Name: bilayer microfluidic device for combinatorial plug production
Uploaded: 2023-12-01T12:30:00.000+00:00
Duration: 7 min 3 s
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We would like to thank Stacey Martina of the NanoLab TuE for help with HMDS vapour deposition. This research was funded by the Institute for Complex Molecular Systems (ICMS) at TU/e and by the Netherlands Organization for Scientific Research (NWO) Gravitation programme IMAGINE! (project number 24.005.009).

1. Soft lithography
NOTE: The microfluidic device is composed of two layers, flow layer and control layer (Figure 1A), and each layer is molded from individually patterned wafers using a positive and negative photoresist respectively (Refer to Table of Materials for details of photoresist and developers).
<ol>
	<li>Perform wafer fabrication for the flow layer as described below.
	<ol>
		<li>Dehydrate a silicon wafer (100 mm diameter, &#60;1-0-0&#62; oriented, 525) overnight (12-16 h) at 250 &#176;C.</li>
		<li>Allow the wafer to cool before proceeding to spin-coating. Apply 3-4 mL of the positive photoresist to the center of the wafer.</li>
		<li>Spin for 40 s at 1400 rpm (344 rpm/s) to obtain a feature height of 45 &#181;m.</li>
		<li>Soft bake on a hotplate using a temperature ramp, increasing at the rate of 450 &#176;C /h, from 35 &#176;C to 105 &#176;C. This step can also be carried out on microfiber tissues to prevent direct contact and minimize the bubbling of the photoresist. Remove the wafer from the hotplate and allow it to cool on microfiber tissues.</li>
		<li>Place the photomask (commercially produced) corresponding to the flow layer (emulsion side down) onto the resist-coated silicon wafer and expose it under a UV lamp, at 10&#160;mW/cm2, until a total exposure of 200 mJ/cm2 is reached.</li>
		<li>Use two hotplates - one at 65 &#176;C and the other at 95 &#176;C - to perform a post-exposure bake - for 1 min and 7 min respectively - on the plates.</li>
		<li>Develop the wafer by transferring it to a Petri dish filled with developer for positive photoresist. Agitate the Petri dish by shaking it on a benchtop shaker with the wafer completely submerged and refresh the developer solution periodically until the wafer is completely developed, and the features can be clearly seen.</li>
		<li>Use demineralized water to rinse off residual resist from the wafer and check under a stereo microscope for any residues inside the channels. Remove residues by returning the wafer to the developer solution or carefully adding the developer to the wafer with a micropipette. Once completed, dry the wafer using a nitrogen spray gun.</li>
		<li>Reflow the wafer by placing it on a hotplate set to 110 &#176;C for 25 min. This process results in rounded features.</li>
		<li>Proceed to silanization of the wafer as detailed in step 1.3. 
		&#8203;NOTE: Hexamethyldisilazane (HMDS) vapor deposition can also be carried out on the silicon wafers prior to application of the resist to improve adhesion between the resist and the wafer.</li>
	</ol>
	</li>
	<li>Perform Wafer fabrication for the control layer as described below.
	<ol>
		<li>Take another silicon wafer and dehydrate by placing it on a hotplate set at 110 &#176;C for 15 min.</li>
		<li>Remove the wafer and allow it to cool to room temperature before proceeding with spin coating.</li>
		<li>Apply 5 mL of the negative photoresist to the center of the wafer.</li>
		<li>Use the following spin protocol to obtain a feature height of 40 &#181;m: 5 s at 500 rpm (100 rpm/s acceleration), 33 s at 1400 rpm (300 rpm/s), and finally decelerate to 0 rpm for 5 s at 300 rpm/s.</li>
		<li>Soft bake using two separate hotplates set to 65 &#176;C and 95 &#176;C for 1 min and 15 min respectively. Remove the wafer from the hotplate and allow it to cool on microfiber tissues.</li>
		<li>Place the photomask (commercially produced) corresponding to the control layer (emulsion side down) onto the resist-coated wafer and expose the wafer under a UV lamp, set at 15&#160;mW/cm2, until a total exposure of 250 mJ/cm2 is reached.</li>
		<li>Use two hotplates - one at 65 &#176;C and the other at 95 &#176;C - and perform a post-exposure bake of the wafer for 2 min and then 5 min respectively. Remove the wafer from the hotplate and allow it to cool on microfiber tissues.</li>
		<li>Develop the wafer by transferring it to a Petri dish filled with developer for negative photoresist for 4 min. Refresh the developer and continue the process for 4 min more.</li>
		<li>Rinse the wafer with isopropanol to remove residual photoresist and use a stereo microscope to check the wafer for any residue inside the channels.</li>
		<li>Remove residues by returning the wafer to the developer solution or carefully adding the developer to the wafer with a micropipette. Once completed, dry the wafer using a nitrogen spray gun.</li>
		<li>Once fully developed, hard bake the photoresist by placing the wafer on a hotplate set at 95 &#176;C for 10 min.</li>
		<li>Proceed to silanization as detailed in step 1.3.</li>
	</ol>
	</li>
	<li>Carry out silanization as described below.
	<ol>
		<li>Place the wafer in a desiccator. Place a glass bottle in the desiccator and add 4-5 drops of 1,1,3,3 tetramethyldisiloxane. 
		CAUTION: 1,1,3,3 tetramethyldisiloxane is not toxic but is flammable. Other silanes can be used, but they might be toxic. It is recommended to carry out silanization in a fume hood while wearing necessary Personal Protective Equipment (PPE) such as lab coat, glasses, and nitrile gloves.</li>
		<li>Pull the vacuum for 15 min and seal the desiccator for 12-16 h to allow the silane to deposit on the wafer.</li>
		<li>Open the desiccator and dispose of the glass bottle. Place the wafer in a clean Petri dish.</li>
	</ol>
	</li>
	<li>Perform microfluidic device fabrication as described below. 
	NOTE: The following protocol has been adapted from previous works23.
	<ol>
		<li>Prepare two separate PDMS solutions - one for the flow layer and one for the control layer. For each solution, mix the base agent and curing agent of the PDMS kit in a beaker and stir using a mixing rod. The control layer requires 10 g of base agent and 0.5 g of curing agent (20:1 ratio) while the flow layer requires 40 g of the base agent and 8 g of the curing agent (5:1 ratio).</li>
		<li>Degas the PDMS solutions in a desiccator until the solutions are gas-free.</li>
		<li>Place the silanized flow layer wafer in a Petri dish covered with foil and pour the corresponding PDMS solution over the wafer. Place the Petri dish back in the desiccator and pull the vacuum to degas further (for approximately 20 min).</li>
		<li>Spin coat the silanized control layer wafer with its corresponding PDMS solution. Pour 3-4 mL of the solution onto the center of the wafer and spin for 20 s at 1500 rpm at 408 rpm/s. Place the wafer on a level surface in a closed Petri dish for 20 mins.</li>
		<li>Place both the flow and control layers in an oven at 80 &#176;C for 18-20 min. Periodically monitor the two layers to check if they are cured. The layers are ready when they are tough enough to be malleable yet slightly sticky, as this improves the bonding between the two layers.</li>
		<li>Cut out the PDMS around each of the devices on the flow layer wafer with a scalpel. Make sure to not cut too close to the features and leave approximately 2 cm of space between the feature and the edges of the PDMS. Once detached from the silicon wafer, cover the PDMS block with tape on the feature side to avoid any dust contamination.</li>
		<li>Once all PDMS blocks have been cut out, place them one by one on the corresponding control layer wafer performing a rough alignment by eye.</li>
		<li>After all the blocks have been placed on their corresponding areas on the control layer, adjust the position of each of the blocks such that the control valves overlap over the corresponding flow channels to complete the alignment. This can also be carried out with the help of a stereo microscope.</li>
		<li>Remove air pockets between the two layers by applying pressure. If the air pocket is on or near a feature, take care to not collapse the channels while applying pressure.</li>
		<li>Place the devices in the 80 &#176;C oven and leave them to bond for 12-16 h. Place 100 g weights on each of the devices to improve the bonding between the two layers.</li>
		<li>Take the wafer out and cut out each individual device. Peel the devices off the control layer wafer and cover the feature side with tape.</li>
		<li>Place each individual device on a cutting mat with the feature side facing upwards and punch a hole for each of the eight flow layer inlets, eight control layer channel inlets, the oil inlets, and the outlet using a 0.75 mm biopsy punch with the feature side facing upwards.</li>
		<li>Load the plasma asher with a microscope slide and a single device with the tape removed and the feature side facing upwards. Perform the oxygen plasma ashing with a power of 30 W for a duration of 20 s.</li>
		<li>Take the device and the glass slide out as soon as the ashing is complete and place the device with the feature side downwards onto the slide. The adhesion between PDMS and glass should be immediately visible to the naked eye. Apply pressure to any regions with air pockets to squeeze the air out.</li>
		<li>Place the devices on a hotplate set to 110 &#176;C for 60 min with a weight on top to improve the bonding of the PDMS to the glass.</li>
	</ol>
	</li>
</ol>
2. Hardware setup
