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120 protocols using nanozoomer s60

1

Histological Analysis of Footpad and Tail Lesions

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Footpad lesions and 5 mm long tail pieces were fixed in 4% PFA. Tail pieces were also decalcified with Shandon TBD-1 Decalcifier (Thermofisher Scientific) for 24 hrs at 4°C. All samples were embedded into paraffin and 5 μm transversal sections were obtained. Sections were stained with Masson’s Trichrome Blue by the Mouse Pathology Facility at the University of Lausanne. Entire sample area was acquired on AxioScan.Z1 scanner (Zeiss) with Plan Apochromat 20x/0.80 objective using Brightfield contrast or NanoZoomer S60 (Hamamatsu Photonics K.K.) scanner with Nikon Plan Apochromat 20x/0.75 objective using Brightfield contrast. Images were obtained using the following software: Zen Blue (Zeiss) for AxioScan.Z1 scanner or NPD.scan3.3 (Hamamatsu Photonics K.K.) for NanoZoomer S60 scanner. Representative images of the sections are shown.
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2

Immunostaining of MICA/B and HLA-E in Formalin-Fixed Spheroids

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The formalin-fixed spheroids were first embedded in Histogel (Thermo Scientific) and then in paraffin. Blocks were sliced in 5 μm-thick sections and immunostainings performed on a Discovery Ultra automaton (Ventana). After pre-treatment with cell conditioning 1 (Ventana), sections were incubated 1 h at 37 °C with anti-MICA/B (clone MIA4, Innate Pharma) or anti-HLA-E (clone MEM-E/02, Exbio) primary antibodies at 2 μg/mL and 1 μg/mL, respectively. Anti-mouse IgG detection system (discovery OmniMap anti-mouse HRP, Ventana) was used for HLA-E staining and an additional amplification step using tyramide was used for MICA/B staining (discovery Amp HQ kit, Ventana). After revelation with 3,3-diaminobenzidine and counterstaining with hematoxylin, sections were washed, dehydrated, cleared and mounted using a coverslipper (ClearVue, Thermo Scientific). Stained sections were finally scanned on a slide scanner (S60 Nanozoomer, Hamamatsu).
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3

Immunohistochemical Analysis of MICA/B

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Formalin-fixed paraffin embedded blocks were sliced in 5 µm-thick sections and immunostainings performed on a Discovery Ultra or a Benchmark Ultra (Ventana). All samples except breast cancer tissues were stained on a Discovery Ultra automaton. After pre-treatment with cell conditioning 1, sections were incubated for 1 hour at 37°C with anti-MICA/B (clone Mia4, Innate Pharma) primary antibody or mouse IgG1 isotype control at 2 µg/mL (for staining on the Discovery Ultra) or at 6.6 µg/mL (for staining on the Benchmark Ultra). Then, signal amplification using the discovery Amp HQ kit (760-052) or the UltraView kit (760-500) was performed. After revelation with 3,3-diaminobenzidine, counterstaining with hematoxylin and bluing, sections were washed, dehydrated, cleared and coverslipped. Stained sections were finally scanned on a slide scanner (S60 Nanozoomer, Hamamatsu or a Pannoramic scan II, 3DHistech). Staining was interpreted and scored by trained pathologists that determined the MICA/B expression on the tumor cells. Samples with more than 1% of MICA/B positive tumor cell were considered MICA/B positive.
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4

MICA/B Immunohistochemical Staining Protocol

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Formalin-fixed paraffin embedded blocks were sliced in 5 μm-thick sections and immunostainings performed on a Discovery Ultra or a Benchmark Ultra (Ventana). All samples except breast cancer tissues were stained on a Discovery Ultra automaton. After pre-treatment with cell conditioning 1, sections were incubated for 1 hour at 37°C with anti-MICA/B (clone Mia4, Innate Pharma) primary antibody or mouse IgG1 isotype control at 2 μg/mL (for staining on the Discovery Ultra) or at 6.6 μg/mL (for staining on the Benchmark Ultra). Then, signal amplification using the discovery Amp HQ kit (760-052) or the UltraView kit (760-500) was performed. After revelation with 3,3-diaminobenzidine, counterstaining with hematoxylin and bluing, sections were washed, dehydrated, cleared and coverslipped. Stained sections were finally scanned on a slide scanner (S60 Nanozoomer, Hamamatsu or a Pannoramic scan II, 3DHistech). Staining was interpreted and scored by trained pathologists that determined the MICA/B expression on the tumor cells. Samples with more than 1% of MICA/B positive tumor cell were considered MICA/B positive.
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5

Histological Evaluation of Adipose and Liver Tissues

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Parts of VAT, SCAT, and liver were fixed in 4% paraformaldehyde (Sigma-Aldrich) overnight at 4 °C, dehydrated and embedded in paraffin as previously described [32 (link)]. Tissue Sections (5 μm) were prepared by using a microtome and stained with hematoxylin and eosin (Sigma-Aldrich). VAT and SCAT were acquired using the Axiovision Zeiss software (10 × magnification). The quantification of adipocytes area was performed using ImageJ software with the Adiposoft plugin [33 (link)]. For the liver section, whole slices were acquired with the Nanozoomer S60 slide scanner (Hamamatsu, Tokyo, Japan). The images were then magnified and saved at 20 × with the NDPview2 software (Hamamatsu) to show only the considered area, which was then quantified with ImageJ software. Area covered by small lipid droplets within hepatocytes was evaluated as microsteatosis, whereas area covered by large lipid droplets disrupting the cell morphology (small nuclei pushed to the cell border) was quantified as macrosteatosis [34 (link)]. Inflammatory foci were evaluated as groups of > 5 close non-hepatocytic nuclei [35 (link)].
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6

