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16 protocols using eclipse ti microscope system

1

Live-cell and Superresolution Imaging

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Live-cell imaging was performed on a Nikon Eclipse Ti Microscope System (Nikon Instruments, Melville, NY) at 37°C and 5% CO2. Images were captured using an electron-multiplying charge-coupled device camera (Photometrics Evolve 512; Photometrics, Tucson, AZ) and a Plan Apo VC 60× H objective (numerical aperture [NA] 1.40). Diffraction-limited fixed-cell imaging was performed with a Zeiss 780 (Carl Zeiss). Superresolution imaging was performed using a Zeiss 880 Airyscan microscope and a 63×/1.40 NA Plan-Apochromat Oil DIC M27 objective lens (Carl Zeiss) and processed at setting 6. Image processing was performed in ImageJ (http://imagej.nih.gov/ij/), including cropping and average/maximum intensity projections. Photobleaching experiments were performed at 37°C and 5% CO2 on a Nikon Eclipse Ti Microscope System equipped with a Galvo miniscanner to allow photobleaching and subsequent spinning-disk confocal imaging. TIRF images were acquired with an Apo TIRF 100× objective.
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2

Immunohistochemical Analysis of Xenograft Tumors

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The xenograft tumors were fixed in 2% paraformaldehyde for 24 hours. The paraffin-embedded tissue was cut into 5-µm sections. The sections were deparaffinized, rehydrated, and then subjected to high pressure for antigen retrieval (pressure, 15PSI; temperature, 121 °C) in EDTA antigen retrieval buffer (1 mM EDTA; pH 8.0). Endogenous peroxidase was inactivated with 3% hydrogen peroxide, and 1% bovine serum albumin (Sigma) was used to block non-specific binding for 1 hour. Anti-Ki-67 (1:200; Abcam), anti-MCM2 (1:200; Abcam), and anti-PCNA (1:1,000; Cell Signaling Technology) antibodies were used to detect the expression levels of the corresponding proteins in the mouse xenograft tissues. These antibodies were the same as those used for western blotting and have been described previously. Tissue samples were incubated in a primary antibody solution overnight at 4 °C. The secondary antibody Biotin Conjugated AffiniPure Donkey Anti-Rabbit IgG (1:200; Wuhan Boster Biological Technology) was incubated for 1 hour . Finally, the tissue slices were visualized with a Nikon ECLIPSE Ti microscope system (Nikon Corporation), and the images were processed using Nikon software (NIS-Elements v.AR4.10, Nikon Corporation). IHC Profiler (an ImageJ plugin) was used to perform automatic quantitative analysis in line with the manufacturer’s instructions.
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3

Quantifying Ki67 Expression in Xenografts

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The scores from immunohistochemistry experiments were calculated as described previously48 (link). We used anti-Ki67 antibodies (ready to use; Zhongshan Bio-Tech) to detect the expression of Ki67 in the mouse xenografts. The sections were visualized using a NikonECLIPSE Ti microscope system and were processed with Nikon software.
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4

Immunohistochemical Analysis of LC3 and Cleaved Caspase-3

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Paraffin sections were deparaffinized and hydrated. After serial incubation with primary antibodies anti-LC3 (1:400, ab48394, Abcam), anti-cleaved caspase3 (1:50, #9661, Cell signaling, Danvers, MA, USA) and secondary antibody, then subjected to the liquid DAB substrate-chromogen system. Images were visualized using a Nikon ECLIPSE Ti microscope system and processed with Nikon software.
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5

Advanced Microscopy Techniques for Live-Cell Imaging

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Immunofluorescence microscopy was performed as previously described61 (link),62 (link) on a Zeiss LSM710 microscope (Carl Zeiss, Thornwood, NY). Live-cell imaging was conducted with a NIKON Eclipse Ti Microscope System equipped with an environmental chamber (temperature controlled at 37°C and CO2 at 5%), high-speed EM charge-coupled device cameras (iXon DU897 from Andor and Evolve 512 from Photometrics), and NIS-Elements Ar Microscope Imaging Software. TIRF Images were acquired with an Apo TIRF 100X objective (N.A. 1.49) and iXon DU897. Spinning-disk confocal z-stacks were taken with a Plan Apo VC 60x H objective (N.A. 1.40) and Evolve 512. Dual-color imaging was achieved by fast switching excitation lasers so that images from green and red channels were aligned automatically.
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6

Live-Cell Imaging of Clathrin-Mediated Endocytosis

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Live cell and immunofluorescence imaging of clathrin and AP-2 at endocytic sites was performed by TIRF microscopy using a NIKON Eclipse Ti Microscope System equipped with an environmental chamber (temperature controlled at 37 °C and CO2 at 5%), Apo TIRF ×100 objective (NA 1.49), high-speed EM charge-coupled device camera (iXon DU897 from Andor), and NIS-Elements Ar Microscope Imaging Software.
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7

Immunohistochemical Analysis of Tumor Markers

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All steps were conducted as described in the previous study [23 (link)]. All tissue specimens were fixed with 37% formalin and then paraffin-embedded, haematoxylin and eosin were used for staining. For IHC, the antibodies were listed as follows: HMMR (1:300, Proteintech, Wuhan, China), phosphor-AKT (Ser473) (1:100, Service Bio, Wuhan, China), N-cadherin (1:100, Service Bio, Wuhan, China), and Ki-67 (1:100, Service Bio, Wuhan, China). All images were captured by an ECLIPSE Ti microscope system (Nikon, Japan).
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8

Live-cell Imaging of Transfected Cells

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Live-cell imaging was conducted with an Eclipse Ti Microscope System (Nikon, Tokyo, Japan) equipped with an environmental chamber (temperature controlled at 37°C and CO2 at 5%) and NIS-Elements AR microscope imaging software. Cells were kept in microscopy medium (DMEM without phenol red, 1% bovine serum albumin [Sigma-Aldrich] and 25 mM HEPES [Corning] [pH 7.4], sterile filtered) during the entire imagining time. Spinning disk confocal images were taken with a Plan Apo VC 60× objective (NA 1.40) and a high-speed electron-multiplying charge-coupled device camera (Evolve 512; Photometrics, Tucson, AZ, USA). The focus on the sample was maintained using the Perfect Focus system. Dual-color imaging was done by fast switching of the excitation lasers, and images from green and red channels were aligned automatically. Laser power and exposure times were optimized depending on transfection efficiency and frame-rate acquisition.
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9

Murine Tumor Ki67 IHC Protocol

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The immunohistochemistry (IHC) experiment and IHC score calculations were conducted as previously described [22 (link)]. Briefly, an anti-Ki67 antibody (1:100, Service Bio, Wuhan, China) was used to detect the Ki67 expression in paraformaldehyde-fixed, paraffin-embedded murine tumour tissue. Images were obtained by ECLIPSE Ti microscope system (Nikon, Japan).
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10

Immunohistochemical Analysis of PD-L1 in HSCC

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HSCC tumor tissues were fixed in 4% paraformaldehyde for 24 h, then routinely embedded in paraffin and sectioned into 4 µm sections. Sections were deparaffinized, hydrated, and immersed in blocking solution (prepared using Triton X-100) in the dark for 1 h. After incubating with anti-PD-L1 (1:500, ab228415, Abcam) overnight, sections were incubated with horseradish peroxidase-labeled secondary antibody (1:5000, ab205718, Abcam) for 30 min. After developing with a diaminobenzidine substrate, sections were counterstained with hematoxylin. Images were visualized using a Nikon ECLIPSE Ti microscope system and processed with Nikon software (Version 5.02).
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