NOTE: A schematic of the connections to the microfluidic device is shown in Figure 1B and a realization of such a scheme using the necessary hardware is shown in Figure 2.
<ol>
	<li>Set up the Pneumatic valves as described below. 
	NOTE: Each control channel, which regulates a PDMS valve on the chip is in turn controlled by a single solenoid valve. The prototype presented here consists of eight control channels (Figure 1A), and hence eight solenoid valves are required.
	<ol>
		<li>The solenoid valves are controlled using a custom LabVIEW software program (Main Interface Program; Figure 3 and Supplementary File 1, Supplementary File 2, Supplementary File 3, Supplementary File 4). This program sends MODBUS commands via a TCP connection (Supplementary File 5, Supplementary File 6), to a WAGO controller. Connect the WAGO device to the computer with the LabVIEW program using an ethernet cable. Proceed to connect the solenoid valves sequentially to the ports on the WAGO controller. For a more detailed description, please refer to previously described protocols23.</li>
		<li>Connect the solenoid valve array to a compressed air source using 1/4 in tubing and set the pressure of the valve array to 3.5 bar. In this system, the eight valves marked 9-16 were used.</li>
	</ol>
	</li>
	<li>Set up pressure regulators&#160;as described below. 
	NOTE: A commercially available pressure pump is used to control fluid flow (Figure 2). An eight-port and a four-port pump set were used to accommodate eight aqueous inlets and two oil inlets in the device. The pressure of each port is regulated via software that is provided by the manufacturers.
	<ol>
		<li>Connect the pressure pump to a compressed air source ensuring that the supplied pressure does not exceed the maximum pressure permitted by the pump (2.2 bar for both the eight-port and the four-port controllers).</li>
		<li>Connect the pressure pumps to a computer using a USB-connector.</li>
		<li>Once the pumps are switched on, they should be visible in the corresponding software. Set the pressures to zero while setting up the pumps.</li>
		<li>Connect a male luer to 3/32 in barb connector to each of the 12 female luer lock output ports on the controllers.</li>
		<li>Connect a piece of soft tubing (OD: 3 mm, ID: 1 mm, L: 15 cm) to the barb. Connect another male luer to 3/32 in barb connector to the other end of the soft tubing.</li>
		<li>Connect a luer stub (23 G, 0.5 in) to the barb connector. At this point, the pressure regulator is set up and ready to be used.</li>
	</ol>
	</li>
</ol>
3. Microfluidic device setup
<ol>
	<li>Connect the control channel tubing as described below (Figure 2).
	<ol>
		<li>For each control channel, cut a length of PolyTetraFluoroEthylene (PTFE) tubing (OD: 0.042 in, ID: 0.022 in). Insert the pin of a 23 G, 0.5&#160;in luer stub at one end.</li>
		<li>Connect the luer stub to a male luer to&#160;3/32 in barb nylon connector. Insert the barb of the connector into a length of polyurethane tubing (OD: 4 mm, ID: 2.5 mm). Connect the other end of the polyurethane tubing directly to a solenoid valve.</li>
		<li>Fill a syringe with water and connect a 23 G, 0.5 in luer stub at the end.</li>
		<li>Connect the free end of the PTFE tubing to this syringe and inject water until approximately halfway through the tubing.</li>
		<li>Disconnect the tubing from the syringe and insert the free end of the tubing into a punched hole of the corresponding control channel (Figure 1A-C1-8). Repeat until each control channel has been connected to its corresponding solenoid valve. 
		NOTE: In this paper, the solenoid valves 9-16 were connected to the control channels corresponding to C1 to C8, respectively. While these can be connected in any manner, it is important to remember the order and sequence of the connections, especially while operating the Main Interface program.</li>
		<li>Use the Main Interface program (Figure 3) to open all the solenoid valves (Pressurize all control channels). This will push the fluid from the tubing into the control channels of the microfluidic device and thereby filling it up. An example of pressurized and depressurized valves is shown in Figure 4.</li>
	</ol>
	</li>
	<li>Connect reagents and prime the device as described below.
	<ol>
		<li>Ensure that all control channels are pressurized by pressing the Pressurize all Control Channels button in the Main Interface program (Figure 3).</li>
		<li>For each of the aqueous reagents, cut a segment of PTFE tubing (OD: 0.042 in, ID: 0.022 in) long enough to connect the pumps to the inlets of the microfluidic device inlets. Connect one of the tubing to the luer stub from step 2.2.6.</li>
		<li>Fill a syringe with the required reagent and connect a 23 G, 0.5 in luer stub at the end.</li>
		<li>Inject the reagent into the corresponding PTFE tubing until the tubing is full. Take care that the reagent does not enter the output port on the pump set.</li>
		<li>Insert the free end of the tubing into a corresponding inlet in the microfluidic chip.</li>
		<li>Apply a pressure of 400 mbar to each of the inlet aqueous reagents using the software provided.</li>
		<li>Sequentially depressurize the control channels individually using the Main Interface program (Figure 3) to ensure that all the reagents have reached the T-junction of the device. Actuate individual valves , if needed, by pressing the corresponding buttons on the program in the box Control Channels Manual Pressurization.</li>
		<li>Repeat steps 3.2.3 to 3.2.5 for the oil reagents. Apply a pressure of 400 mbar to each of the inlet oil reagents.</li>
		<li>Simultaneously depressurize all the control channels by pressing Depressurize All Control Channels (Figure 3) until all the air has been removed from the device. This is observable by the naked eye or under a microscope.</li>
		<li>Pressurize all the control channels by pressing Pressurize All Control Channels button (Figure 3). At this stage, all reagents have been connected and the device is primed and ready to use.</li>
	</ol>
	</li>
	<li>Program and execute the experiment as described below.
	<ol>
		<li>Encode the composition, sequence, and replicates of each plug population to be produced in a .csv file as shown in Supplementary File 7 which serves as the input for the Automatic Experiment in the Main Interface program (Figure 3). Mark the necessary control channels with a 0 if its corresponding to an inlet needs to be open and a 1 if it needs to be closed. Each row in the .csv file corresponds to one distinct plug population.</li>
		<li>Load the .csv on to the Main Interface program by clicking on the Folder button in the Experiment File tab.</li>
		<li>Enter the relevant fields in the program such as Iterations of experiment (to determine how many times the given sequence of plugs are produced), Time of depressurization (to determine how long the inlet channels need to be open and the corresponding control channel needs to be depressurized in milliseconds), Time of pressurization (to determine how long the inlets need to be closed between sequences of plug population in milliseconds).</li>
		<li>Select the inlet channel(s) corresponding to barcode production in the Barcode Inlets (up to 3 channels) section along with the duration for which they need to be open (Time for Barcoding (ms)). Alternatively, these barcodes can also be hardcoded into the input .csv file as shown in Supplementary File 7.</li>
		<li>Reduce the pressure of the inlet oil reagents to 200 mbar.</li>
		<li>Connect a PTFE tubing (OD: 0.042 in, ID: 0.022 in) of the desired length at the outlet to collect the plugs. In order to ensure uniform plug production, use tubing of approximately 100 cm prefilled with plugs for collection. This is to neutralize the difference in pressure at the outlet which is exerted by the collection of plugs in the tubing.</li>
		<li>Press Run Experiment to start the program and plug production.</li>
	</ol>
	</li>
	<li>Perform data recording and analysis as described below (see Figure 5). 
	NOTE: This section specifically outlines a method for analyzing fluorescent plugs. Depending on the nature of the plugs generated, this section can be altered as required.
	<ol>
		<li>Fill a syringe with oil (either mineral oil or fluorinated oil) and connect a 23 G 0.5 in luer stub at the end. Fasten the syringe to a pump.</li>
		<li>Connect one of the ends of the filled collection tubing to the luer stub on the syringe. Affix the other end of the filled collection tubing above the objective lens of a microscope.</li>
		<li>Place a waste reservoir below the end of the tubing near the objective.</li>
		<li>Focus the microscope on a given region of the tubing and set it to record fluorescence in the desired channel(s).</li>
		<li>Set the pump to a flow rate of 50 &#181;L/min.</li>
		<li>Record the video of the fluorescent channel as an .avi file.</li>
		<li>Analyze the .avi file using the provided python script (Supplementary File 8) to extract the average fluorescence in a predefined region of interest (ROI) per frame of the .avi file (an example of which is given in Supplementary File 9).</li>
		<li>Use the provided customized R script (Supplementary File 10) to extract the conditions and plot the raw data and the peak heights. 
		NOTE: The R script in Supplementary File 10 was used for analysis in this paper. The custom-made R functions used in this script to cut data, detect conditions using barcodes, and analyze the peak heights for individual plugs and plotting are provided in Supplementary File 11.</li>
	</ol>
	</li>
</ol>

