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83 protocols using 90i microscope

1

Histological Analysis of Infected Murine Lungs

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Infected murine lungs were excised, fixed using 4% phosphate-buffered formalin solution and stained with hematoxylin and eosin as previously published [36 ]. Four individual sections were taken per mouse for downstream analysis via histology. Analysis of lung sections and assessment of alveolar space was performed using NIS advanced software on a Nikon (Tokyo, Japan) 90i microscope.
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2

RNA-ISH Assay Protocol with Fluorescent Imaging

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RNA-ISH was performed according to the Affymetrix ViewRNA ISH Tissue-2 Plex Assay. Fluorescent images were taken in using a Nikon 90i microscope. See Supplemental Experimental Procedures for details.
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3

Immunostaining of Pancreatic Organoids

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Pancreas tissue were fixed with 4% paraformaldehyde at 4°C overnight. Fixed tissue were incubated with 30% sucrose in PBS overnight and then embedded in freezing medium. Tumor organoids cultured in matrigel in a 96-well plate were fixed with 4% paraformaldehyde for 10 min and the matrigel containing organoids was embedded in freezing medium. We made cryosections (7 μm) with a Cryostat (CM1900, Leica, Buffalo Grove, Ill). Cryosections were blocked with 5% donkey serum and 0.2% bovine serum albumin for 30 min and incubated with primary antibodies at 4°C overnight. The primary antibodies used were CDH1 conjugated with AlexaFluor 488 (100-fold dilution, 560061, BD Biosciences, San Jose, Calif), doublecortin like kinase 1 (DCLK1, 100-fold dilution, PA5–20908, ThermoFisher Scientific), PROM1 (50-fold dilution, 14–1331), EPCAM (100-fold dilution, G88, DSHB), and KRT19 (50-fold dilution, TROMA-III). The unconjugated primary antibodies were detected with secondary antibodies conjugated with AlexaFluor 488 and 568 dyes (ThermoFisher Scientific). The sections were counterstained with DAPI. Images were captured with a 90i microscope (Nikon, Melville, NY).
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4

Immunohistochemistry of Mouse Liver Tissues

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Mouse liver tissues were embedded in freezing medium without fixation or after fixation with 4% paraformaldehyde. Cryosections (7 µm) were used for immunohistochemistry. After blocking, the sections were incubated with primary antibodies for 1 hour. The primary antibodies and additional treatment are listed in Supplementary Table 1. The primary antibodies were detected with secondary antibodies conjugated with AlexaFluor dyes. Nuclei were counterstained with DAPI. Signals were captured with 90i microscope (Nikon, Melville, NY).
The paraffin-embedded specimens for normal human livers (n=2) and alcohol-induced fibrosis (n=2) at the Harbor-UCLA Medical Center or biliary atresia (n=3) at Children’s Hospital Los Angeles were used for immunohistochemistry under study protocols approved by the institutional review boards (HS-11-00476, CCI-10-00148). The primary antibodies were detected with SuperPicure HRP Polymer (Life Technologies, Grand Island, NY).
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5

Single-cell fluorescence quantification

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Cells were spotted on agar pads containing 1% agarose in PBS and imaged with a Nikon 90i microscope using 100x phase contrast. Exposure times were 30 msec for phase contrast, and 20 msec for mCherry. Fluorescence intensity of ~500 single cells per experiment was determined using ImageJ and plotted with Prism.
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6

Quantifying Larval Fluorescence Intensity

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Imaging was done as previously described12 (link). Briefly, third instar larvae were immobilized by cold treatment in glycerol, imaged with a NIKON 90i microscope, and the fluorescence intensity was quantified with ImageJ software.
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7

Detecting Neutrophil Granules in Zebrafish

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VE DIC microscopy was done with 60×/1.00 NA water-immersion objective mounted on Nikon 90i microscope according to previously described (25 (link)). In 2-dpf live embryos, the neutrophil granule status is easy to be detected with DIC assay since the neutrophil granules are abundant and neutrophils are accessible to be observed by the lens.
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8

Immunostaining Protocol for Quantifying pH2AX Foci

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For immunostaining, cells were washed with PBS and then incubated with pre-extraction buffer [10 mM Pipes (pH 6.8), 100 mM NaCl2, 300 mM sucrose, 3 mM MgCl2, 1 mM EGTA, and 0.2% Triton X-100] for 5 min. After wash with PBS, the cells were fixed with 3% paraformaldehyde in PBS for 15 min, washed with PBS, and fixed with cold methanol (−20°C) for 10 min. Subsequently, cells were washed with PBS, permeabilized with 0.5% Triton X-100 for 5 min, washed a second time with PBS, and blocked in PBST (1× PBS containing 0.05% Tween 20) containing 3% bovine serum albumin (BSA) or 10% milk and 2% BSA for 1 hour at room temperature. Cells were further incubated with the primary antibody diluted in PBST containing 3% BSA or 10% milk and 2% BSA at 4°C for overnight. Coverslips were washed three times with PBST before the incubation with the fluorescent secondary antibody for 1 hour. Coverslips were washed three times with PBST and stained with 4′,6-diamidino-2-phenylindole (DAPI) at the second time. The images were acquired using a Nikon 90i microscope with a Nikon Plan Apo Lambda 20× or 60× objective. Signals of pH2AX of each nucleus in DAPI-stained area were quantified using the Fiji software.
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9

Quantifying Intracellular Parasite Development

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For imaging sporozoite invasion and confocal imaging of developing exoerythrocytic forms, cells were visualized using a Nikon 90i microscope at 100× magnification, and images were acquired with a Hamamatsu Orca-ER camera using the Volocity 3D Image Analysis Software with image stacks deconvolved prior to combining and focused along the plane of the parasites. Epifluorescence imaging of exoerythrocytic forms was performed using an Olympus BX-53 upright microscope at 100× magnification. Imaging of hepatocytes following protein staining was performed using either a Zeiss Axioskop 2 microscope with a ProgRes MFcool camera using the ProgRes CapturePro software version 2.10.0.1 or using a BZ-X710 (Keyence, Osaka, Japan) All-in-One Fluorescence Microscope. BZ-X700 Analyzer Software (version 1.31.1) was used for Z-stack analyses to yield a single compressed fully focused image at 600× magnification from 9 to 11 planes, with each plane at 0.2 μm thickness.
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10

Transgenic P. berghei ANKA Expressing P. falciparum MSP1

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Transgenic P. berghei ANKA parasites expressing P. falciparum MSP1 in place of the endogenous allele (de Koning-Ward et al., 2003 (link)) were grown in C57Bl/6 mice (Jackson Laboratories) housed under specific pathogen–free conditions. All animal work was performed with the approval of the University of Washington Institutional Care and Use Committee in accordance with the guidelines of the National Institutes of Health Office of Laboratory Animal Welfare. When parasitemia reached ∼5%, blood was harvested from euthanized animals by cardiac puncture, and red blood cells were washed and fixed in 4% paraformaldehyde with 0.0075% glutaraldehyde. Fixed cells were permeabilized with 10% Triton X-100 in PBS, blocked with BSA and incubated with MaliM03 IgM or IgG antibody along with a rabbit polyclonal anti-BIP antibody (kindly provided by Ashley Vaughan, Seattle Children’s Research Institute, Seattle, WA), followed by anti-rabbit antibody and anti-human IgM or IgG antibody conjugated to af488 and af594, respectively (Invitrogen). Finally, nuclei were stained with 6′-diamidino-2-phenylindole. PBS washes were performed between each step. Stained samples were applied to a slide and coverslipped using VectaShield. Images were obtained on a Nikon 90i microscope at 100× magnification.
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