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80 protocols using diluent c

1

Isolation and Characterization of Extracellular Vesicles

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The CM of M-protein-treated and untreated BCC MDA-MB-231 cells was collected and centrifuged at 300×g for 5 min, followed by 1200×g for 20 min. The supernatant was ultracentrifuged at 140,000×g for 70 min at 4°C using an Optima XE-100 ultracentrifuge to collect the EV pellet. EV pellets were collected in 100 μL of PBS; these were considered to be isolated EV. The EV collected from the M-protein-treated BCC were called MpEV, and the EV collected from the untreated breast cancer cells were called nEV. For PKH26 labeling of EV, of 120 µg was resuspended in 250 µL of Diluent C (Sigma-Aldrich) and mixed with 250 µL of Diluent C containing 1 µL of PKH26 (Sigma-Aldrich). The mixture was then incubated in the dark for 5 min and neutralized by adding 40 ml of PBS containing 0.25% FBS. The solution was then ultracentrifuged at 140,000×g for 70 min at 4°C to collect stained EV pellet, then resuspended in 100 µL PBS and stored at -80°C. The protein concentration of EV was measured using a Bradford assay (Bio-Rad, Hercules, CA, USA) and was considered to be the EV concentration. The size of collected EV was measured by dynamic light scattering (Zetasizer Nano ZS, Melvern Instruments, United Kingdom). EV markers expression was characterized by Western Blotting.
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2

Labeling Apoptotic Jurkat Cells

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Jurkat cells were irradiated under a 254-nm UV lamp for 15 min, followed by incubation under normal cell culture conditions for 2–3 h. This method routinely yields more than 85% Annexin V+ cells. The apoptotic cells (ACs) were rinsed once with serum-free DMEM, resuspended at a concentration of 2 × 107 cells/mL in Diluent C (Sigma-Aldrich), and incubated for 3 min with four mL of Diluent C containing concentrated PKH or CellVue Claret membrane-intercalating dyes (Sigma-Aldrich). The cells were then rinsed twice with DMEM containing 10% heat-inactivated FBS and used for experiments. Alternatively, ACs were rinsed with PBS twice, resuspended at a concentration of 4 × 106 and incubated for 30 min with 20 ng/mL pHrodo green or pHrodo red (Life Technologies), rinsed twice with DMEM containing 10% heat-inactivated FBS, and then used for experiments.
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3

Labeling Leishmania Amastigotes with PKH67

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After isolation or rapid thawing, the amastigotes to be labeled were washed in plain RPMI medium (Gibco, Invitrogen) and in DPBS (Mg2+ and Ca2+ free; Gibco, Invitrogen) before resuspension in 100 μL diluent C (Sigma) per 108 amastigotes. An equivalent volume of diluent C containing 1:250 PKH67 membrane linker dye (Sigma) was added to the suspension and incubated for 3 min at room temperature. The staining reaction was stopped by adding an equivalent volume to the total amount of diluent C of FBS to the parasites and incubating at room temperature for 1 min. The thus-stained parasites were washed in plain RPMI medium and complete IMDM before use in subsequent experiments.
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4

Apoptotic Cell Labeling and Tracking

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Jurkat cells were irradiated under a 254-nm UV lamp for 15 min, followed by incubation in 1X PBS for 2–3 h, and then used for experiments. For some experiments, the apoptotic cells (ACs) were rinsed once with serum-free DMEM, resuspended at a concentration of 2 × 107 cells/mL in Diluent C (Sigma-Aldrich), and incubated for 5 min with 1 mL of Diluent C containing concentrated PKH26 dye (Sigma-Aldrich). The reaction was stopped with 2 mL FBS, and the ACs were then rinsed twice with DMEM containing 10% heat-inactivated FBS and used for experiments. For other experiments, ACs were stained with pHrodo dye (ThermoFisher) as described by the manufacturer's protocol. For experiments using apoptotic human macrophages, HMDMs were made apoptotic by treatment with 1 μM staurosporine in DMEM media for 48 h.
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5

Exosome Labeling with PKH67 Dye

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Exosomes were labeled with PKH67 (Sigma-Aldrich) according to the manufacturer’s protocol. Briefly, 250 μg of exosomes was resuspended in 1 ml of diluent C (Sigma-Aldrich) and mixed with PKH67 diluted in diluent C for a final concentration of 2 × 10–6 M PKH67. The exosomes was incubated in dye suspension for 5 min. Excessive dye from the labeled exosomes was neutralized with 2 ml of 5% BSA/PBS. Finally, the supernatant was removed by centrifugation (100,000 g for 70 min at 4 °C) and resuspended in 50 μl PBS. A mixture without exosomes was used as a negative control to examine any carryover of PKH67 dye. For the negative control, labeling was performed as described but without exosomes.
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6