Setup of a Microfluidic Device for Combinatorial Plug  Production

F. E. is a freelancer for TheraMe! AG. The authors declare they have no competing financial interests.

In this paper, a set of protocols for the fabrication and operation of a PDMS-based microfluidic device for the automated generation of combinatorial libraries in water-in-oil compartments called plugs has been presented. The combination of microfluidics with droplet technology provides a powerful technique to encapsulate small quantity of reagents in a large number of compartments, therefore opening avenues for large-scale combinatorial screening.
Previously, several technologies have been described to generate chemically distinct compartments using microfluidics, each with its advantages and limitations. Kulesa et al.50, described a strategy to encapsulate cells with barcodes in droplets using microtiter plates and merging these droplets using an electric field to create a combinatorial library. While such an approach can generate a lot of combinations of droplets, it is limited by the need for manual handling steps in the workflow. Tomasi et al.51 developed a microfluidic platform to merge a spheroid (free floating cell aggregates)-containing droplet with a stimulus droplet, thereby allowing the manipulation of the spheroid microenvironment. This method allows for the study of important phenomena such as cell-cell interactions and the effect of drugs, but it is relatively low throughput. Eduati et al.46 and Utharala et al.47 developed a microfluidic valve-based platform that can generate high-throughput combinatorial libraries in an automated fashion. However, in these studies, the valves are operated using a Braille device, which necessitates cumbersome alignment steps between the microvalve and the microfluidic chip. A key feature of the system described in this paper is the implementation of pneumatic PDMS valves to regulate the flow of fluid in the input channels. Since these valves are PDMS-based, they can be incorporated rather smoothly into the fabrication steps of the microfluidic chip. Additionally, they are a relatively straightforward option to control the flow of liquids in the inlet channels, as they can be actuated by applying pressure through an external gas source. Finally, the duration and sequence of pressurization and depressurization of these valves can be programmed, thereby automating the production of distinct populations of plugs in a high-throughput manner. Another important feature is the use of constant pressure regimes for the injection of reagents through the inlet, which allows one to opt out of incorporating waste channels to relieve any pressure accumulation that arises in a constant flow rate regime. This simplifies the device design, reduces the need for additional valves and hardware to control the valves of the waste channel, and minimizes reagent wastage.
While the fabrication of devices with PDMS is relatively uncomplicated, the implementation of such devices does require the usage of extensive hardware paraphernalia such as the pneumatic solenoid valves (to control the actuation of the PDMS valves), pressure pumps (to control the flow of inlet and oil reagents) and software programs (to regulate the solenoid valves). While they represent a significant investment, such a setup provides consistency and reliability for the successful operation of the device. Additionally, the hardware components and architecture outlined in this protocol are set up in a modular way. Therefore, alternatives can be used for some modules to reduce costs or to adapt them to a specific need. For example, there exists a variety of pumps that can be used based on utility, budget, availability, and convenience52,53,54. Additional components such as fluid reservoirs and temperature regulators can be incorporated for sensitive inlet reagents23. Furthermore, this design can be scaled up or down to address specific scientific needs. For example, in this paper, an eight-inlet prototype is described which allows eight unique reagents to be combined to produce plugs. This can be upscaled to a 16-inlet device which allows for a higher number of inlets and larger combinations thereof. Consequently, it will need extra control channels and solenoid valves to address the inlets, but such a prototype allows larger and more diverse combinatorial libraries to be generated. Finally, in this paper, each plug population is produced by the opening of three out of the eight aqueous inlets of the microfluidic device. It was observed that for such a configuration, a pressure of approximately 200 mbar for the oil reagents and 400 mbar for the aqueous reagents corresponded to a regime of plug production, which is driven solely by valve actuation. When higher pressures were applied to the oil(s), a breakup of plugs was observed, and the application of lower pressures led to a fusion of plugs. The optimal pressure regime for plug production depends on a wide range of factors, such as the number of inlets contributing to the formation of a plug, the nature and viscosity of the fluids, and the dimensions of the channels, and should be optimized as and when necessary.
One of the drawbacks of operating in a constant-pressure regime is that fluids with different viscosities have different flow rates under constant pressure. Therefore, it needs to be ensured that the aqueous reagents flowing through the inlets are of comparable viscosities. The use of fluids of different viscosities will affect not only fluid flow in the inlet channels but also plug formation at the T-junction, thereby compromising the composition of the plug populations. Another drawback is the contamination of a plug population from residual reagents at the T-junction. When the device switches between the production of different plug populations, the first/last plug in the sequence of each population tends to be contaminated by the previous or the following population. This can be overcome by producing extra replicates of each population and discounting the contaminated plug during analysis. Finally, there is also the potential for variation between individual devices arising from inconsistencies in fabrication and/or external sources (pressure fluctuations). This issue can be mitigated by reusing a single microfluidic chip multiple times and ensuring that a complete run of a combinatorial library is performed on a single chip to minimize the effect of these inconsistencies.
The microfluidic device and the accompanying set of operational protocols presented in this paper have been used to demonstrate the production of a quantitative combinatorial library of plugs. This platform can, therefore, rapidly generate combinatorial libraries of distinct plug populations in a high-throughput manner. As a result, such technologies can be used for a variety of screening purposes including, but not limited to, combinatorial drug screening on patient biopsy samples - whereby a small number of cells retrieved from a biopsy can be distributed in a large number of droplets and treated with a large combination of the anti-cancer drug to optimize individual therapy for a given patient sample - and therefore accelerate personalized cancer therapy46,48,55.

