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16 protocols using polyvinylidene fluoride filter

1

Lentiviral Transduction of HUVECs

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Lentiviral particles were produced by transfecting HEK293T cells with the third-generation HIV-1 packaging plasmids (Addgene) using Trans IT (Mirus). Cell culture medium containing virus particles was collected at 48 and 72 h after transfection, centrifuged, and filtered through 0.45-µm polyvinylidene fluoride filter (Millipore). Supernatant containing lentivirus was used to infect subconfluent HUVECs. Infected HUVECs were used for experiments at 72 h after infection. All shRNA clones that were used in the study were verified by sequencing (45 clones targeting 22 proteins) and are shown in Fig. S1 B . The identity of 7 clones used in the screen could not be validated by sequencing and is therefore omitted from Fig. S1 B and the phenotype analysis. The efficiency of the knockdown in several cases was assessed by immunoblotting.
For KCTD10 lentiviral overexpression, KCTD10 cDNA was cloned into a CSII-CMV-MCS-IRES2-Bsd vector and packed into lentivirus particles as described previously (Sakaue et al., 2017b (link)). Lentiviral expression and packaging vectors were kindly provided by H. Miyoshi (RIKEN BioResource Center, Wako, Japan). Template cDNA (product ID FHC07641) was purchased from Kazusa DNA Research Institute.
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2

Lentiviral Transduction of HEK293T and A549 Cells

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On day 1, HEK293T cells were seeded into 100mm dishes (Corning). On day 2, cells were ∼50%–70% confluent at the time of transfection. For each dish, 6 μg of pHR vector containing the construct of interest, 4 μg of dR8.91 and 1 μg of pMD2.G (Addgene) were mixed in 1 mL of Opti-MEM reduced serum media (GIBCO) with 30 μL of Mirus TransIT-LT1 reagent and incubated at room temperature for 30 minutes. The transfection complex solution was distributed evenly to HEK293T cultures dropwise. On day 5, lentiviruses are harvested from the supernatant with a sterile syringe and filtered through a 0.22-μm polyvinylidene fluoride filter (Millipore).
For A549 cells, lentivirus precipitation solution (Alstem) was added and precipitated as per the manufacturer’s protocol. One well of a 6-well plate (Corning) of A549 cells at ∼50% confluency was transduced with the precipitated lentivirus. After 2-3 days of growth, the cell supernatant containing the virus was removed and the cells were expanded. Cells were then sorted for mCherry+ cells using a Sony SH800S cell sorter.
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3

Generating Stable Cell Lines via Lentiviral Transduction

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Stable cell lines were generated using lentiviral transduction. For lentiviral production, HEK293T cells were transfected with 1.51 μg of pHR vector with construct of interest, 1.32 μg of dR8.91 and 165 ng of pMD2 with 7.5 μL of Mirus TransIT-LT1 (for 6 well plate format, scaled up or down as appropriate). Two days post transfection lentivirus was harvested and filtered through a 0.45 μm polyvinylidene fluoride filter (Millipore). Following filtration, 1 volume lentivirus was mixed with 4 volumes Lentivirus Precipitation Solution (Alstem) and refrigerated overnight. The next day, lentivirus was pelleted at 1500xg for 30 minutes at 4°C. HEK cells were seeded the day before transduction at 1×105 cells/well of a 12-well plate and transduced with precipitated lentivirus resuspended in 1/100 of original volume of PBS. For Jurkat cell transduction, cells were seeded the day of transduction at 1×106 cells/mL in 100μL in a 96-well plate, and transduced with precipitated lentivirus resuspended in 100μL RPMI. When appropriate, transduced cells were selected for with 2ug/mL Puromycin (Gold Biotech) or 150ug/mL Hygromycin (Sigma).
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4

Generating Stable Cell Lines via Lentiviral Transduction

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Stable cell lines were generated using lentiviral transduction. For lentiviral production, HEK293T cells were transfected with 1.51 μg of pHR vector with construct of interest, 1.32 μg of dR8.91 and 165 ng of pMD2 with 7.5 μL of Mirus TransIT-LT1 (for 6 well plate format, scaled up or down as appropriate). Two days post transfection lentivirus was harvested and filtered through a 0.45 μm polyvinylidene fluoride filter (Millipore). Following filtration, 1 volume lentivirus was mixed with 4 volumes Lentivirus Precipitation Solution (Alstem) and refrigerated overnight. The next day, lentivirus was pelleted at 1500xg for 30 minutes at 4°C. HEK cells were seeded the day before transduction at 1×105 cells/well of a 12-well plate and transduced with precipitated lentivirus resuspended in 1/100 of original volume of PBS. For Jurkat cell transduction, cells were seeded the day of transduction at 1×106 cells/mL in 100μL in a 96-well plate, and transduced with precipitated lentivirus resuspended in 100μL RPMI. When appropriate, transduced cells were selected for with 2ug/mL Puromycin (Gold Biotech) or 150ug/mL Hygromycin (Sigma).
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5