Tracking Exosome Internalization by Confocal Microscopy

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Confocal microscopy was performed for detection of the uptake of exosomes, milk-exosome/cis were stained with PKH26 Dye (PKH26 Red Fluorescent Cell Linker Kits, Sigma-Aldrich, Merck KGaA, Darmstadt, GER) to evaluate the internalization by A2780CP cells. Milk-exosomes diluted in 1.5 mL Diluent C (PKH26 Red Fluorescent Cell Linker Kits, Sigma-Aldrich, Merck KGaA, Darmstadt, GER), then were mixed with the mixture containing 6 μL PKH26 dye and 1.5 mL Diluent C following the protocol of the manufacturer. After 10 min, 6 mL ultracentrifuged exosome-free-FBS was added and incubated for 5 min to bind the excess dye. Then 15 mL DMEM were added to wash the product, followed ultracentrifugation again at 1,25,000 g for 60 min at 4°C. The supernatant was removed as completely as possible and purified PKH26-labeled-milk-exosome/cis were resuspended with 1 mL DMEM. Then, 1 mL of 5,000-ng/mL PKH26-labeled-milk-exosome/cis in DMEM were incubated with A2780CP cells/3 × 104 per well in 24-well-plate containing round coverslips at 37°C under 5% CO2 condition. Anti-fluorescence-quenching agent with DAPI (6-diamidino-2-phenylindole) (DAPI Fluoromount-GTM; Yeasen Biotechnology, Shanghai, China) was used to mount the slides and label nuclei. Images were captured with a TCS SP5 confocal laser scanning microscopy (Leica Microsystems, Wetzlar, GER).
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7

PKH26 Labeling and Purification of EVs

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100μg of EVs were resuspended in 250 μL of Diluent C (Sigma) and then mixed with 250 μL of 8 μM of PKH26 (Sigma) in Diluent C. The dye mixture and EVs were incubated for 10 minutes protected from light with gentle mixing by pipetting every minute. Excess dye was removed with 50μL of exosome-depleted fetal bovine serum (Sigma-Aldrich). Then, PKH26-labeled EVs were diluted in 1mL of PBS and transferred to Amicon Ultra-2 centrifugal filters 100 kDa MWCO filters (Merck Millipore, Darmstadt, Germany) and centrifuged at 3000×g for 15 min at 4°C. This step was repeated twice then the sample was diluted to the necessary concentration for the experiments.
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8

Induction and Labeling of Apoptotic Jurkat Cells

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Jurkat cells were irradiated with 254-nm UV lamp for 15 minutes, followed by incubation at 37°C 5% CO2 for 2-3 hours. This method typically generates 85% annexin-V+ cells. The apoptotic cells (ACs) were resuspended in 1x PBS at a concentration of 2 X107 cells/mL with 5 μL of Vybrant® DiD cell-labeling solution (Invitrogen) for 10 minutes. For efferocytosis assays involving the sequential uptake of differentially labeled ACs added at 2 different times, ACs were suspended at the same concentration, but in Diluent C (Sigma-Aldrich), and incubated for 5 minutes with 4 mL of Diluent C containing concentrated PKH67 or PKH26 membrane-intercalating dyes (Sigma-Aldrich). Cells were rinsed twice with 1x PBS and resuspended at a concentration 4 X 106 cells/mL in DMEM containing 10% heat-inactivated FBS, and then used for experiments.
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9

PKH26 Cell Proliferation Kinetics

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For proliferation assays in parallel to infection kinetic experiments, a fraction of cells was stained with PKH26 in Diluent C (both Sigma Aldrich), according to manufacturer’s instructions (2.5 × 107 cells in a total volume of 4 ml Diluent C with 2 µM PKH26 for 2 min at room temperature). Labeling reaction was stopped by adding equal volumes of heat-inactivated FCS for 1 min, followed by centrifugation and further washing steps in serum containing medium. Cells were then cultured in suspension or collagen for 0, 2, 4, and 7 days. At these time points cells were processed for flow cytometry (viability dye, CD8 PE-Vio770, CD3 PE, no permeabilization, see above), fixed and analyzed with FACSVerse. The sample at day 0 served to verify uniform labeling and to identify the parent population. Generations were modeled using ModFit LT (Verity Software).
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10

Labeling Leishmania Amastigotes with PKH67

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After isolation or rapid thawing, the amastigotes to be labeled were washed in plain RPMI medium (Gibco, Invitrogen) and in DPBS (Mg2+ and Ca2+ free; Gibco, Invitrogen) before resuspension in 100 μL diluent C (Sigma) per 108 amastigotes. An equivalent volume of diluent C containing 1:250 PKH67 membrane linker dye (Sigma) was added to the suspension and incubated for 3 min at room temperature. The staining reaction was stopped by adding an equivalent volume to the total amount of diluent C of FBS to the parasites and incubating at room temperature for 1 min. The thus-stained parasites were washed in plain RPMI medium and complete IMDM before use in subsequent experiments.
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