Microfluidics allows for the manipulation of small amounts of fluids in microchannels1. The scale of operation of typical microfluidic devices is tens to hundreds of micrometers which allows the miniaturization of chemical and biological reactions, thereby enabling such reactions to be carried out with relatively small quantities of reagents. Initially, microfluidic devices were fabricated with materials such as silicon2 and glass3. Although they are still in use4, they pose certain issues, such as solvent compatibility, high cost of manufacture, and difficulties in integrating controls for fluid flow5,6. PDMS-based fabrication methodologies, termed soft-lithography, offer an inexpensive alternative for the rapid prototyping of devices7 and an avenue to fabricate complex multilayered devices8. The addition of valves and pumps to PDMS devices allows for the ability to control the routing and speed of fluids in devices9,10. Several methods to design and actuate microvalves in a reversible or irreversible manner have been developed - for example, bimetallic valves made from silicon and aluminum, which are thermally actuated11 or using gas generated from an electrochemical reaction to deflect a silicon nitride membrane12. Gu et al.&#160;demonstrate the use of the mechanical pins of a Braille display to apply pressure on microchannels to regulate flow13. One set of microvalves that has gained popularity is the pneumatic PDMS-based valves pioneered by the group of Stephen Quake14. Typically, such valves are composed of two orthogonal microchannels - a flow channel and a control channel. Upon pressurization of the control channel, a thin PDMS membrane deflects upon the flow channel, closing it off and thereby interrupting fluid flow. Once depressurized, the membrane relaxes, thereby opening the flow channel and allowing the resumption of fluid flow. PDMS valves thereby allow flow regulation in a robust and reversible manner since the control channel can be pressurized and depressurized multiple times15. Additionally, since such valves can be actuated by the application of pressure, they open up avenues for digital control and automation16. Furthermore, as they are of the same material, they can be integrated seamlessly into the fabrication of PDMS-based devices using soft-lithography techniques8,17,18. These features make PDMS valves an attractive choice for flow regulation in microfluidic devices. Thorsen et al. used the principle of such valves to design a fluidic multiplexer - a combinatory array of pneumatic valves - to address nearly a thousand input flow channels with twenty control channels19. This principle has been extended to selectively route fluids to in-chip microfluidic chemostats such that unique reactions can be carried out simultaneously in each reactor20,21,22,23. However, such microreactors, while useful in optimizing the usage of limited reagents, cannot parallelize multiple reactions and are not sufficient for high-throughput studies.
Droplet microfluidics is a subcategory of microfluidics that involves the production of droplets through the manipulation of immiscible, multiphasic liquid flow in microfluidic devices24. Droplet formation involves the breakup of a continuous fluid by the introduction of an immiscible fluid, resulting in a pinch-off due to instability in the interfacial energy and in the formation of an emulsion25. Surfactants aid in the formation of rounded droplets when emulsions leave the microchannel by stabilizing the interfacial energies26. Larger droplets, called plugs, are less stable and can be collected in a holding compartment (such as a length of tubing) as an array of aqueous compartments spaced on either side by one or more immiscible liquids27. In addition to miniaturization and compartmentalization, droplet microfluidics also offers increased throughput of biological reactions, as a large number of monodisperse droplets can be produced - each serving as a nanoreactor28. Droplets, once generated, can also be subjected to further manipulations, such as splitting29,30, fusion31,32, sorting33,34, and assemblage into higher order structures35,36. Droplet microfluidics has revolutionized several scientific fields and technologies - from PCR37 to single-cell transcriptomics38, from drug-discovery39,40 to virology41, from next-generation sequencing42 to chemical synthesis43.
Integration of PDMS-based soft-lithography and microvalves with droplet technology is a potent combination that allows for the regulation of fluid flow in microchannels and subsequent control over droplet contents. Depending on the opening and closing of channels, it is possible to produce distinct populations of droplets, each with a specific composition. Such a platform could miniaturize, compartmentalize, and parallelize biochemical reactions and therefore be a useful technique for combinatorial screening44. Combinatorial screening is a high-throughput method to generate tens of thousands of combinations of selected reagents to produce libraries which consist of individual populations of known composition. Combinatorial screening has been used to discover synergistic effects between drugs and antibiotics for bacterial growth inhibition45. In the field of cancer therapy, combinatorial screening has been used to test combinations of anti-cancer drugs for a given patient thereby advancing personalized therapy46,47. Mathur et al. have built on this technology by integrating a combinatorial DNA barcoding approach to assess transcriptome changes in high-throughput drug screening48. Thus, combinatorial screening is a powerful yet nascent technology, and there is a need for developing diverse microfluidic technologies to execute and facilitate such screening procedures.
The goal of this manuscript is to present a complete set of protocols for the fabrication of a bilayer microfluidic device capable of generating a combinatorial library of water-in-oil plugs and describe the hardware and software needed for the operation of such a device. The fluid flow is regulated using pressure-controlled PDMS-based pneumatic valves, which are in turn controlled by a custom LabVIEW program. Flow of reagents in the device is achieved using commercially available pressure pumps. An eight-inlet prototype is presented wherein a plug is formed by the contents of three inlets, each containing an aqueous reagent. The aqueous phase meets a continuous oil phase, and plugs are produced at a T-junction with a frequency of 0.33 Hz. The functioning of the system is demonstrated by producing a quantitative library containing three distinct populations of fluorescent plugs. This technology and set of protocols will help to expedite the production of combinatorial libraries for high-throughput screening purposes.

<table><tbody><tr><td>1,1,3,3 tetramethyldisiloxane</td><td>Merck Life Science NV</td><td>MFCD00008256</td><td></td></tr><tr><td>4 channel digital input/output module</td><td>WAGO Kontakttechnik GmbH</td><td>750-504</td><td></td></tr><tr><td>Acetone</td><td>Boom Labs</td><td>BOOMSKEUZW3</td><td></td></tr><tr><td>Analysis Software</td><td>Eindhoven University of Technology</td><td>https://github.com/SysBioOncology/BilayerMicrofluidicsAnalysis_JoVE</td><td></td></tr><tr><td>AZ 40XT 11D</td><td>Merck Life Science NV&amp;nbsp;</td><td>212299</td><td>&amp;nbsp;Positive photoresist&amp;nbsp;</td></tr><tr><td>AZ 726 MIF developer</td><td>Merck Life Science NV</td><td>10055824960</td><td>Developer for positive photoresist</td></tr><tr><td>Biopsy Punch, Rapid Core</td><td>World Precision Instruments Germany, GMBH</td><td>504529</td><td>0.75 mm ID, W/Plunge</td></tr><tr><td>Blue food dye</td><td>PME</td><td>FC1036</td><td></td></tr><tr><td>Controller end module&amp;nbsp;</td><td>WAGO Kontakttechnik GmbH&amp;nbsp;</td><td>750-600</td><td></td></tr><tr><td>Ethernet Controller&amp;nbsp;</td><td>WAGO Kontakttechnik GmbH&amp;nbsp;</td><td>750-881</td><td></td></tr><tr><td>FC-40</td><td>Merck Millipore</td><td>F9755-100ML</td><td></td></tr><tr><td>Fluigent flow unit</td><td>Fluigent</td><td>FLU-S-D</td><td></td></tr><tr><td>Fluigent pressure system&amp;nbsp;</td><td>Fluigent&amp;nbsp;</td><td>MFCS-EZ&amp;nbsp;</td><td>0 - 2 bar</td></tr><tr><td>Fluorescein</td><td>Merck Life Science NV</td><td>MFCD00005050</td><td></td></tr><tr><td>Hot plate&amp;nbsp;</td><td>Torrey Pines Scientific&amp;nbsp;</td><td>HP61</td><td></td></tr><tr><td>Inverted microscope&amp;nbsp;</td><td>Nikon Instruments&amp;nbsp;</td><td>Eclipse Ti-E</td><td></td></tr><tr><td>Isopropanol</td><td>Boom Labs</td><td>BOOMSKEUZE3</td><td></td></tr><tr><td>LabVIEW (Software Version 20)</td><td>Eindhoven University of Technology</td><td>https://github.com/SysBioOncology/BilayerMicrofluidicsAnalysis_JoVE/tree/main/LabVIEW_8_inlet_device_&lt;br/&gt; VERSION_1</td><td>All files have been saved for LabVIEW version 20. It is advised to use this version or higher to open the files.</td></tr><tr><td>Luer stubs&amp;nbsp;</td><td>Instech Laboratories, Inc.&amp;nbsp;</td><td>LS23</td><td>23 ga, 0.5&quot;</td></tr><tr><td>Male Luer to barb connectors&amp;nbsp;</td><td>Cole Parmer&amp;nbsp;</td><td>45505-32&amp;nbsp;</td><td>3/32&quot; ID</td></tr><tr><td>MasterFlex PTFE tubing</td><td>Avator/VWR</td><td>48634</td><td></td></tr><tr><td>Microscope Slides</td><td>VWR</td><td>470150-480</td><td></td></tr><tr><td>Microscope slides,&amp;nbsp; Plain</td><td>Corning</td><td>2947-75X50</td><td></td></tr><tr><td>Mineral Oil</td><td>Merck Millipore</td><td>330760-1L</td><td></td></tr><tr><td>mr DEV 600</td><td>Micro resist Technology</td><td>R815100</td><td>Developer for negative photoresist</td></tr><tr><td>Oven</td><td>Thermo Scientific</td><td>&amp;nbsp;Heraeus T6P 50045757</td><td></td></tr><tr><td>Oxygen plasma asher</td><td>Quorum Technologies</td><td>K1050X</td><td></td></tr><tr><td>Photomask</td><td>CAD/Art Services, Inc.</td><td></td><td></td></tr><tr><td>Photomask Design</td><td>Eindhoven University of Technology (Adapted from Merten Lab, EPFL)</td><td>https://github.com/SysBioOncology/BilayerMicrofluidicsAnalysis_JoVE/blob/main/8_inlet_JoVE_device_design.dwg</td><td></td></tr><tr><td>Pneumatic valve array</td><td>FESTO</td><td></td><td>1x 8 valve array, Normally closed valves</td></tr><tr><td>Silicon Wafers</td><td>Silicon Materials</td><td></td><td>&amp;lt;1-0-0&gt;, 100 mm diameter, 525 &amp;mu;m thickness</td></tr><tr><td>Single edge blades&amp;nbsp;</td><td>GEM Scientific</td><td></td><td></td></tr><tr><td>Soft tubing</td><td>Fluigent</td><td></td><td>1 mm ID, 3 mm OD</td></tr><tr><td>Spin coater&amp;nbsp;</td><td>Laurell Technologies Corporation&amp;nbsp;</td><td>WS-650MZ-23NPPB</td><td></td></tr><tr><td>Stereo microscope&amp;nbsp;</td><td>Olympus Corporation&amp;nbsp;</td><td>SZ61</td><td></td></tr><tr><td>SU-8 3050</td><td>Kayakli Advanced Materials</td><td>Y311075 1000L1GL</td><td>Negative photoresist</td></tr><tr><td>Sylgard 184 Silicone Elastomer Kit (PDMS)</td><td>Dow</td><td>1317318</td><td></td></tr><tr><td>Syringe</td><td>B Braun Injekt - F Fine Dosage Syringe</td><td>10303002</td><td></td></tr><tr><td>UV-LED exposure system</td><td>Idonus</td><td>UV-EXP150S-SYS</td><td></td></tr><tr><td>Vacuum pump</td><td>&amp;nbsp;Vacuumbrand GmbH&amp;nbsp;</td><td>MD1C</td><td></td></tr><tr><td>Weighing scales&amp;nbsp;</td><td>Sartorius&amp;nbsp;</td><td>M-prove</td><td></td></tr></tbody></table>

