the PDMS device near the inlet and outlet to avoid introducing air bubbles into the microchannel. Then, use a 0.75 millimeter biopsy puncher to punch two holes from the top of the PDMS device near the ends of the microchannel. Be sure to only punch through the top layer of the device.Next, fill a one milliliter plastic syringe containing fresh prewarmed medium, and use a 23 gauge blunt needle and PTFE tubing to connect it to the newly created inlet port. Slowly flow approximately 120 microliters of fresh medium into the device over five minutes to replace the old medium. When finished, seal the inlet and outlet ports using two plugs, and return the device to the cell culture incubator.The number of cells that end up in the capture-wells ranges from about 68%to 85%depending on the type of cell. In addition, most of the capture-wells contain only a single cell, for all three of the cell types. Following the transfer of captured KT98 cells to the culture-wells, about 77%of the wells had only a single cell, 16%had no cells, 6%had two cells, and less than 1%of the wells had three or more cells.Over the course of seven days, isolated single cells exhibited heterogeneous growth patterns. While some of the cells multiplied, others did not. Once mastered, this technique can be done in approximately 20 minutes if it is performed properly.After watching this video, you should have a good understanding of how to use this high-throughput single cell isolation endocrinal culture platform to boost the productivity of your single cell experiments. While attempting this procedure, it's important to remember to avoid air bubbles getting into the microchannel and to prevent cells from aggregating together as time goes on.

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Bioengineering

11.1K vistas.  National Health Research Institutes, Taiwan. The overall goal of this protocol is to demonstrate the fabrication and operation of a microfluidic chip, which allows for high-efficiency single-cell isolation and culture. This method provides a useful tool for any area that would benefit from single-cell isolation and culture. The main advantage of this technique is that it is highly efficient at loading single cells into large microwell arrays.Additionally, only gentle flow and the gravitational force are used to operate the device...