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25 protocols using m5904

1

Specific Virus Transduction in Mouse Brain

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In 3 male and 1 female CaMKII-tTA × tetO-GCaMP6s mice, AAV1-CaMKIIα0.4-NLS-tdTomato-WPRE (custom made by Vigene Biosciences, MD, USA) was injected during the cranial window procedure. For Scnn1a-Cre mice, AAV1-Syn-Flex-GCaMP6s-WPRE-SV40 (a gift from Douglas Kim & GENIE Project (Addgene viral prep # 100845-AAV1; http://addgene.org/100845; RRID: Addgene_100845)) was injected. We pulled a glass capillary (Wiretrol® II, Drummond) into 10–20 μm in tip diameter using a micropipette puller (Model P-97, Sutter Instrument), and beveled the tip to about 30°. After filling the capillary with mineral oil (M5904, Sigma-Aldrich), we withdrew virus solution (titrated to 1012 GC/mL using 0.001% Pluronic F-68 in saline) from the tip using a plunger. Care was taken not to introduce an air gap between mineral oil and virus solution. We injected virus solution at the 4 corners of a 200 μm square whose center matched to that of identified C2 region, 50 nL per site over 5 min. We waited for 2 min after each virus injection before withdrawing. Depth of the pipette tip was 400 μm for Scnn1a-Cre mice, and 200 and 400 μm for others.
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2

PDMS-based cell culture chambers

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Reaction chambers for imaged cells in sample 3 are shown in Figure S1BC. PDMS was mixed at a ratio of 1:10 w/w cross-linker:potting reagent as before, and mixed/degassed 3 minutes at 2000 rpm. Uncured PDMS of mass 33–35 g was immediately dispensed into 10 cm petri dishes and degassed under vacuum for 1 hour. PDMS was then cured at 80 C for 150 minutes, and holes were punched using Integra biopsy punches with diameter 6 mm in the pattern indicated (Figure S1B). Cut PDMS blocks were then bonded with oxygen plasma to plain glass slides (VWR 16004–422) and cured at 80 C for 3 hours. 100–120 ul of mineral oil (Sigma M5904) was then added to all wells and degassed 45 minutes. Slides were then baked at 80 C for 5 hours, then allowed to cool, and mineral oil was aspirated. Slides were washed heavily with acetone and isopropanol to get rid of residual mineral oil and allowed to dry. 2% APTES solution was prepared in acetone as above, and the bottom of the wells were immersed with 35 ul of this solution for 60 seconds. Wells were immediately rinsed 5 times with 120 ul water, 2 times with isopropanol, allowed to dry, and stored sealed at room temperature until further use.
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3

Single-Molecule Fluorescence Imaging Protocol

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Secondary hybridizations were performed using 1 μM of secondary probe in 2x SSC +30% (v/v) formamide, and allowed to hybridize for 30 minutes at RT. Following hybridization, a wash solution (40% v/v formamide + 2x SSC) was introduced for 12 minutes to the flow cell and incubated for 3 minutes without flow. Wash solution was then replaced with imaging buffer consisting of 10% (w/v) glucose, 2x SSC, 50 mM Tris, 1% (v/v) β-mercaptoethanol, and 2% (v/v) of a GLOX stock solution consisting of 75 mg/mL glucose oxidase (Sigma G2133-250KU), 7.5 mg/mL catalase (Sigma C40-500MG), 30 mM Tris, and 30 mM NaCl. A thin layer of mineral oil (Sigma M5904) was added at the top to prevent oxygen from penetrating the imaging buffer. Imaging was initiated after the imaging buffer was allowed to incubate for 2 minutes without flow.
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4

Quantifying CSF Production in Mice

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CSF production rate was quantified as previously described in rats(70 (link), 71 (link)). Anesthetized mice were fixed on a stereotactic apparatus and a 0.5mm burr hole was made over the left lateral ventricle (AP=−0.1mm, ML= −0.85mm). A 30-gauge needle connected to PE-10 tubing was lowered through the burr hole to −2.00 mm DV. The mouse then received a MCAO as before. The rCBF drop was confirmed with laser Doppler flowmetry for five minutes and then the mouse was placed back in a stereotactic head frame and the cisterna magna was surgically exposed with the mouse’s neck flexed at 90 degrees. A 30-gauge needle connected to PE10 tubing filled with mineral oil (Sigma Aldrich, M5904) was inserted into the cisterna magna and advanced gently 2mm through the foramen of Magendie into the 4th ventricle. One microliter of mineral oil was infused at a rate of 1μl/min for 1 min with a syringe pump (Harvard Apparatus) to block outflow from the ventricular system. The location of CSF within the intraventricular PE-10 tubing was marked at 10 min intervals. The volume of CSF was calculated as: CSF volume=π x (internal radius: 0.14mm)2 x length. The rate of CSF production (μl/min) was calculated as the slope of the linear regression from each mouse.
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5

Lipid-in-Oil Mixture Preparation Protocol

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The preparation of the lipid-in-oil mixture is based on published protocols27 (link),71 (link). We use POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, Avanti Polar Lipids, Inc.) with 1% DSPE-PEG(2000) biotin (1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[biotinyl(polyethyleneglycol)-2000], Avanti Polar Lipids, Inc.; both 25 mg/ml in chloroform) and give 77 µl thereof in a 10 ml vial with 600 µl chloroform. In experiments with labeled membranes, 3 µl DOPE-ATTO655 (0.1 mg/ml in chloroform) is added. While being mixed on a vortex mixer, 10 ml of a silicon oil and mineral oil (Sigma Aldrich, M5904) mix (4:1 ratio) is slowly added to the lipid solution. Since the lipids are not fully soluble in this mix of silicon oil, mineral oil, and chloroform, the resulting liquid is cloudy.
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6