bilayer microfluidic device for combinatorial plug production

Droplet microfluidics is a versatile tool that allows the execution of a large number of reactions in chemically distinct nanoliter compartments. Such systems have been used to encapsulate a variety of biochemical reactions - from incubation of single cells to implementation of PCR reactions, from genomics to chemical synthesis. Coupling the microfluidic channels with regulatory valves allows control over their opening and closing, thereby enabling the rapid production of large-scale combinatorial libraries consisting of a population of droplets with unique compositions. In this paper, protocols for the fabrication and operation of a pressure-driven, PDMS-based bilayer microfluidic device that can be utilized to generate combinatorial libraries of water-in-oil emulsions called plugs are presented. By incorporating software programs and microfluidic hardware, the flow of desired fluids in the device can be controlled and manipulated to generate combinatorial plug libraries and to control the composition and quantity of constituent plug populations. These protocols will expedite the process of generating combinatorial screens, particularly to study drug response in cells from cancer patient biopsies.

One of the crucial features of the microfluidic chip are the PDMS valves and their ability to regulate fluid flow was characterized as it influences the operational paradigm of the device. To this end, the flow rate of distilled water (measured using a commercial flow rate sensor) through the inlet channels was recorded as a function of different input pressures whilst periodically pressurizing (3.5 bar for 2000 ms) and depressurizing (1000 ms) the PDMS valves (Figure 6A). It was observed that the valves were able to regulate fluid flow until approximately 800 mbar of input pressure, as indicated by the drop in flow rate to zero when the valves are actuated (Figure 6 B-D). This validates the use of such PDMS-based valves to regulate the flow of reagents inside the channels. Furthermore, at 1200 mbar, the input pressure is too high for the valves to regulate the flow, as is evidenced by the flow rate not reducing to zero (Figure 6E). Whilst the duration of pressurization and depressurization of the PDMS valves can be modified, the rate of change of fluid flow upon the current conditions of pressurization (2000 ms) and depressurization (1000 ms) was calculated. For an input pressure of 400 mbar, the flow can be switched on and off at the rate of 1.26 Hz and 1.44 Hz respectively (Figure 6C).
Previous iterations of a similar combinatorial high-throughput microfluidic device also incorporated a waste channel coupled to every flow channel46,47. These devices were operated in a constant flow rate regime (where reagents were injected into the device at constant flow rates rather than constant pressure), and the waste channels were programmed to open when their corresponding inlet channels were closed to alleviate any pressure build-up. Such channels, while useful, result in a loss of reagents as the contents of the waste channel do not contribute toward plug formation. Furthermore, additional control channels - and thereby additional pumps - are also required to regulate the opening and closing of the waste channels. In the prototype presented here, the waste channels were removed, and an operational paradigm was established that allows for reduced wastage of reagents and a scale-down of design and operational complexity. This involves injecting the aqueous reagents in constant pressure mode as opposed to constant flow rate mode. To better understand the two regimes, the relationship between pressure and flow rate in the channels during valve actuation was assessed in each case (using the same setup as shown in Figure 6A), the results of which are shown in Figure 7. In Figure 7A, the flow rate of distilled water was measured while being injected at a constant pressure (300 mbar) and it was observed that during valve actuation, the flow rate drops to zero and upon depressurization of the valve the flow rate recovers to pre-actuation levels. However, in a constant flow rate regime, wherein the pressure in the channels was recorded whilst injecting the distilled water at a constant flow rate (2.5 &#181;L/min; Figure 7B), valve actuation did not result in complete inlet closure - evidenced by the flow rate not dropping to zero - and a build-up of pressure in the channel was observed. This is the pressure that is relieved by the opening of waste channels. Since a constant input pressure regime allows the operation of the device without back pressure upon valve actuation, thereby negating the need for waste channels, this regime was adopted for the operation of the microfluidic chip.
To demonstrate the functionality of the microfluidic device, a quantitative combinatorial library of fluorescent plugs was generated. To the eight inlets of the device, three aqueous reagents - fluorescein (50 &#181;M) in four inlets (I1, I3, I5, I7), distilled water in three inlets (I4, I6, I8), one inlet with a blue color dye (I2; to act as a barcode) - and two oil reagents - fluorinated oil (FC-40) and mineral oil (MO) in inlets O1 and O2, respectively - were plugged in (Figure 1A, Figure 8A). The fluorinated oil serves as the carrier phase in which the aqueous plugs are dispersed, and the mineral oil aids in plug stability and minimizes adhesion of plug content to the walls, thereby minimizing cross-contamination between plugs46. With three inlets contributing to the composition of a single plug population, this configuration can generate three distinct fluorescent populations: FFF - composed of fluorescein from three channels, FFW - composed of fluorescein from two channels, and water from one channel, and FWW - composed of fluorescein from one channel and water from two channels. With this setup, there are 12 distinct conditions (plug populations produced with a distinct combination of three inlets) that can produce FWW plugs, 18 distinct conditions that can produce FFW plugs, and four distinct conditions that can produce FFF plugs. Therefore, the chip was programmed to produce these 34 different conditions with five different replicate plugs each, along with five replicates of barcode plugs separating them. It is recommended to intersperse the fluorescent plug populations with a barcode population, i.e., a set of colored (ideally non-fluorescent) plugs (in this case formed by opening the inlet channels corresponding to the blue dye and two distilled water channels) which are visible to the naked eye. It allows the user to monitor the plug production for issues such as plug break-up or fusion and helps in the downstream analysis of plugs. Therefore, a total of 340 plugs - 170 experimental plugs and 170 barcoding plugs separating the different conditions - were generated and collected in PTFE tubing, a sample of which is shown in Figure 8B. The time of depressurization and time of pressurization were set at 1000 ms and 2000 ms, respectively. The fluorescence of the plugs and their variability within and across the different experimental conditions were analyzed, the results of which are shown in Figure 8C,D. Figure 8C shows the fluorescence per frame of the .avi file generated in step 3.4.6, which highlights the 34 experimental conditions in consideration (demarcated by a blue line). The mean fluorescent value of peaks within a condition is shown in red, and the dashed lines indicate the standard error within that condition. The heights of the peaks of all the plugs in each population, obtained by subtracting the baseline fluorescence from the maximum fluorescence detected in each peak, were plotted in Figure 8D. The last peak in each condition was neglected for the calculations as it was a contaminated plug due to the intermixing of reagents at the T-junction (since the fluorescence of the plugs was recorded in reverse order of plug production, the first plug in a population during production is the last plug in a population during analysis). It was evident that the height of the FWW plugs is about one-third (mean = 40.9, standard deviation = 3.1) and that of the FFW plugs is about two-thirds (mean = 78.4, standard deviation = 5) of the height of the FFF plugs (mean = 117, standard deviation = 10). These results match the expected proportions of fluorescence in different populations of FFF/FFW/FWW plugs, which highlights the robustness of the device and its functioning.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/66154/66154fig01.jpg" /> 
Figure 1: Schematic of the device design and microfluidic set up. (A) The flow layer of the chip is shown in blue and the control layer is shown in red. A total of eight unique aqueous reagents can flow through the inlets (I1-8) towards the T-junction, where they encounter the oil phases from the oil inlets (O1-2) to form plugs which are collected at the outlet. Each inlet flow channel is under the control of a unique control channel (C1-8). (B)&#160;Schematic of the microfluidic chip along with the tubing connections to the inlets, control channels, and oil reagents is shown along with the outlet tubing. Arrows indicate the direction of fluid flow in the tubing. The inset shows the working principle of PDMS valves. Dashed lines indicate that the control layer is beneath the flow layer. This figure has been modified from Dubuc et al49. <a href="https://www.jove.com/files/ftp_upload/66154/66154fig01large.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/66154/66154fig02.jpg" /> 
