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32 protocols using dp manager

1

Histological Evaluation of Lung Tissue

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Lung tissue was fixed using 10% formalin for 2 weeks at room temperature. The tissues were embedded in paraffin, cut into sections (5-µm thick) and stained with hematoxylin and eosin (H&E). Tissue slides were deparaffinized at 65°C for 5 min, put into xylene for 20 min. Deparaffinized slides was hydrated in a descending alcohol series (100, 90, 75 and 60% for 5 min) and tap water (10 min). Hydrated slides were stained with hematoxylin for 15 sec, washed with tap water for 10 min and stained with eosin for 30 sec at room temperature. Stained slides were dehydrated in an ascending alcohol series (60, 75, 80, 90 and 100%) and xylene for 5 min. Dehydrated slides were mounted with Canadian balsam. To investigate thickening of the bronchiolar wall, all tissue samples were examined and visualized using a light microscope (BX51; Olympus Corporation, Tokyo, Japan) at ×200 magnification. Images was captured using an Olympus DP21 camera, DP controller and DP manager (Olympus Corporation).
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2

Imaging Adult Fly Eyes with Leica Microscope

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Adult fly eyes were imaged with a Leica MZ6 microscope equipped with an Olympus DP73 camera and controlled by Olympus DP Controller and Olympus DP Manager software. Individual images were processed using Adobe Photoshop CS6 (Adobe).
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3

Comprehensive Cytogenetic Imaging Protocol

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We captured Giemsa-stained metaphases with an Axio Imager Z2 microscope (Zeiss, Oberkochen, Germany), equipped with automatic Metafer-MSearch scanning platform and a CoolCube 1 b/w digital camera (MetaSystems, Altlussheim, Germany). Karyograms were assembled using the software Ikaros (MetaSystems, Altlussheim, Germany). Fluorochrome-stained metaphases were examined under Provis AX70 microscope (Olympus, Tokyo, Japan) equipped with DP30BW camera (Olympus, Tokyo, Japan). The photos from FISH experiments were pseudo-colored and merged in DP Manager (Olympus, Tokyo, Japan). The color of C-banded metaphases was inverted.
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4

Fluorescence Microscopy of N27 Cells

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N27 cells were plated in 8-well glass slides (Millicell EZ Slide) at a density of 3.0 × 104 cells in each well. Cells were fixed after treatment exposures (testosterone-BSA-FITC). The cells on the slides were washed with cold 1× Phosphate Buffered Saline (PBS) twice for 1 minute each followed by 100% cold methanol fixation at −20 °C for 10 minutes. Afterwards, the slides were washed with 1× cold PBS, and then sealed with mounting VECTASHIELD medium containing DAPI. Once sealed with coverslips, the slides were stored at 4 °C. A fluorescence microscope (Olympus BX41, Olympus Corporation) equipped with wide UV and FITC filters was used to visualize fluorescence of the cells on the slides. Images of the cells at 40× magnification were captured using a digital camera (Olympus DP70, Olympus Corporation) and imaging software (DP Controller—version 3.3.1.292 and DP Manager—version 3.3.1.222, Olympus Corporation).
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5

Capillary-like Structure Formation Assay

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To capillary-like structure formation, cells were cultured on Matrigel, thawed at 4 °C for overnight and 50 μL added to Matrigel on 96 wells plate. Plates coated with Matrigel were incubated at 37 °C for 30 min. Cells were counted to 2 × 104 and then seeded on Matrigel. All images were acquired using an Olympus fluorescence microscope (Olympus, DP70) and performed with the DP manager (Olympus, version 3.1.1.208).
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6

Quantitative Analysis of Nerve Fibers

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Image analysis software Olympus DP Controller and DP Manager (Olympus Corp., Toyko, Japan) was used with 400-power random observation for 50 visual fields. All the immunoreactive fibers were numbered and the density of the nerve fibers was calculated (fibers/cm2). The data collection was completed by two pathological physicians in a double-blind manner.
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7

Immunofluorescence Staining of Estrogen Receptor Alpha

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Immunofluorescence staining was performed as reported previously [9 (link)]. In brief, rat CMECs on coverslips were washed once with PBS, fixed in 4% paraformaldehyde (pH 7.2~7.6) for 20 min at room temperature, washed with PBS, and then blocked with 5% bovine serum albumin in TBST for 15 min. The cells were incubated with PBS (negative control) or mouse antibody against estrogen receptor alpha (1: 100, Santa Cruz, Santacruz, CA, US) overnight at 4°C and then for 1 h at 37°C, then washed with PBS 3 times for 5 min each. The cells were then incubated with FITC-labeled goat anti-mouse IgG (1: 200 in TBST, Santa Cruz, Santacruz, CA, US) for 45 min and washed 3 times. Coverslips were analyzed using DPController and DPManager software (Olympus, Tokyo, Japan).
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8

Chromosome Analysis and Karyotyping Protocol

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At least 50 metaphase spreads per individual were analyzed to confirm the diploid chromosome number (2n), karyotype structure, and FISH results. Giemsa-stained preparations were analyzed under Axio Imager Z2 microscope (Zeiss, Oberkochen, Germany), equipped with an automatic Metafer-MSearch scanning platform. Photographs of the chromosomes were captured under 100 × objective using CoolCube 1 b/w digital camera (MetaSystems, Altlussheim, Germany). The karyotypes were arranged using Ikaros software (MetaSystems, Altlussheim, Germany). Chromosomes were classified according to their centromere positions,98 modified as metacentric (m), submetacentric (sm), subtelocentric (st), or acrocentric (a). FISH preparations were inspected using an Olympus BX53 epifluorescence microscope (Olympus, Tokyo, Japan), equipped with an appropriate fluorescence filter set. Black-and-white images were captured under 100 × objective for each fluorescent dye with a cooled DP30BW CCD camera (Olympus) using Olympus Acquisition Software. The digital images were then pseudo-colored (blue for DAPI, red for Cy3, green for FITC) and merged in DP Manager (Olympus). Composed images were then optimized and arranged using Adobe Photoshop CS6.
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9

Imaging Adult Fly Eyes with Leica Microscope

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Adult fly eyes were imaged with a Leica MZ6 microscope equipped with an Olympus DP73 camera and controlled by Olympus DP Controller and Olympus DP Manager software. Individual images were processed using Adobe Photoshop CS6 (Adobe).
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10

Chromosome Analysis of Plant Species

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Raw images were processed using the DP Manager (Olympus Corporation, Tokyo, Japan) and Photoshop CC 2015 (Adobe Systems Incorporated, San Jose, CA, USA) software. At least ten slides of each plant were observed, and at least fifteen cells with good chromosome spread were used for chromosome counting and length measurement. All chromosomes were aligned from longest to shortest. The chromosome ratio was determined by comparing the length of the longest chromosome to that of the shortest chromosome. Further karyotype analysis could not be carried out due to the small chromosome size and unclear centromere location of many of the species.
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