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12 protocols using ca2 mg2

1

Protein Identification by Aptamer Pulldown

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Protein identification was performed with an adapted protocol described previously by Berezovski et al.41 (link) To isolate protein targets, 6 million GSCs (#1 and #83) were lysed with sodium deoxycholate (Sigma-Aldrich) at 0.1% (w/v) in 10 mM PBS with Ca2+, Mg2+ (Sigma-Aldrich) and incubated with a biotinylated-scrambled oligonucleotide (TriLinK Biotechnologies, San Diego, CA, USA) at 200 nM for 30 min at room temperature, as a counterselection step. Then, lysates were incubated with streptavidin MagneSphere paramagnetic particles (Promega, Milan, Italy) for 30 min at 4°C. Afterward, unbound proteins were incubated with biotinylated A40s (TriLinK Biotechnologies) at 200 nM for 30 min at room temperature. A40s-protein complexes were incubated with streptavidin MagneSphere paramagnetic particles (Promega) for 30 min at 4°C. Collected beads were washed twice with cold 10 mM PBS with Ca2+, Mg2+ (Sigma-Aldrich). Thus, incubation with 8 M urea for 1 h at 4°C led to protein denaturation and release from the aptamer and magnetic beads. Pull-down proteins were separated by SDS-PAGE (10% polyacrylamide gel), transferred to nitrocellulose membranes (Millipore, Bedford, MA, USA), and immunoblotted for EphA2 antibody (Santa Cruz Biotechnology).
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2

Isolation and Culture of Ovarian Cells

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Ovarian carcinoma cells (OvCa) and normal epithelial ovarian cells (OvEp) were isolated from biopsies derived from ovarian tissue. The tissue was finely minced with a cutter, incubated with a digestion solution composed by 0.5% trypsin (Sigma-Aldrich, Milan, Italy) and 50 µg/ml DNase I (Roche, Milan, Italy) in Hanks’ Balanced Salt solution containing 0.5 mM Ca2+Mg2+ (Sigma-Aldrich) overnight at 4°C. Next, the enzymatic solution was changed to collagenase type 1 (1.5 mg/ml) (Worthington Biochemical Corporation, DBA) diluted in Medium 199 with Hank’s salts (Euroclone Spa, Milan, Italy) for 30 min at 37°C. The digestion was blocked with 10% v/v fetal bovine serum (FBS; GIBCO, Life Technology) and the cell suspension was passed through a 100 µm pore filter (BD Biosciences, Italy). The cells were seeded in a 25 cm2 flask, coated with bovine gelatine, and cultured using Human Endothelial cells serum-free medium (HESF; Life Technologies), 10% heat-inactivated FBS supplemented with EGF (10 ng/ml), basic FGF (20 ng/ml) and Penicillin–Streptomycin (Sigma-Aldrich). Fresh medium was replaced every 2–3 days. The cells were maintained at 37°C in humidified atmosphere with 5% v/v CO2 and used at their fifth to eighth passage for in vitro experiments.
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3

Quantifying Osteogenic Differentiation by ALP

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On day 14, osteogenic differentiation of cells incubated in 25 cm2 cell culture flasks were determined quantitatively by measuring the alkaline phosphatase (ALP) enzyme activity using a fluorometric Alkaline Phosphatase Assay Kit (Abcam, Cambridge, UK). In total, 4 × 105 cells were centrifugated at 300× g at 4 °C for 5 min, washed with DPBS with Ca2+/Mg2+ (Sigma-Aldrich, Taufkirchen, Germany) and centrifuged again (300× g, 4 °C, 5 min). The cell pellet was dissolved in 400 µL ALP Assay Buffer. After centrifugation at 13,000× g at 4 °C for 3 min, supernatant was removed and the cell pellet was processed according to the ALP assay kit protocol. Measurements of the fluorescence intensities of the samples, which were pipetted in duplicate into 96-well plates, were performed using a 2300 EnSpireTM multiplate reader at excitation and emission wavelengths of 360 nm and 440 nm, respectively.
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4