Immunohistochemical Staining of Cytochrome P450 Enzymes

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Immunohistochemical staining with monoclonal mouse anti-human mitochondria (hMIT) (clone 113-1, Merck Millipore, Burlington, MA, 1:2000), antihuman CYP1A2 (clone 3B8C1, Abcam plc., Cambridge, UK, 1:1000), antihuman CYP2C9 (clone 2C8, LifeSpan Biosciences, Inc., Seattle WA. USA, 1:150), and rabbit antihuman CYP3A4 (clone EPR6202, Abcam Plc., 1:300) antibodies was performed as described previously14 (link). Tissues were fixed in 4% (v/v) phosphate-buffered formalin (Mildform 10 NM; Wako Pure Chemical Industries). The sections were autoclaved for 10 min in a target retrieval solution (0.1 M citrate buffer, pH 6.0; 1 mM EDTA, pH 9.0), equilibrated at room temperature for 20 min, and then incubated with an anti-POR (HPA010136, Sigma) primary antibody. Primary antibodies were visualized using amino acid polymer/peroxidase complex-labeled antibodies (Histofine Simple Stain MAX PO [MULTI]; Nichirei Biosciences Inc.) and diaminobenzidine (DAB; Dojindo Laboratories, Kumamoto, Japan) substrate (0.2 mg/mL 3,3-diaminobenzidine tetrahydrochloride in 0.05 M Tris–HCl, pH 7.6, and 0.005% H2O2). The sections were counterstained with hematoxylin. Images were captured using a digital slide scanner (NanoZoomer S60; Hamamatsu Photonics, KK Hamamatsu, Japan).
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7

Apoptosis Detection in Intestinal Epithelial Cells

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TUNEL was used to detect the apoptosis of intestinal epithelial cells. TUNEL staining was processed by an apoptosis two-step assay kit. The slides of the TUNEL stain were sealed by an anti-fluorescence quenching sealer. The images of the slides above were collected by NanoZoomer-S60 (Hamamatsu Photonics (China) Co., Ltd.) and analyzed by ImageJ.
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8

NIR Imaging of Lymph Nodes

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With each rat under general anesthesia, 10 μ L of ICG aqueous solution (50 µg/mL) or SnC–ICG (final ICG concentration: 50 µg/mL) was administered to the right foot pad of four animals each and the injection site was massaged a few times. Eighteen hours later, each rat was laparotomized and regional LNs were observed using an NIR fluorescence camera. Next, all fluorescent LNs were retrieved and embedded in a Tissue-Tek® Optimal Cutting Temperature Compound (O.C.T. compound; Sakura Finetek Japan Co., Ltd., Inc., Tokyo, Japan) and subsequently frozen in liquid nitrogen.
Tissue sections (7  μ m thick) were prepared and the distribution of fluorescence in the specimen was examined under the NIR fluorescence microscope. Next, the samples were stained with hematoxylin/eosin (HE) and their images were obtained using a digital slide scanner (NanoZoomer S60; C13210-01, Hamamatsu Photonics K.K., Shizuoka, Japan).
The fluorescence intensity of the LN images on the NIR fluorescence camera was estimated using the ImageJ software (NIH, DC, USA). The mean brightness of the fluorescent area determined by a five-time repeated discriminant analysis in the CIE Lab color space on an apparent LN image was used as the representative fluorescence intensity.
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9

Immunohistochemical Analysis of MnPV E4 in FFPE Tumors

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Staining of formalin-fixed, paraffin-embedded tumors was performed as previously described (16 (link)). Briefly, deparaffinized sections were subjected to heat-induced epitope retrieval (citrate buffer pH6.0), blocked with 5% goat serum in PBS and incubated with a self-made anti-MnPV E4 mouse monoclonal antibody overnight at 4°C. After washing, slides were incubated with Alexa594-conjugated anti-mouse antibody (Invitrogen, Carlsbad, CA, USA) and nuclei were stained with DAPI. Sections were mounted with Dako Faramount Aqueous Mounting Medium (Dako North America, Inc, CA, USA) and imaged with a Keyence BZ-9000 Microscope (Keyence Deutschland GmbH, Neu-Isenburg, Germany) or a Hamamatsu NanoZoomer S60 (Hamamatsu, Hamamatsu City, Japan).
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10

Cytogenetic Biomarkers Analysis Protocol

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Micronuclei (MNi) multiple MNi (≥2), nucleoplasmic bridges (NPBs), nuclear buds (NBUDs), and fused nuclei (Fused) were scored in binucleated cells using the cytokinesis-block micronucleus cytometry assay (CBMNcyt) [35 (link)]. Briefly, following treatment with MGO for 24 or 48 h, cells were washed twice with Hanks balanced salt solution and resuspended in RPMI-1640 containing 4.5 µg/mL cytochalasin-b (cyt-b) for 24 h. After cytokinesis block, cells were harvested onto slides by cytocentrifugation [35 (link)]. Slide preparation and scoring of the CBMNcyt assay were performed as described previously using a NanoZoomer S60 (Hamamatsu Photonics, Shizuoka, Japan) [35 (link),36 (link)]. Enlarged, misshapen, and multinucleated cells were prepared the same as for the CBMNcyt assay, except cytochalasin-b was not added following treatment of MGO. Scoring criteria for the above biomarkers has previously been described [18 (link),35 (link)]. For mitotic index, cells which possessed condensed chromosomes were distinguished from interphase cells microscopically, as previously described [37 (link)].
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