Figure 2: Schematic of the hardware setup for plug production. The pressure pumps control the flow of reagents (both aqueous and oil) in the inlet channels, and the solenoid valves control the actuation of the PDMS valves. <a href="https://www.jove.com/files/ftp_upload/66154/66154fig02large.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/66154/66154fig03.jpg" /> 
Figure 3: The main interface program to control the microfluidic device. This custom-made program enables manual pressurization of individual pneumatic valves (white panel). It also allows the execution of a complete experiment (blue panel) where it accepts a .csv file with the desired plug populations and necessary parameters such as valve pressurization and depressurization times and displays the status of the experiment execution, including which control channels are pressurized and not, in real-time. <a href="https://www.jove.com/files/ftp_upload/66154/66154fig03large.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/66154/66154fig04.jpg" /> 
Figure 4: Pressure-driven valve actuation. Bright-field microscopy images of (A) PDMS-valve (horizontal) being depressurized and the inlet channel (vertical) being open and (B) PDMS-valve being pressurized and closing off the inlet channel. <a href="https://www.jove.com/files/ftp_upload/66154/66154fig04large.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/66154/66154fig05.jpg" /> 
Figure 5: Schematic of the data recording setup. The collection tubing is connected to a syringe with oil, which is affixed to a pump. The plugs are flown through the collection tubing, and images/videos are captured using a fluorescence microscope. <a href="https://www.jove.com/files/ftp_upload/66154/66154fig05large.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/66154/66154fig06.jpg" /> 
Figure 6: Effect of valve actuation on flow rate at a given input pressure. (A) Schematic of the hardware setup used to monitor flow rate in the microfluidic channels. The response of the flow rate in the channels when operated at different input pressures of (B) 200 mbar, (C) 400 mbar, (D) 800 mbar, and (E) 1200 mbar. Duration of valve actuation is shown in the red shaded region. Distilled water was used for all experiments. Standard deviation of three independent measurements is shown by the green shaded region. <a href="https://www.jove.com/files/ftp_upload/66154/66154fig06large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 7" class="xfigimg" src="/files/ftp_upload/66154/66154fig07.jpg" /> 
Figure 7: Relationship between pressure and flow rate of reagents in the inlet channels upon valve actuation. (A) In a constant input pressure regime (300 mbar) valve the flow rate reduces to zero upon valve actuation. (B) In a constant flow rate regime (2.5 &#181;L/min) valve actuation results in rapid pressure build up in the channel until the valve is depressurized. Duration of valve actuation is shown in the red shaded region. Distilled water was used for all experiments. <a href="https://www.jove.com/files/ftp_upload/66154/66154fig07large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
<img alt="Figure 8" class="xfigimg" src="/files/ftp_upload/66154/66154fig08.jpg" /> 
Figure 8: Production of fluorescent plug populations. (A) Schematic of the experimental setup depicting the connection of the different reagents to the device. Abbreviations: F = Fluorescein, W = distilled water, B = Blue food dye, FC-40 = fluorinated oil, and MO = mineral oil. (B) Sample picture of collection tubing containing plugs. (C) Raw data obtained from the analysis shows the average fluorescence intensity measured in a specified region of interest (ROI) vs the frame number of the video file. Red lines show the mean of the peak fluorescence for each condition (population of plugs produced with a specific combination of three inlets), and the dashed lines show the corresponding standard error. (D) Boxplots of the height of the peaks in the different conditions. Dots correspond to individual peaks, boxes for each condition range from the first to the third quartile of the distribution of the corresponding peaks, and the thick line is used for the median value. <a href="https://www.jove.com/files/ftp_upload/66154/66154fig08large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Supplementary File 1: The main interface program for device operation. The control interface for manual pressurization of the control channels and running an automatic experiment in the eight-inlet device. <a href="https://www.jove.com/files/ftp_upload/66154/8_inlet_device_with_barcode.zip" target="_blank">Please click here to download this File.</a>
Supplementary File 2: Alternate main interface program for device operation. The control interface for running an eight-inlet device without a barcoding function. <a href="https://www.jove.com/files/ftp_upload/66154/8_inlet_device_without_barcode.zip" target="_blank">Please click here to download this File.</a>
Supplementary File 3: LabVIEW sub-program with global variables. SubVI of the main interface&#160;program listing and displaying the status of the global variables in the main interface program, namely the control channels. <a href="https://www.jove.com/files/ftp_upload/66154/Global_Valves.zip" target="_blank">Please click here to download this File.</a>
Supplementary File 4: LabVIEW program to save values of global variables. SubVI of the main interface&#160;program that saves the current state of the valves as an array, which will be used to maintain the same state of the valves in case of the user being inactive for more than 30 seconds. <a href="https://www.jove.com/files/ftp_upload/66154/Save_current_command.zip" target="_blank">Please click here to download this File.</a>
Supplementary File 5: Transmission Control Protocol (TCP) LabVIEW program. SubVI for maintaining the TCP connection between the main interface program and the WAGO controller. <a href="https://www.jove.com/files/ftp_upload/66154/TCP_WRITE_READ_SV.zip" target="_blank">Please click here to download this File.</a>
Supplementary File 6: TCP global variable LabVIEW sub-program. Program to store the TCP output variable. <a href="https://www.jove.com/files/ftp_upload/66154/TCP_GV.zip" target="_blank">Please click here to download this File.</a>
Supplementary File 7: Input for carrying out automatic experiment. The&#160;.csv file encoding composition, sequence, and replicas of plug populations for carrying out experiments to produce quantitative fluorescent plugs, as detailed in this paper. <a href="https://www.jove.com/files/ftp_upload/66154/Sequence of plug production.zip" target="_blank">Please click here to download this File.</a>
Supplementary File 8: Python script for analysis of fluorescent plug population. Custom&#160;python script to readout fluorescence values from the recording of plugs (.avi file). <a href="https://www.jove.com/files/ftp_upload/66154/extract_fluorescence.zip" target="_blank">Please click here to download this File.</a>
Supplementary File 9: Output of fluorescence analysis of plugs. Output from the Python script containing fluorescence values for a 5x5 ROI from the recording of the plugs. <a href="https://www.jove.com/files/ftp_upload/66154/Data_0727_Raw Data_Analysis5x5.zip" target="_blank">Please click here to download this File.</a>
Supplementary File 10: R program to read output file. Custom program used in this work to read the output fluorescent values and plot raw data, peak heights, and standard deviations. <a href="https://www.jove.com/files/ftp_upload/66154/main_peaks_analysis.zip" target="_blank">Please click here to download this File.</a>
Supplementary File 11: R functions for analyzing and plotting fluorescent data. Custom&#160;R functions which are used to 1. cut the raw data of the fluorescent values, 2. define different experimental conditions, 3. identify peaks from the given conditions, 4.plot the raw data and the detected conditions overlapped, and 5. plot the identified peaks and the raw data overlapped. <a href="https://www.jove.com/files/ftp_upload/66154/functions_peak_analysis.zip" target="_blank">Please click here to download this File.</a>

Watch this Scientific Journal Video about Author Spotlight: Integrating Computational and Experimental Approaches in Precision Oncology at JoVE.com

Author Spotlight: Integrating Computational and Experimental Approaches in Precision Oncology

The fabrication of a polydimethylsiloxane (PDMS)-based bilayer device for the production of combinatorial libraries in water-in-oil emulsions (plugs) is presented here. The necessary hardware and software required to automate plug production are detailed in the protocol, and the production of a quantitative library of fluorescent plugs is also demonstrated.