Isolation of Stromal Vascular Fraction from Lipoaspirate

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The lipoaspirate [16 ] was diluted with sterile phosphate-buffered saline (PBS), Sigma-Aldrich, St. Louis, MO, USA) supplemented with antibiotics and centrifuged at 430 × g for 10 min (without brakes) to remove contaminating debris and red blood cells. The wash step was repeated 2–3 times depending on the quality of the specimen. The floating adipose tissue was digested with an equal volume of collagenase type I [10 mg/mL in PBS containing 5 mM Ca2+/Mg2+ (C0130, Sigma-Aldrich), final concentration 0.5%] at 37 °C for 30 min with shaking (250 rpm). The collagenase was inactivated by adding an equal volume of autologous serum, and the sample was centrifuged at 600 × g for 10 min. After centrifugation, the supernatant was discarded and the cell pellet was resuspended in NaCl 0.9% (Alpha Laboratories, Eastleigh, UK) and filtered through a 100 μm cell strainer (CS003 – PNC International Co. Ltd., Seoul, Korea) to remove debris. After centrifugation (300 RCF/5 min), 5 ml of the stromal vascular fraction were collected. All the processing must be realized within a maximal time of 90 min. The number of viable cells were determined manually (Trypan blue method) and validated on MACSQuant analyzer (Miltenyi-Biotech, Bergisch Gladbach, Germany) (7AAD staining method). All the quality control tests and injections were done with the obtained fresh samples.
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5

Isolation of Extracellular Vesicles from Conditioned Media

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Fetal dermal cells and adult dermal cells, previously cryopreserved in Dulbecco's modified Eagle's medium (DMEM) (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 10% dimethyl sulfoxide (DMSO) (CryoSure, WAK-Chemie Medical GmbH, Steinbach, Germany) and 30% fetal bovine serum (FBS), were grown in 75 cm2 tissue flasks (SARSTEDT, Numbrecht, Germany) as previously described [11 (link)]. For CM collection, serum-free alpha-minimum essential medium (MEM) (Gibco, Thermo Fisher Scientific) was added to 80% confluent cells and collected 24 hours later. EVs were isolated by differential ultracentrifugation of CM according to a protocol [17 (link)] and as previously described [18 (link)]. In brief, CM was centrifuged at 1800 × g for 10 minutes to remove cell debris, centrifuged again at 17000 × g for 15 minutes, and then at 160000 × g for 1 hour in the ultracentrifuge (Optima MAX-XP, Beckman Coulter Inc., Irving, TX, USA). All centrifugation steps were done at 4°C. The pellet was resuspended in phosphate-buffered saline (PBS) without Ca2+/Mg2+ (Sigma-Aldrich) or subjected to total protein extraction or total RNA extraction.
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6

Isolation and Characterization of Extracellular Vesicles

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EVs were isolated by differential ultracentrifugation of CM, according to a protocol (53 (link)), and analyzed as previously described (37 (link)). In brief, cell culture was centrifuged at 300g for 10′ to remove cells, and the supernatant harvested was subsequently centrifuged at 1,800g for 10′ to remove debris, again at 20,000g for 30′, and then at 160,000g for 90′ in the ultracentrifuge (Optima MAX-XP, Beckman Coulter Inc., Irving, TX, USA). All centrifugation steps were performed at 4°C. The pellets were resuspended in phosphate-buffered saline (PBS) without Ca2+/Mg2+ (Sigma-Aldrich) or subjected to protein or RNA extraction.
Pellet particles resuspended in PBS were analyzed for size and concentration by nanoparticle tracking analysis (NTA) using the NanoSight (NS300, Malvern Instruments, Westborough, MA, USA). Samples were diluted in PBS, 300 μl of samples was loaded into the chamber, and five videos for each sample were recorded. Data analysis was done with the NTA software, and data were presented as mean ± standard deviation (SD) of the five videos.
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7

Isolation and Culture of Murine Colonoids

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Mice were killed and colon was collected, cut open longitudinally in a Petri dish with cold PBS without Ca2+/Mg2+ (Sigma-Aldrich), vigorously washed using forceps, and cut in 2- to 5-mm pieces. Next, the pieces were collected in a 50-mL Falcon tube filled with 30 mL Dulbecco′s Phosphate Buffered Saline (DPBS) plus 120 μL ethylenediaminetetraacetic acid 0.5 mol/L (Sigma-Aldrich) and incubated for 45 minutes at 4ºC. Subsequently, colon pieces were collected in 4 fractions of 25 mL DPBS. The 4 fractions were inspected under a microscope (10× objective) to identify the fractions enriched in crypts and with low level of debris. The chosen fraction was spun down (450 × g for 10 minutes at 4ºC). The supernatant was removed and the pellet was resuspended in 150 μL Intesticult (STEMCELL Technologies) and 150 μL Matrigel basement membrane matrix (Corning, Inc, Corning, NY). Aliquots of 40 μL of this solution then were plated in a prewarmed 48-well plate (VWR, Radnor, PA) into the center of the well and incubated for 10 minutes at 37ºC, allowing the Matrigel to polymerize. Finally, 350 μL Intesticult was added in each well of the plate. Colonoids were cultured for 10 days and passaged once after 6 days. Total RNA was extracted on day 10 and gene expression was measured by NanoString analysis.
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8

