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82 protocols using perfection v700 photo

1

Quantitative Cell Colony Formation Assay

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Cells were plated at 250 (SK-N-BE) or 100 (U2OS) cells/well in 6-well plates, in full growth medium. Media were replaced by fresh culture medium every 4 days. After 15 days, cells were washed with PBS, fixed with methanol and stained with 0.5% crystal violet. Digital images of cell colonies were obtained using a scanning device (Epson Perfection V700 Photo). Quantification of the clonogenic assay was performed with the ImageJ plugin “ColonyArea” [27 (link)] to determine the area covered by colonies in the well and the colony intensity percentage.
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2

Root Morphometrics Measurement Protocol

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The primary root length was measured with a ruler. Then, counts were taken for the lateral root number. After that, the whole root was scanned with a desktop scanner (EPSON Perfection V700 Photo), and root pictures were taken. Finally, WinRHIZO was used to analyze the length (cm), surface area (cm2), volume (cm3), and diameter (mm) of the root samples.
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3

Crystal Violet Cell Staining

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Cells were stained with crystal violet on the last day of experiments. After a short wash step with PBS, cells were fixed for 2 min with 100% methanol and stained 20 min with 0.05% crystal violet in 20% ethanol. Stained cells were then washed at least three times with tap water and finally dried. Pictures of the staining were taken with an Epson Perfection V700 Photo scanner (Epson).
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4

Wheat Seedling Growth Analysis

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We harvested plants after 30 days of sowing grown under control, T1 and T2 conditions for measuring the different growth parameters. Root length was measured using Root Scanner (Model, Epson Perfection V 700 Photo, Win-RHIZO Programme V. 2009 c 32-bit Software) following the manufacturer's protocol and shoot height was measured using a standard scale.
After washing with deionized water, roots were placed on a 150 mm wide Petri plate filled with distilled water to manually observe the primary root and the first-order lateral root characteristics in each plant. To determine root characteristics, we used six wheat seedlings for each of the treatments, including three biological replicates. Each sample's leaf area was determined using a Digital Leaf Area Meter (YMJ-C Series, China) following the manufacturer's instructions. Three technical replicates were evaluated for each parameter.
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5

Clonogenic Assay for Radiotherapy Response

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Clonogenic assays were performed as described in [5 (link)] with minor modifications. Briefly, T47D cells from sub-confluent monolayer cultures were detached by trypsin treatment, counted using a hemocytometer and seeded in 6-well plates using standard medium enriched with 33% T47D conditioned growth medium. After 24 hours the cells were exposed to different doses of gamma-rays. For each treatment at least 4 replicates were performed. After 16 days the colonies were fixed with methanol and stained with Giemsa stain. Images were acquired using a desktop scanner (Epson Perfection V700 Photo; resolution settings: 1200 DPI) and analyzed using the ImageJ 1.47v software (NIH, USA; website: http://imagej.nih.gov/ij/). Colonies containing more than 50 cells were counted and scored positive for growth. Overall we counted 973 colonies with an average of 195 colonies for each treatment condition. Plating efficiency was determined dividing the number of counted colonies by the number of plated cells (plating efficiency of control samples was ~25%). The surviving fraction was calculated as the ratio of plating efficiency for irradiated and control samples. Data were fitted with the linear-quadratic model [4 (link)]:
S(D)=e(αD+βD2)
where S(D) is the surviving fraction of cells at a given dose of radiation D (Gy) and α and β are non-negative parameters.
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6

Mammosphere Formation Efficiency Assay

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After seven days of culture, 8-bit grayscale images of the mammospheres were acquired by placing the cell culture plate on a scanner (Epson Perfection V700 PHOTO, Epson, Tokyo, Japan). Low-resolution images (300 dpi) were loaded using the software program NICE (ftp://ftp.nist.gov/pub/physics/mlclarke/NICE) [40 (link)]. For counting, regions of interest (ROIs) were created by choosing the desired number of rows and columns (e.g., 2 × 3 for a six-well plate), and individual ROIs were defined by moving and resizing the provided ROI shapes after selecting the elliptical setting in the NICE program. The background signal of the images was negated using thresholding algorithms, and the selected images were automatically counted. The results of the mammosphere formation assay are reported as the mammosphere formation efficiency (MFE, % of control), which corresponds to the number of mammospheres per well/the number of total cells plated per well ×100, as previously described [40 (link)].
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7

