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8 protocols using 15 cm dishes

1

Mycolactone-Induced Membrane Fraction Isolation

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HDMEC (1 × 107 cells) were seeded onto 15cm dishes (Corning) and grown to 90% confluency then exposed to solvent carrier DMSO or 10ng/ml mycolactone for 24 hours. Cells were washed four times in PBS and once in lysis buffer (10mM Tris pH 7.5, 250mM Sucrose, protease inhibitor cocktail). Cells were incubated for 20min on ice in 10ml lysis buffer then lysed in by 20 strokes dounce homogenisation. Lysates were centrifuged at 1,000×g for 10min at 4°C then the post-nuclear supernatant was centrifuged at 100,000×g for 1 hour at 4°C. Pellets were resuspended in 110 μl lysis buffer. Protein concentration was determined by BCA assay and 50 μg aliquots were subjected to acetone precipitation. Triplicate samples were prepared from 3 independent assays.
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2

Lentiviral Particle Production in HEK293T Cells

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HEK293T cells were seeded in 15 cm dishes (Corning). The medium was replaced with 10 mL of the complete medium after the cells reached 80% confluence. Next, 20 µg of transfer plasmids carrying the target gene, 15 µg of psPAX2, 10 µg of pMD2.G, and 130 µL of LipoFiter Liposomal Transfection Reagent (Hanbio) were vortexed with 434 µL of DMEM and incubated at room temperature for 10 min. The plasmid and liposome mixtures were then gently added to the cells. After 12 h of transfection, the supernatant was replaced with fresh medium. The supernatant containing the viral particles was harvested after 48 h and 72 h, and the lentiviruses were purified by ultracentrifugation and then aliquoted before storage at -80 °C.
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3

Lentiviral Transduction of 293T Cells

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2.5 X 106 293T cells were seeded in 15-cm dishes (Corning Falcon). After 48 h, cells were co-transfected with second-generation packaging lentiviral plasmids pMD2G, pPAX2, and either pGIPZ encoding shRNAs (Thermo Scientific) in the presence of polyethylenimine (4.1 μmol/L) and NaCl (2.25 × 10−4 mol/L). Supernatant containing the virus was collected 48 and 72 h after transfection and concentrated using Lenti-X concentrator (Takara bio, Cat# 631232) and resuspended in a final volume of 300 μL of STFL medium. Cells were infected at a functional MOI of 10.
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4

EGF Stimulation of A431 Cells

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A431 cells were grown in Dulbecco’s modified Eagle’s medium (DMEM)
(A.T.C.C., VA) supplemented with 10% FBS (Atlas Biologicals, CO), and
penicillin/streptomycin (ThermoFisher, MA). Trypsin/EDTA was
obtained from Gibco (ThermoFisher, MA). Unless otherwise noted, chemicals were
obtained from Sigma Chemical Co. (Sigma, MO). Recombinant EGF and c-Fos were
obtained from Active Motif (Active Motif, CA). Recombinant Ras was obtained from
Cytoskeleton, Inc. (Cytoskeleton, CO). Human EGF was obtained from Cytoskeleton,
Inc. (Cytoskeleton, CO). For EGF stimulation experiments, A431 cells were serum
restricted for 24 h with serum-free DMEM in order to synchronize the cells. The
cells were then treated with 33 ng/ml EGF for 0.5, 2, 5, 15, and 60 min
in individual 15-cm dishes (Corning, NY), followed by subsequent lysis with
BlastR lysis buffer (Cytoskeleton, CO).
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5

Culturing SKBR3B Cells in McCoy's 5A Media

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SKBR3B cells were seeded in 15 cm dishes (Corning) and cultured in McCoy’s 5A medium supplemented with 10% FBS, L-glutamine (2 mM), and antibiotics (100 U/ mL penicillin and 100 μg/mL streptomycin), and grown in a humidified air with 5% CO2 at 37 °C. Cells were further maintained in McCoy’s 5A media supplements with 3% dFBS (which had been depleted of bovine-derived exosomes by ultracentrifugation for 16 h at 100 000g twice, prior to filtration through a 0.22 μm filter (Millipore, Billerica, MA) in the same incubation conditions.
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6

SILAC Labeling of C2C12 Myoblasts

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Mouse muscle myoblast cells C2C12 were obtained from American Tissue and Cell Culture (ATCC, Manassas VA, USA) and maintained in DMEM supplemented with 20% FBS and penicillin/streptomycin at 37 °C and 5% CO2. For differentiation, the cells were grown to confluency in 15 cm dishes (Corning, NY), switched to DMEM with 2% FBS, and allowed to differentiate for five days. The proliferating C2C12 cells were labeled with SILAC amino acids. Briefly, the C2C12 cells were cultured in DMEM supplemented with 20% FBS and SILAC amino acids such as L-lysine (13C615N2) and L-arginine (13C615N4). After five doubling cycles, all the proliferating C2C12 cells were fully labeled. The SILAC-labelled proliferating C2C12 cells and the non-labelled differentiated C2C12 cells were prepared separately.
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7

Oxidative Stress Response in A431 Cells

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A431 human epidermoid carcinoma cells and 3T3-swiss mouse fibroblast cells were obtained from ATCC. Cells were grown in DMEM media (ATCC, Manassas, VA, USA) supplemented with 10% FBS (Atlas Biologicals, Fort Collins, CO, USA) and penicillin/streptomycin (ThermoFisher, Waltham, MA, USA). TrypLE Express was obtained from Gibco (ThermoFisher, Waltham, MA, USA). Unless otherwise noted, chemicals were obtained from Sigma Chemical Co. (Sigma, St. Louis, MO, USA). For all Western blot and IP analysis experiments, A431 cells at 60% confluency, post 5 days of cell passage, were treated with 100 μM H2O2 for 2 h in individual 15 cm dishes (Corning, Corning, NY, USA).
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8

Isolation and Characterization of Extracellular Vesicles from MCF-7 Cells

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MCF-7 (Bioresource Collection and Research Center, Hsinchu, Taiwan) cells were cultured and grown in 15 cm dishes (Corning). When cells reached approximately 80% confluence, cells were washed with phosphate buffered saline (PBS) (Gibco) and transferred to fresh media containing 1% EV-free serum (Gibco) for 24 h. Media was then collected and subjected to centrifugation at 500×g for 5 min to pellet cells, then 2000×g for 15 min to remove cellular debris (Eppendorf, Hamburg, Germany). The supernatant was then transferred to ultracentrifuge tubes (Beckman Coulter, Pasadena, CA, USA) and ultracentrifuged (Beckman Coulter) at 10,000×g for 30 min twice to pellet and remove large vesicles. The supernatant was then transferred to new ultracentrifuge tubes and ultracentrifuged twice at 100,000×g for 60 min to pellet EVs. EVs were resuspended in PBS and then stored at 4 °C. Protein content of EVs was determined by BCA (Thermo Fisher Scientific) and treatment dosing was determined by EV protein concentration. Particle size was measured using qNano Gold (Izon, Science Ltd., Burnside, New Zealand) by Tunable Resistive Pulse Sensing. Data was recorded and analyzed using Izon Control Suite Software (version 2.2.2.111). Particle size reported are representative of three separate measurements of EVs.
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