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27 protocols using scepter 2

1

Murine Colon and Lung Cancer Cell Cultures

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Cells of the murine colon carcinoma cell line CT26 (harboring a ras mutation but wild type for p53 [14 (link)]) and the Lewis lung carcinoma cell line LLC (harboring mutations in both ras and p53 [15 (link), 16 (link)]) were obtained from the American Type Culture Collection (ATCC; Manassas, Virginia, USA) and the Riken BioResource Center (Ibaraki, Japan), respectively. Both lines were cultured in RPMI1640 medium (Sigma-Aldrich Inc., Tokyo, Japan) containing 10% fetal bovine serum (FBS; Thermo Fisher Scientific, Tokyo, Japan), 100 mg/mL streptomycin and 100 U/mL penicillin (FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan). Cells were incubated in a humidified atmosphere at 37°C with a 5% CO2. For subculturing, cells were rinsed with Ca2 + − and Mg2+ − free phosphate-buffered saline (PBS; FUJIFILM Wako) and dispersed with 0.25% trypsin containing 0.5 mM ethylenediaminetetraacetate (FUJIFILM Wako). The number of cells were counted with a Countess II FL (Thermo Fisher Scientific) or a Scepter 2.0 (Merck KGaA, Darmstadt, Germany).
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2

Lipidomic Analysis of Red Blood Cell Membrane

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Fatty-acid-based membrane lipidome analyses were performed by the Lipidomic Laboratory of Lipinutragen (Bologna, Italy). Blood samples (0.5 mL) collected in vacutainer tubes with ethylenediaminetetraacetic acid (EDTA) were treated according to the ISO17025 certified procedure (accredited Lab. #1836L) by robotic equipment and processed as described in previous studies [21 (link),22 (link),36 (link),46 (link)]. Briefly, the mature cell fraction was isolated based on the higher density of the aged cells with control of diameter controlled by cell counter (Scepter 2.0 with Scepter Software Pro, EMD Millipore, Darmstadt, Germany) [47 (link)]. After phospholipid extraction, derivatization to fatty acid methyl esters (FAME) was performed, transforming membrane glycerophospholipids (mainly phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidyl inositol, and plasmalogens) to examine up to 80% of the RBC membrane lipidome [48 (link)]. Fatty acids analysis was performed by gas chromatography (GC), and percentages are given as % relative quantitative (% rel. quant.), as previously described [21 (link),22 (link),36 (link),46 (link)], comparing with the benchmark of the interval values of each fatty acid and index [15 (link)].
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3

LNCaP Cell Culture and Treatment

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LNCaP cells (from ATCC) were grown in RPMI1640 (Gibco) supplemented with 10% fetal bovine serum (FBS), 1% penicillin/streptomycin and 2 mM L-glutamine. In signal induction experiments cells were maintained in RPMI 1640 medium with 10% charcoal-stripped FBS for 2 days to deplete androgen actions and then exposed to vehicle (DMSO), DHT (5α-dihydrotestosterone, 100 nM, Steraloids Inc.), TNFα (1000 U/ml, a kind gift from prof. Claude Libert, Ghent University) or both DHT and TNFα. In proliferation assay, the cell numbers were counted using Scepter 2.0 (Merck Millipore).
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4

Isolation and Differentiation of Monocyte-Derived Osteoclasts

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Buffy coats were purchased from the German Red Cross Dresden and PBMC were isolated by density gradient centrifugation, followed by lysis of erythrocytes as previously described [42 (link)]. Monocyte content of the PBMC was analyzed using an automated cell counter (scepter 2.0., Merck Millipore, Darmstadt, Germany). Cells containing 5 × 105 monocytes were seeded into 48 well plates and supplemented with α-MEM containing 10% heat inactivated fetal calf serum (Corning, a trademark of Thermo Fisher Scientific, Waltham, MA, USA), 2 µM L-glutamine and 100 U/mL penicillin and 100 µg/mL streptomycin (all from Gibco, a trademark of Thermo Fisher Scientific, Waltham, MA, USA) (PS) (adhesion medium). After one day of cultivation the medium was changed to α-MEM, 5% heat inactivated FCS, 5% human serum, L-Glu, PS, 25 ng/mL MCSF and 50 ng/mL RANKL (both from Peprotech, Hamburg, Germany) (osteoclast differentiation medium). Cu2+ containing medium was prepared by adding different volumes of a 3 mM stock solution of Cu(NO3)2 (Sigma-Aldrich, Munich, Germany) in water to the respective medium. For the generation of osteoclasts PBMC were cultivated for 14 days with medium changes twice per week.
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5

NSCLC Cell Culture and Characterization

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We cultured NSCLC cells (H358, H1975)
in 2 mM l-glutamine (Thermo Fisher Scientific), 10% (v/v)
FBS (Biowest), and 1% (v/v) penicillin/streptomycin solution (Thermo
Fisher Scientific) at 37 °C for 3–4 days in RPMI 1640
medium containing 5% CO2 in a humidified atmosphere. Confluent
cells were trypsinized and resuspended in phosphate-buffered saline
(PBS) immediately prior to each experiment. Cell diameter of H358
was measured with a handheld automated cell counter (Merck Scepter
2.0).
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6