Bilayer Microfluidic Device for Combinatorial Plug Production

Droplet microfluidics is a versatile tool that allows the execution of a large number of reactions in chemically distinct nanoliter compartments. Such ...

bilayer-microfluidic-device-for-combinatorial-plug-production

Research

JoVE Journal

Bioengineering

769 Views.  Eindhoven University of Technology. Wij van de leerstoelgroep Systeembiologie voor Oncologie gebruiken een gecombineerde computationele en experimentele benadering om het ingewikkelde mechanisme te ontrafelen dat de micro-omgeving van de tumor vormgeeft. We gebruiken wiskundige modellen op basis van klinische gegevens en kankerbiologie om factoren te identificeren die van invloed zijn op de individuele respons op therapie, met als uiteindelijk doel de precisie-oncologie te verbeteren. Gezien de heterogene en dynamische aard van...

Video: Auteur in de schijnwerpers: integratie van computationele en experimentele benaderingen in precisie-oncologie

Microfluidic Chips Controlled with Elastomeric Microvalve Arrays

Miniaturized microfluidic systems provide simple and effective solutions for low-cost point-of-care diagnostics and high-throughput biomedical assays. Robust flow control and precise fluidic volumes are two critical requirements for these applications. We have developed microfluidic chips featuring elastomeric polydimethylsiloxane (PDMS) microvalve arrays that: 1) need no extra energy source to close the fluidic path, hence the loaded device is highly portable; and 2) allow for microfabricating deep (up to 1 mm) channels with vertical sidewalls and resulting in very precise features.

The PDMS microvalves-based devices consist of three layers: a fluidic layer containing fluidic paths and microchambers of various sizes, a control layer containing the microchannels necessary to actuate the fluidic path with microvalves, and a middle thin PDMS membrane that is bound to the control layer. Fluidic layer and control layers are made by replica molding of PDMS from SU-8 photoresist masters, and the thin PDMS membrane is made by spinning PDMS at specified heights. The control layer is bonded to the thin PDMS membrane after oxygen activation of both, and then assembled with the fluidic layer. The microvalves are closed at rest and can be opened by applying negative pressure (e.g., house vacuum). Microvalve closure and opening are automated via solenoid valves controlled by computer software.

Here, we demonstrate two microvalve-based microfluidic chips for two different applications. The first chip allows for storing and mixing precise sub-nanoliter volumes of aqueous solutions at various mixing ratios. The second chip allows for computer-controlled perfusion of microfluidic cell cultures.

The devices are easy to fabricate and simple to control. Due to the biocompatibility of PDMS, these microchips could have broad applications in miniaturized diagnostic assays as well as basic cell biology studies.

We demonstrate protocols for manufacturing and automating elastomeric polydimethylsiloxane (PDMS)-based microvalve arrays that need no extra energy to close and feature photolithographically defined precise volumes. A parallel subnanoliter-volume mixer and an integrated microfluidic perfusion system are presented.

Miniaturized microfluidic systems provide simple and effective solutions for low-cost point-of-care diagnostics and high-throughput biomedical assays.  ...

Biology

High-throughput Protein Expression Generator Using a Microfluidic Platform

Rapidly increasing fields, such as systems biology, require the development and implementation of new technologies, enabling high-throughput and high-fidelity measurements of large systems. Microfluidics promises to fulfill many of these requirements, such as performing high-throughput screening experiments on-chip, encompassing biochemical, biophysical, and cell-based assays1. Since the early days of microfluidics devices, this field has drastically evolved, leading to the development of microfluidic large-scale integration2,3. This technology allows for the integration of thousands of micromechanical valves on a single device with a postage-sized footprint (Figure 1). We have developed a high-throughput microfluidic platform for generating in vitro expression of protein arrays (Figure 2) named PING (Protein Interaction Network Generator). These arrays can serve as a template for many experiments such as protein-protein 4, protein-RNA5 or protein-DNA6 interactions.
The device consist of thousands of reaction chambers, which are individually programmed using a microarrayer. Aligning of these printed microarrays to microfluidics devices programs each chamber with a single spot eliminating potential contamination or cross-reactivity Moreover, generating microarrays using standard microarray spotting techniques is also very modular, allowing for the arraying of proteins7, DNA8, small molecules, and even colloidal suspensions. The potential impact of microfluidics on biological sciences is significant. A number of microfluidics based assays have already provided novel insights into the structure and function of biological systems, and the field of microfluidics will continue to impact biology.

We present a microfluidic approach for the expression of protein arrays. The device consists of thousands of reaction chambers controlled by micro-mechanical valves. The microfluidic device is mated to a microarray-printed gene library. These genes are then transcribed and translated on-chip, resulting in a protein array ready for experimental use.

Rapidly increasing fields, such as systems biology, require the development and implementation of new technologies, enabling high-throughput and ...

A Microfluidic Device for Studying Multiple Distinct Strains

The study of cell responses to environmental changes poses many experimental challenges: cells need to be imaged under changing conditions, often in a comparative manner. Multiwell plates are routinely used to compare many different strains or cell lines, but allow limited control over the environment dynamics. Microfluidic devices, on the other hand, allow exquisite dynamic control over the surrounding conditions, but it is challenging to image and distinguish more than a few strains in them. Here we describe a method to easily and rapidly manufacture a microfluidic device capable of applying dynamically changing conditions to multiple distinct yeast strains in one channel. The device is designed and manufactured by simple means without the need for soft lithography. It is composed of a Y-shaped flow channel attached to a second layer harboring microwells. The strains are placed in separate microwells, and imaged under the exact same dynamic conditions. We demonstrate the use of the device for measuring protein localization responses to pulses of nutrient changes in different yeast strains.

We present a simple method to produce microfluidic devices capable of applying similar dynamic conditions to multiple distinct strains, without the need for a clean room or soft lithography.

The study of cell responses to environmental changes poses many experimental challenges: cells need to be imaged under changing conditions, often in a ...

Microfluidic Pneumatic Cages: A Novel Approach for In-chip Crystal Trapping, Manipulation and Controlled Chemical Treatment

The precise localization and controlled chemical treatment of structures on a surface are significant challenges for common laboratory technologies. Herein, we introduce a microfluidic-based technology, employing a double-layer microfluidic device, which can trap and localize in situ and ex situ synthesized structures on microfluidic channel surfaces. Crucially, we show how such a device can be used to conduct controlled chemical reactions onto on-chip trapped structures and we demonstrate how the synthetic pathway of a crystalline molecular material and its positioning inside a microfluidic channel can be precisely modified with this technology. This approach provides new opportunities for the controlled assembly of structures on surface and for their subsequent treatment.

Herein, we describe the fabrication and operation of a double-layer microfluidic system made of polydimethylsiloxane (PDMS). We demonstrate the potential of this device for trapping, directing the coordination pathway of a crystalline molecular material and controlling chemical reactions onto on-chip trapped structures.

The precise localization and controlled chemical treatment of structures on a surface are significant challenges for common laboratory technologies. ...

Chemistry

High Throughput Microfluidic Rapid and Low Cost Prototyping Packaging Methods

In this work, 3 different packaging and assembly techniques are presented. They can be classified into two categories: one-time use and reusable packaging techniques.
The one-time use packaging technique employs UV-based and temperature curing epoxies to connect microtubes to access holes, wire-bonding for integrated circuit connections, and silver epoxy for electrical connections. This method is based on a robust assembly technique that can support relatively high pressure close to 1 psi and does not need any support to strengthen the microfluidic architecture.
Reusable packaging techniques consist of PDMS-based microtube interconnectors and anisotropic adhesive films for electrical connections. These devices are more sensitive and fragile. Consequently, Plexiglas support is added to the microfluidic structure to improve the electrical contact when anisotropic adhesive films are used, and also to strengthen the microfluidic architecture. In addition, a micromanipulator is needed to maintain tubes while using a thin PDMS layer to connect them to the access holes. Different PDMS layer thicknesses, ranging from 0.45-3 mm, are tested to compare the best adherence versus injection rates. Applied injection rates are varied from 50-300 &#956;l/hr for 0.45-3 mm PDMS layers, respectively. These techniques are mainly applicable for low-pressure applications. However, they can be extended for high-pressure ones through plasma-oxygen process to permanently seal the PDMS to glass substrates. The main advantage of this technique, besides the fact that it is reusable, consists of keeping the device observable when the microchannel length is very short (in the range of 3 mm or lower).