Quantification of Plasma CoQ10 Levels

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The plasma concentration of CoQ10 was determined as described in our previous study.[17 (link),18 (link)] Briefly, frozen plasma samples were thawed on ice and then maintained at 4°C during handling. Thawed plasma was pipetted into Eppendorf microcentrifuge tubes, deproteinized with methanol, and then treated with n-hexane. The mixture was vortexed for 5 minutes and then centrifuged at 2500 × g and 4°C for 15 minutes, after which the clear n-hexane layer was transferred to another tube for another round of n-hexane extraction. The plasma extracts were combined and evaporated to dryness under a gentle stream of nitrogen gas. The dry residue was dissolved in the mobile phase, filtered through a membrane (polyvinylidene fluoride filter, 4 mm, 0.45 μm; Millipore, Bedford, MA), and injected into a high-performance liquid chromatography system. A microBondapak C18 3.9-mm × 30.0-cm stainless steel column with a 3 × 22–mm guard column packed with microBondapak C18 was used with the mobile phase of methanol–n-hexane 85:15 (v/v). The flow rate was 1 mL/min. The wavelength of the ultraviolet detector was fixed at 276 nm. To determine the amount of CoQ10 in plasma, a calibration curve was constructed by plotting the peak areas versus the concentration. Linearity was achieved in the concentration range of 0.12 to 1.92 μg/mL.
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6

Synthesis and Characterization of NIR-II CL Nanoprobe

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BPN‐BBTD was synthesized according to the literature, with minor modifications.[30] The different micelles were prepared using a nanoprecipitation method, and the amounts of ingredients are shown in Table S4 (Supporting Information). In a typical procedure for the NIR‐II CL nanoprobe, different amounts of F127, CPPO, PFODBT, and BPN‐BBTD were dissolved in THF (1 mL) to obtain a stock solution. Under intense sonication for 2 min, the stock solution was quickly injected into the water to produce a clear micellar solution. After THF was removed by heating the micelle solution at 45 °C for 12 h, to get rid of big aggregates, the aqueous solution was filtered through a polyvinylidene fluoride filter (0.22 µm, Millipore, USA). The obtained suspension was finally concentrated to 500 µL through ultrafiltration (Amicon Ultra‐15 30 KD, Millipore, USA) and used immediately for experiments.
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7

Exosome Isolation from Serum and Media

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Serum and cell medium were treated with polyvinylidene fluoride filter (Millipore, Billerica, Mass). Then subsequently ExoQuick solution (System Biosciences, Mountain View, CA) was added incubating at room temperature for 0.5 h. By centrifugation at 1500g for 30 min. Exosome pellets were collected and resuspended in 25 μl DEPC water.
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8

Lentiviral Transduction of ITGA2 in Ovarian Cancer Cells

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For preparation of lentiviral particles, HEK293T cells were seeded at 50% confluency in a T75 flask one day before transfection. 4 μg of plasmid pUltra-Chili-ITGA2-HA (or ITGA2-mutants) and 2 μg of pMD2.G (Addgene #12259) and 2 μg of pCMVR8.74 (Addgene #22036) were co-transfected using 24 μL of jetPEI reagent in 1 mL of 150 mM NaCl solution (Polyplus-transfection, Chemie Brunschwig AG, Switzerland). Medium was changed 24 h after transfection. Virus supernatant was collected 48 h later and filtered with a 0.45 μm polyvinylidene fluoride filter (Millipore). 3 mL of lentivirus-containing medium was used to transduce previously established ΔITGA2 ovarian cancer cells (Huang et al., 2020 (link)) to preclude the functional impact of endogenous ITGA2 expression. dTomato + transduced cells were sorted by BD FACS Aria Cell Sorter (BD Bioscience). In addition, pUltra-Chili-ITGA2-HA and pUltra-Chili-10NQ-HA plasmids were used to transduce OVCAR4 cancer cell lines. Plasmid-encoding dTomato + transduced cells were sorted by BD FACS Aria Cell Sorter (BD Bioscience).
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9

Lentiviral Transduction of HEK293T and A549 Cells

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On day 1, one confluent 100mm dish (Corning) of HEK293T cells were seeded into three 150mm dishes (Corning). On day 2, cells were ∼50%–70% confluent at the time of transfection. For each dish, 27.18 μg of pHR vector containing the construct of interest, 23.76 μg of dR8.91 and 2.97 μg of pMD2.G (Addgene) were mixed in 4.5 mL of Opti-MEM reduced serum media (GIBCO) with 150 μL of Mirus TransIT-LT1 reagent and incubated at room temperature for 30 minutes. The transfection complex solution was distributed evenly to HEK293T cultures dropwise. On day 5, lentiviruses are harvested from the supernatant with a sterile syringe and filtered through a 0.22-μm polyvinylidene fluoride filter (Millipore).
For A549 cells, lentivirus precipitation solution (Alstem) was added and precipitated as per the manufacturer’s protocol. One well of a 6-well plate (Corning) of A549 cells at ∼50% confluency were transduced with the precipitated lentivirus. After 2-3 days of growth, the cell supernatant containing the virus was removed and the cells were expanded. Cells were then sorted for mCherry+ cells using a Sony SH800S cell sorter.
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10

Characterization of Glycodendrimer Size and Charge

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The dendrimer diameter was determined by dynamic light scattering (DLS) using a Malvern Nano ZS (Malvern Panalytical, U.K.) instrument equipped with a 633 nm laser. Compounds 6, 8 and 10 were dissolved at a 150 µM concentration in 25 mM Tris buffer (pH 8, 150 mM NaCl) both in the presence and absence of 4 mM CaCl2. All the solutions were passed through a 0.22 μm PVDF (Polyvinylidene Fluoride) filter (Millipore) before the DLS measurements. Samples were recorded at a 173º scattering angle and data were analyzed using the number distribution mode. The reported mean diameter values resulted from at least 6 measurements.
The zeta potential was also measured using a Malvern Nano ZS equipment. In this case, glycodendrimers were dissolved in MilliQ water. At least 3 measurements per sample were recorded and the mean and standard deviation from these measurements were reported.
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