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4 protocols using gt x980 scanner

1

Dental Pulp Stem Cell CFU-F Assay

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Isolated cells (10 × 103) from the deciduous dental pulp tissue were seeded into a 100-mm culture dish (Corning) and were cultured in 10 mL of XFM (Biological Industries) for 14 days. The culture dish was treated with 3 mL of 4% paraformaldehyde (Merck, Darmstadt, Germany) and 0.1% toluidine blue (Merck) in PBS (pH 7.4; Nacalai Tesque) for 18 h. After washing five times with 1 mL of PBS, the dish was air-dried and was imaged with a GT-X980 scanner (Epson, Suwa, Nagano). Numbers of CFU-F, which contained > 50 cells, were counted using a Primovert inverted microscope (Carl Zeiss Microscopy).
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2

Evaluating Colony Formation in Cancer Cell Lines

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T98G, HCT116 p53−/−, HepG2, and H1299 cells were transduced with control lentivirus or lentivirus expressing FUCA1 or mutant FUCA1 (Q422X). Colony formation assay was carried out using cells selected in blasticidin‐containing medium for 6–10 days in 6‐well plates (2 × 104 cells per well). Subsequently, cells were fixed with 100% methanol for 10 min and stained with Giemsa for 40 min. Images were obtained with a GT‐X980 scanner (Epson, Nagano, Japan). Colonies were analyzed using ImageJ software. Briefly, the images were converted into binary format using ImageJ's binary convert function, and analyzed by ImageJ's batch measure function.
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Maintenance and Differentiation of 3T3-L1 Preadipocytes

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Maintenance and differentiation of 3T3-L1 preadipocytes (provided by Dr. Howard Green) (23 (link)) were carried out as described previously (24 (link)). Deferoxamine (DFO) (Sigma-Aldrich, D-9533) was freshly diluted in Dulbecco's modified Eagle's medium (DMEM), and added to the culture medium at the indicated concentrations. Stock solutions of PIK-III (Selleck Biotech, S7683), bafilomycin A1 (Cayman Chemical Company, 11038), and 2,2’-bipyridyl (FUJIFILM Wako, 042–04241) were prepared by diluting them in dimethyl sulfide (DMSO) at 10, 1 and 100 mM, respectively and added to the medium at the indicated concentrations, where final DMSO concentrations were 0.01%, 0.01% and 0.02%, respectively. Oil red-O (ORO) staining was performed as described previously (25 (link)), and photographed with a GT-X980 scanner (EPSON) and an inverted microscope Primovert (Zeiss). The cell number counting assay was performed at the indicated time points during adipocyte differentiation by detaching cells using 0.25% trypsin (FUJIFILM Wako, 200-13953), 0.75 mg/ml collagenase (FUJIFILM Wako, 17105-041), and 0.5 mg/ml Dispase II (Thermo Fisher, 17105-041) in DMEM.
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4

Quantifying Apoptosis in Grey Matter

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Small pieces of gray matter, 70–100 mg in total (wet mass), were dissolved in 2× Laemmli Sample Buffer and applied on 4–15% precast polyacrylamide gel (Criterion TGX), together with prestained Protein ladder EXtended PS13 (5–245 kDa, GeneON, Ludwigshafen, Germany) and positive control samples (cultured primary neurons from adult goat spines treated with the apoptosis-inducing agent staurosporine). Separation was performed in Criterion™ Vertical Electrophoresis Cell (BioRad, Hercules, CA, USA) with a constant voltage 140 V. Proteins from the gel were transferred onto Immobilon-FL PVDF membranes (0.45 µm, Millipore now Merck KGaA, Darmstadt, Germany) blocked with Pierce Protein-Free Blocking Buffer (Thermo Scientific, Waltham, MA, USA), cut on the level of 75 kD standards lines and stained separately with primary antibodies against active caspase 3 (ab214430, AbCam, Cambridge, UK) and neurofilaments (anti-Neurofilament M antibody, Merck/Chemicon, Darmstadt, Germany) as loading control. They were then developed with Amersham ECL Prime Reagent and visualized from contact-exposed X-ray film. Only areas of interest were manually scanned (with GT-X980 scanner, Epson, Suwa, Nagano, Japan) from the films due to constraints of file size and optical density processing.
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