Synthesis of Iron Oxide-Gold Core-Shell Nanoparticles

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For the synthesis of the core-shell nanoparticles, iron oxide nanoparticles were firstly synthesized within the droplets of the reactor, as previously described24 (link),34 (link). Briefly, through the first two fused silica capillaries of the reactor, two aqueous solutions were injected at a flow rate of 10 µL/min. The first solution was 0.06 M of FeCl3·6H2O (Alfa Aesar, USA) and 0.03 M of FeCl2∙4H2O (Sigma-Aldrich, USA) dissolved in DI water, and the second solution was 4 M ammonia (Alfa Aesar, USA). As a continuous phase mineral oil (M5904, Sigma-Aldrich USA) with 0.075 vol % Triton X-100 (Samchun Chemical, Korea) and 1.75 vol % Abil EM 90 (Evonik Industrial, Germany) was used, the flowrate injected through the central Tygon tubing was 10 µL/min. For the synthesis of the gold shell around the iron cores, a gold precursor solution was injected into the existing droplets through the single capillaries at 100, 130, and 160 cm. The gold precursor solution consisted of 0.03 M HAuCl4 (Sigma-Aldrich USA) dissolved in DI water. For all three injections, the same flowrate was used and flowrate was determined by a self-optimizing algorithm based on the transmission of the droplets and two initial guesses for the flowrate. To quench the reaction, core-shell nanoparticles were collected in a vial filled with water, once they left the capillary droplet reactor.
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7

Preparation of Alginate Hydrogel Droplets

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Originally, the experiment would have alginates from Sigma Aldrich (W201502) of various concentrations between 0 to 5%. However, any concentration above 2% proved detrimental to the droplet’s stability and some trials showed no formation of droplets. To prepare the alginate in water solutions of 1% and 2% w/w, two steps were conducted. Firstly, a mixture of 0.5–1.0 g alginate with 50 mL of distilled water was prepared in a beaker glass. Secondly, stirring with a magnetic bar was performed for 1 day at room temperature. Then, the alginate solution was ready to use. The solution was stored in a refrigerator at a temperature of around 6–7 °C. The oil phase used was from Sigma Aldrich (St. Louis, MO, USA) (M-5904). Properties for fluids in this experiment are presented in Table 1.
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8

Microfluidic Synthesis of Monodisperse Microdroplets

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Deionized water was used as the dispersed phase, and 97 wt % mineral oil (M5904, Sigma Aldrich, St. Louis, MO, USA) and 3 wt % SPAN®80 (S6760, Sigma Aldrich, USA) were used as the continuous phase. SPAN®80 was used to prevent merging with each microdroplet in the microchannel before coming out from the device. The dispersed and continuous phases were injected into the fabricated microfluidic device using syringe pumps (Pump 11 Elite & Pico Plus, Harvard Apparatus, Holliston, MA, USA). Microdroplets in the microchannel were inspected using an optical inverted microscope (CSB-IH5, Samwon Scientific Ind. Co., Ltd., Seoul, Korea) as shown in Figure 1c. The diameter of microdroplets was analyzed using the Image J program with at least 30 samples. The microdroplet production rate was measured using a high-speed camera (Motionxtra N3, IDT, Tallahasse, FL, USA).
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9

Effects of Temperature on Giant Unilamellar Vesicles

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GUVs solution were incubated in the dark at temperatures of 4 °C, 25 °C, 37 °C, and 45 °C. Samples were taken on day 0, day 1, day 3, day 5, and day 7 of incubation, respectively. Before sampling, the homogenous solution was thoroughly mixed. Then, 10 μL of the GUVs solution was dropped into the glass bottom cell culture dish (801001, NEST, China), sealed with mineral oil (M5904, Sigma, USA), and allowed to settle for 3 h in the dark. The samples were viewed using an inverted fluorescence microscope (RVL-100-G, ECHO, San Diego, CA, USA) or a confocal laser scanning microscope (CLSM, A1R; Nikon, Tokyo, Japan), and the center of the GUVs solution and eight directions around it were photographed and recorded. Experiments were repeated three or more times and used for subsequent data analysis. Individual GUVs or aggregates were observed with a high-power lens and the Z-axis layer sweep recombination technique of CLSM (thickness is 0.5 μm). The excitation and emission wavelengths of DiO are 488 nm and 500–520 nm, and the excitation and emission wavelengths of DiI are 551 nm and 569 nm, respectively.
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10

Cell-free Reactions in Lipid Vesicles

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The cell-free reactions were encapsulated into large unilamellar phospholipid vesicles by the water-in-oil emulsion transfer method (48 (link)). Briefly, phospholipids (Avanti Polar Lipids, PC 840051, PE-PEG5000 880200) were dissolved in mineral oil (Sigma-Aldrich M5904) at a total concentration of 2 mg/ml (molar proportion: 99.33% PC and 0.66% PE-PEG5000). A few microliters of cell-free reaction was added to 0.5 ml of the phospholipid solution. This solution was vortexed for 5–10 s to create an emulsion. About 100–250 µl of the emulsion was placed on top of 20 µl of the feeding solution. The vesicles are formed by the centrifugation of the biphasic solution for 20 s at 4000 rpm. The phospholipid vesicles were observed with a CCD (charge-coupled device) camera mounted on an inverted microscope (Olympus IX-81) equipped with the proper set of fluorescence filters. The feeding solution contained the same components as the reaction except for the DNA and lysate that were replaced by water. Pure alpha-hemolysin (AH) was purchased from Sigma Aldrich.
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