Lipid Extraction and Quantification Protocol

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Lipid extracts were prepared according to the protocol published by Bligh and Dyer [35 (link)]. Alkaline methanolysis of glycerolipids was performed as described by Bodennec et al. [36 (link)]. Lipids were dried in a SpeedVac vacuum concentrator, dissolved in chloroform/methanol (1:1), and loaded onto HPTLC plates. Lipid standards were loaded onto adjacent lanes of the same HPTLC plate. Chromatograms were developed in the solvent mixture chloroform/methanol/water (70:30:4; v/v/v) or twice in the solvent mixture chloroform/methanol/water (144:25:2.8; v/v/v) using a horizontal developing chamber (CAMAG, Muttenz, Switzerland). Lipids were visualized by spraying plates with 625 mM cupric sulfate (cat# C1297, Sigma-Aldrich) in 8% (v/v) phosphoric acid (cat# 9079, Carl Roth, Karlsruhe, Germany) followed by heating to 180 °C for 5 min [37 (link)]. Immediately after stained plates had been cooled to room temperature, they were scanned using a flatbed scanner (Epson Perfection V700 Photo) and the intensity of lipid bands was quantified using the program AIDA (Elysia-Raytest, Straubenhardt, Germany).
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8

Soybean Root Morphology Analysis

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After exudate collection, soybean plants immediately divided into shoots and roots. Shoots were dried in an oven at 70°C until constant weight. Roots were placed in clear plastic bags filled with 50% ethanol and stored in a refrigerator. Washed roots were gently arranged with minimum overlap using tweezers in a plexiglass tray full with water, and scanned using an Epson perfection V700 photo, Japan. Images were analyzed using WinRhizo (Version 2007d, Regent Instrument Inc., Canada) to estimate total root length, root surface area, and root volume. Several images of one root were analyzed in more detail to determine the root morphology. Roots were dried in an oven at 70°C until constant weight after imaging. Specific root (cm g−1 DW) length was referring to the method of Pang et al. (2010 (link)).
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9

Leaf Nitrogen Allocation and Chlorophyll Determination

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After determination of the gas exchange parameters and fluorescence yield, leaf samples and nearby leaves (30–50 leaves in total per shoot), were taken from each shoot. The surface area of 10–20 leaves was measured by scanner (Perfection v700 Photo, Epson, Nagano-ken, Japan). Leaves were subsequently oven-dried at 80°C for 48 h to constant weight, dry weight was measured using an analytic balance, and then LMA was calculated. Dried leaf samples were ground into a dry flour, nitrogen concentration was determined by a VELP automatic Kjeldahl nitrogen determination apparatus (UDK-139, Milano, Italy), and then leaf nitrogen per mass (Nmass) and leaf nitrogen per area (Narea) were calculated.
The remaining 20–30 leaves were frozen and returned for laboratory analysis. One gram of frozen leaves (5–10 leaves) were cut into small pieces and weighed into 5–10 mg samples. Absolute chlorophyll concentration measurements were conducted using 95% (v/v) alcohol extracts of leaf tissue and a Shimadzu visible-ultraviolet spectrophotometer (UV 2250, Fukuoka, Japan), chlorophyll concentration see S2 Table. The remaining frozen leaves were used to determine cell wall nitrogen content according to Onoda et al. [7 ]. The fraction of leaf nitrogen allocated to cell walls (PCW) represents the ratio of cell wall nitrogen content to total nitrogen content.
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10

Extracting Demineralized Collagen from Irradiated Tibiae

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Tibiae were demineralized in 10% EDTA tetrasodium salt dihydrate for 14 days at 4°C. Demineralized tibiae were rinsed for 30 min in running deionized water, then finely minced into approximately 1 mm pieces with a razor blade. The bone pieces were enzymatically digested (1 mg/ml pepsin in 0.5 M acetic acid; #P7000 and A6283; Sigma-Aldrich) for 72 h at room temperature on an orbital shaker. Insoluble collagen was removed by centrifuging the samples at 4000 rpm for 30 min at room temperature. The supernatant was transferred to a centrifugal concentration device (Millipore Amicon Ultra 15; Thermo Fisher Scientific) with a 10 kDa molecular weight cutoff filter. Samples were centrifuged at 4000 rpm for 30 min. The concentrated sample was rinsed with 10 ml ddH2O and the centrifugation step repeated. The resulting concentrate was lyophilized, then resuspended to a concentration of 2 μg/μl in buffer (0.1 M sodium phosphate pH 7.2, 2.0 M urea, 0.1% sodium dodecyl sulfate; #342483, #51456, and #L3771; Sigma-Aldrich) before running on a 4%–20% TRIS glycine gel (#456-1093; BioRad) and stained with GelCode Blue (#24590; Thermo Fisher Scientific). Gels were imaged on a flat bed scanner (Perfection V700 Photo; Epson). Tibiae exposed to 0 Gy, 20 Gy, and 25 kGy ex vivo radiation, as well as tibiae from mice exposed to 4 × 5 Gy in vivo irradiation or Sham treatment, were analyzed.
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