Isolation and Characterization of Vascular Smooth Muscle Cells

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Primary cells were isolated using tissue explantation and trypsin (Gibco; Thermo Fisher Scientific, Inc., Waltham, MA, USA) enzymatic digestion as described previously (8 (link)). SMCs were isolated into two groups (n=6) and maintained in Dulbecco's modified Eagle's medium (DMEM; Gibco; Thermo Fisher Scientific, Inc.) containing 20% fetal calf serum (FCS; Gibco; Thermo Fisher Scientific, Inc.) in a humidified environment at 37°C with 5% CO2. Subsequent to 3 days incubation, rhomboid-shaped cells grew from the edges of explants, in a radial pattern. Following 7 days of culture, tissue fragments were removed. The remaining SMCs reached near confluence following 7–10 days incubation, exhibiting two distinct populations under an inverted microscope (Leica DMI3000 B, Leica Microsystems, Wetzlar, Germany): Spindle-shaped and rhomboid cells as previously described (7 (link)). The two cell types were separately seeded and proliferation rates were monitored by cell counting (Scepter 2.0, Merck Millipore, Ltd., Carrigtwohill, Ireland).
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7

Evaluating Intracellular Dehydrogenase Activity

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The activity of the intracellular dehydrogenases was evaluated by using the Cell Counting Kit-8 (CCK- 8) (Sigma-Aldrich), a highly sensitive test that utilizes water-soluble tetrazolium salt [34 ,39 (link)]. WST-8 2-(2-methoxy-4-nitrophenyl)-3-(4-nitrophenyl)-5-(2,4-disulfophenyl)-2H-tetrazolium monosodium salt can be reduced by dehydrogenases in cells, producing an orange colored formazan dye soluble in the culture medium. The cells were counted by using Scepter™ 2.0 (Merck Millipore Corporation, New York, NY, USA) cell counter, seeded in 96-well plates at a density of 8 × 103 cells/well, and pre-incubated for 24 h under standard conditions. Then, cells were treated for 72 h with different concentrations of the drug solution. Finally, the activity of the intracellular dehydrogenases was evaluated by adding CCK-8 solution (10 μL) to each well and measuring the absorbance at λ = 450 nm after 2 h of incubation with CCK-8 solution, using the microplate reader Victor® 3V (PerkinElmer®, Waltham, MA, USA). The changes of the cell viability were expressed as percentage (%) changes of intracellular dehydrogenase activity induced by the drug with respect to the control.
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8

Nerve Explant Co-Culture Assay

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Twenty-four hours before nerve explants were harvested, both AD-MSC and dASCs cells from confluent flasks were collected and counted using a Scepter 2.0 (Merck-Millipore). 100,000 cell per well were plated in 24-well plates (three wells for each time point) and 500 μl of either aMEM or d-aMEM media was used for each well.
Nerve explants were collected from four Sprague Dawley rats as described above, with 15–20 nerve explants collected for each condition. All the nerves were de-sheathed under the microscope and cut into 5–10 mm length. Experimental groups were as follow: D0 healthy nerve explants (D0 c), D3 degenerated nerve explants cultured without cells (D3 c), D3 nerves co-cultured with AD-MSC (uASCs) and D3 nerve explants cultured with dASCs (dASCs).
Using an insert with a 0.4 um porous membrane (Greiner Bio-One), the nerve explants were inserted into the 24 well plate containing the plated cells after a media change and HBSS wash. 1200 μl of DMEM media was added to both the cells and the nerves (across the permeable membrane). The well insert ensured that no direct contact between AD-MSC and explants occurred. The co-cultures were kept in the incubator at 37°C at 5% CO2 for 3 days without a media change. The nerve explants were collected at each time point and processed for either gene or protein expression as described above.
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9

Analyzing Immune Cell Populations in Mice

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Leukocytes were harvested from spleens for FACS analysis from uninfected control mice and from infected mice on day 3 post-infection using the gentleMACS Dissociator. Prior to staining, erythrocytes were lysed using ACK lysing buffer (Lonza BioWhittaker). Total cells were counted using the Scepter 2.0 (Millipore). Non-specific antibody binding was blocked using mouse Fc block (BD Pharmingen). The following markers (Biolegend), with the clone listed in parentheses, were used to characterize the cell populations: CD4 (GK1.5), CD8a (53–6.7), NK1.1 (PK136), Ly-6G (1A8), F4/80 (BM8), and CD11c (N418). 7-AAD (BD Pharmingen) was added in the final 10 min of staining for dead cell exclusion. The cells were washed one time with PBS before analysis. A minimum of 20,000 events were collected on a FACSCalibur (BD Biosciences) flow cytometer, and the data was analyzed using Kaluza software (Beckman Coulter, Inc.). The gating strategy was as follows: the stained splenocytes were initially plotted based on SSC vs FSC, and a gate was drawn to eliminate cellular debris. This non-debris gate was then used to create another plot of 7-AAD vs FSC. A gate was drawn on the 7-AAD negative cells (live cells) to further analyze the live populations of each cell type, such as CD4+, CD8+, NK1.1+, Ly-6G+, F4/80+, and CD11c+.
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10

Cell Growth Kinetics Quantification

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Cells (105) were grown in the tested conditions and counted after 48 and 96 h using manual cell counter (Scepter 2.0, Millipore, USA), after prior trypsinization with 0.25 % trypsin–EDTA (1×) solution (Gibco Life Technologies, USA).
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