Cell Membrane Permeability and Resealing

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The shearing buffer consisted of HBSS with Ca2+/Mg2+ and either calcein (629 Da; 3.2 × 10−4 M; Sigma) or fluorescein-5-isothiocyanate (FITC)-conjugated dextran (10−4 M) molecules of different sizes (42 and 464 kDa; Sigma). Cells were incubated at 37°C in buffer containing permeability marker for 10 minutes prior to injury. Sham cultures were placed in the CSID and loaded with the shearing buffer after the cone was lowered as in the injured cultures, but the cone did not rotate. Sham cultures were also incubated for 10 minutes with the shearing buffer after they were taken from the CSID. Naïve controls were cultures that were not placed in the CSID, but were exposed to shearing buffer containing the permeability marker for 10 minutes. These plates were used to establish baseline uptake of permeability marker. In order to reveal the resealing time course; cultures were injured without the presence of permeability marker, which was then added to cells at 1, 2, or 10 minutes after injury (calcein only). calcein- or FITC-conjugated dextrans were in contact with cells for a total of 10 minutes for all groups (Figure 1B). Following incubation with the permeability marker, all plates were rinsed with HBSS.
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9

Immortalized HaCaT Keratinocytes Protocol

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Immortalized human HaCaT keratinocytes were kindly provided by Dr. Petra Boukamp [31 (link)] and were used to generate a HK5-EYFP expressing single cell clone B10 [32 (link)]. The cells were grown at 37 °C in a 5% CO2 humidified atmosphere and DMEM containing l-alanyl-glutamine (Sigma-Aldrich) and 9% (v/v) fetal bovine serum SeraPlus (PAN Biotech). For passaging, cells were washed and incubated for 15 min in PBS without Ca2+/Mg2+ (Sigma-Aldrich) and thereafter trypsinized for ≈ 5 min in a solution of PBS without Ca2+/Mg2+ (Biochrom) containing 0.25% (w/v) trypsin (Biochrom) supplemented with 0.02% (w/v) EDTA (Sigma-Aldrich). Cells were passaged once per week 1 day after reaching confluence and were seeded at a concentration of 40,000–60,000 cells/cm2 for DNA transfection. Cells were transfected on day 2 after seeding with 5 µg of plasmid DNA and 1.5 µl Xfect (Takara) in a total volume of 100 µl Xfect reaction buffer per 2 ml of cell culture medium in 35-mm diameter dishes.
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10

Isolation of Colonic Epithelial Cells

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Mice were killed and colon was collected, cut open, and placed on a Tissue Culture-Treated (TC) dish with a small amount of Hank’s balanced salt solution (GIBCO, Gaithersburg, MD) to keep it moist. The tissue samples then were incubated in a digestive solution containing 3 mL Hank’s balanced salt solution with Ca2+/Mg2+, 150 μL DNase (10 mg/mL; Sigma-Aldrich), 30 μL collagenase (100 mg/mL; Sigma-Aldrich), and 300 μL dispase (STEMCELL Technologies, Vancouver, Canada) for 1 hour at 37ºC at 150 rpm. The cells of each colon sample then were filtered with a 100-μm strainer and collected into a flow cytometry tube. Then, the cells were incubated with 10 μL rat anti-mouse CD16/CD32 antibody (553142; BD Biosciences, Franklin Lakes, NJ) in 6 mL flow cytometry buffer containing EDTA (0.5 mol/L) and HEPES (Sigma-Aldrich) for 10 minutes on ice. After that, each sample was incubated with 5 μL Allophycocyanin (APC) anti-mouse CD326 epithelial cellular adhesion molecule (Ep-CAM) antibody (118213; BioLegend) on a shaker for 1 hour on ice in the dark. Positive cells then were sorted through BD Biosciences Aria and processed for subsequent qRT-PCR analysis.
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