In this article we describe different techniques for microfluidic rapid prototyping platforms. The proposed techniques are based on ultraviolet (UV) sensitive and temperature curing epoxies, polydimethylsiloxane (PDMS) based tubing, wire-bonding, and anisotropic adhesive films. The assembling procedures presented are developed for both one-time use devices as well as reusable microfluidic systems.

In this work, 3 different packaging and assembly techniques are presented. They can be classified into two categories: one-time use and reusable packaging ...

Combining Fluidic Devices with Microscopy and Flow Cytometry to Study Microbial Transport in Porous Media Across Spatial Scales

Understanding the transport, dispersion and deposition of microorganisms in porous media is a complex scientific task comprising topics as diverse as hydrodynamics, ecology and environmental engineering. Modeling bacterial transport in porous environments at different spatial scales is critical to better predict the consequences of bacterial transport, yet current models often fail to up-scale from laboratory to field conditions. Here, we introduce experimental tools to study bacterial transport in porous media at two spatial scales. The aim of these tools is to obtain macroscopic observables (such as breakthrough curves or deposition profiles) of bacteria injected into transparent porous matrices. At the small scale (10-1000 &#181;m), microfluidic devices are combined with optical video-microscopy and image processing to obtain breakthrough curves and, at the same time, to track individual bacterial cells at the pore scale. At larger scale, flow cytometry is combined with a self-made robotic dispenser to obtain breakthrough curves. We illustrate the utility of these tools to better understand how bacteria are transported in complex porous media such as the hyporheic zone of streams. As these tools provide simultaneous measurements across scales, they pave the way for mechanism-based models, critically important for upscaling. Application of these tools may not only contribute to the development of novel bioremediation applications but also shed new light on the ecological strategies of microorganisms colonizing porous substrates.

Breakthrough curves (BTCs) are efficient tools to study the transport of bacteria in porous media. Here we introduce tools based on fluidic devices in combination with microscopy and flow cytometric counting to obtain BTCs.

Understanding the transport, dispersion and deposition of microorganisms in porous media is a complex scientific task comprising topics as diverse as ...

Environment

Double Emulsion Generation Using a Polydimethylsiloxane (PDMS) Co-axial Flow Focus Device

Double emulsions are useful in a number of biological and industrial applications in which it is important to have an aqueous carrier fluid. This paper presents a polydimethylsiloxane (PDMS) microfluidic device capable of generating water/oil/water double emulsions using a coaxial flow focusing geometry that can be fabricated entirely using soft lithography. Similar to emulsion devices using glass capillaries, double emulsions can be formed in channels with uniform wettability and with dimensions much smaller than the channel sizes. Three dimensional flow focusing geometry is achieved by casting a pair of PDMS slabs using two layer soft lithography, then mating the slabs together in a clamshell configuration. Complementary locking features molded into the PDMS slabs enable the accurate registration of features on each of the slab surfaces. Device testing demonstrates formation of double emulsions from 14 &#181;m to 50 &#181;m in diameter while using large channels that are robust against fouling and clogging.

Double Emulsion Generation Using a Polydimethylsiloxane PDMS Co-axial Flow Focus Device

Microfluidic double emulsions generation typically involves devices with patterned wettability or custom-fabricated glass components. Here we describe the fabrication and testing of an all polydimethylsiloxane (PDMS) double emulsion generator that does not require surface treatment or complicated fabrication processes, and is capable of producing double emulsions down to 14 &#181;m.

Double emulsions are useful in a number of biological and industrial applications in which it is important to have an aqueous carrier fluid. This paper ...

Multi-step Variable Height Photolithography for Valved Multilayer Microfluidic Devices

Microfluidic systems have enabled powerful new approaches to high-throughput biochemical and biological analysis. However, there remains a barrier to entry for non-specialists who would benefit greatly from the ability to develop their own microfluidic devices to address research questions. Particularly lacking has been the open dissemination of protocols related to photolithography, a key step in the development of a replica mold for the manufacture of polydimethylsiloxane (PDMS) devices. While the fabrication of single height silicon masters has been explored extensively in literature, fabrication steps for more complicated photolithography features necessary for many interesting device functionalities (such as feature rounding to make valve structures, multi-height single-mold patterning, or high aspect ratio definition) are often not explicitly outlined. 
Here, we provide a complete protocol for making multilayer microfluidic devices with valves and complex multi-height geometries, tunable for any application. These fabrication procedures are presented in the context of a microfluidic hydrogel bead synthesizer and demonstrate the production of droplets containing polyethylene glycol (PEG diacrylate) and a photoinitiator that can be polymerized into solid beads. This protocol and accompanying discussion provide a foundation of design principles and fabrication methods that enables development of a wide variety of microfluidic devices. The details included here should allow non-specialists to design and fabricate novel devices, thereby bringing a host of recently developed technologies to their most exciting applications in biological laboratories.

Multilayer microfluidic devices often involve the fabrication of master molds with complex geometries for functionality. This article presents a complete protocol for multi-step photolithography with valves and variable height features tunable to any application. As a demonstration, we fabricate a microfluidic droplet generator capable of producing hydrogel beads.

Microfluidic systems have enabled powerful new approaches to high-throughput biochemical and biological analysis. However, there remains a barrier to ...

Soft Lithographic Procedure for Producing Plastic Microfluidic Devices with View-ports Transparent to Visible and Infrared Light

Infrared (IR) spectro-microscopy of living biological samples is hampered by the absorption of water in the mid-IR range and by the lack of suitable microfluidic devices. Here, a protocol for the fabrication of plastic microfluidic devices is demonstrated, where soft lithographic techniques are used to embed transparent Calcium Fluoride (CaF2) view-ports in connection with observation chamber(s). The method is based on a replica casting approach, where a polydimethylsiloxane (PDMS) mold is produced through standard lithographic procedures and then used as the template to produce a plastic device. The plastic device features ultraviolet/visible/infrared (UV/Vis/IR) -transparent windows made of CaF2 to allow for direct observation with visible and IR light. The advantages of the proposed method include: a reduced need for accessing a clean room micro-fabrication facility, multiple view-ports, an easy and versatile connection to an external pumping system through the plastic body, flexibility of the design, e.g., open/closed channels configuration, and the possibility to add sophisticated features such as nanoporous membranes.

A protocol for the fabrication of plastic microfluidic devices with transparent view-ports for visible and infrared light imaging is described.

Infrared (IR) spectro-microscopy of living biological samples is hampered by the absorption of water in the mid-IR range and by the lack of suitable ...

Reconfigurable Microfluidic Channel with Pin-discretized Sidewalls

Microfluidic components need to have various shapes to realize different key microfluidic functions such as mixing, separation, particle trapping, or reactions. A microfluidic channel that deforms even after fabrication while retaining the channel shape enables high spatiotemporal reconfigurability. This reconfigurability is required in such key microfluidic functions that are difficult to achieve in existing "reconfigurable" or "integrated" microfluidic systems. We describe a method for the fabrication of a microfluidic channel with a deformable sidewall consisting of a laterally aligned array of the ends of rectangular pins. Actuating the pins in their longitudinal directions changes the pins' end positions, and thus, the shape of discretized channel sidewalls.Pin gaps can cause unwanted leakage or adhesion to adjacent pins caused by meniscus forces. To close the pin gaps, we have introduced hydrocarbon-fluoropolymer suspension-based gap filler accompanied by an elastomeric barrier. This reconfigurable microfluidic device can generate strong temporal in-channel displacement flow, or can stop the flow in any region of the channel. This feature will facilitate, on demand, the handling of cells, viscous liquids, gas bubbles, and non-fluids, even if their existence or behavior is unknown at the time of fabrication.

A microfluidic channel with deformable sidewalls offers flow control, particle handling, channel dimension customization and other reconfigurations while in use. We describe a method for fabricating a microfluidic channel with sidewalls made of an array of pins that allows their shape to change.

Microfluidic components need to have various shapes to realize different key microfluidic functions such as mixing, separation, particle trapping, or ...

Bilayer Microfluidic Device for Combinatorial Plug Production

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