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92 protocols using scn400

1

Histological Analysis of Kidney Tissue

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Kidneys were weighed and examined for gross pathology. A phosphate buffer solution (PBS) was used to wash out blood before preparation for tissue fixation. They were sectioned at 4 μm thickness using Leica RM 2255 microtome. Tissue was stained with Haematoxylin and Eosin (H and E), Periodic Acid Schiff (PAS) and Masson’s Trichome (MT). Slides were digitally scanned using a Leica SCN 400 (Leica Microsystems GmbH, Wetzlar, Germany) and measurements were done at 200 magnification using image analyzer Leica (DMLB) and Leica QWIN software.
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2

Fluorescence Imaging of Transgene Expression

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Fluorescence images of delivered dextran and viral delivery-mediated GFP transgene expression were acquired using 2.5x and 10x dry objectives (Leica DM6 B, Leica Microsystems Inc., Buffalo Grove, IL, USA). Bright-field images of H&E-stained sections were acquired from an automatic whole slide scanning system at 40x magnification (Leica SCN400, Leica Microsystems Inc., Buffalo Grove, IL, USA), and exported using the Aperio ImageScope software (Version 12.4.3, Leica Biosystems Imaging Inc., Buffalo Grove, IL, USA). Immunofluorescence images of IBA1 and GFAP stained brain sections were acquired using a 20x dry objective on a confocal microscope (LSM 700, Zeiss Microscopy, Jena, Germany).
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3

Thoracic Aorta Histology and Immunostaining

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Thoracic aortae obtained from DSS rats (NS, HS, and HS+ASA) were fixed in 10% formalin at a pH of 7.4. Dehydration, clarification, and inclusion were performed soon afterward. After blocks were obtained, sections were obtained using a microtome (Leica RM2235; Leica Microsystems) with a thickness of 5 μm. Thoracic aortae were stained with hematoxylin and eosin. The antibodies eNOS (ab76198), vascular cell adhesion molecule‐1 (ab134047), and collagen I (ab96723) were also used for the primary incubation, while fluorescent antibody rabbit antimouse immunoglobulin G and rabbit antimouse immunoglobulin G (A11059 and A11061; both Thermo Fisher Scientific) were included for the second incubation. From each aorta's description, all sections were obtained using a section‐scanning system (Leica SCN400; Leica Microsystems).
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4

Quantifying Adipocyte Size and Intestinal Morphology

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The visceral adipose tissue was stained with hematoxylin/eosin to quantify the size of the adipocytes. The scanned images were analyzed on ImagenJ software as previously described.31 The cross‐sectional area of each adipocyte was automatically recognized and calculated by the software. Artifacts were manually discarded. At least 700 adipocytes were quantified per measurement and two measurements were done for each mouse.
In the ileum, the crypt depth and villus length were measured after hematoxylin/eosin staining. The sections were digitized (Leica SCN400, Leica Microsystems, Germany), and the images were captured using the Leica Image Viewer Software (Version 4.0.4). Crypt depth and villus length measurements were made on sections (at least 10 measurements per animal).
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5

Immunohistochemical Analysis of Macrophages and Mannose Receptor in Myocardial Specimens

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Myocardial specimens were fixed and the midventricular section was made into paraffin blocks. Primary antibodies used for immunohistochemistry were anti-ED-1 (EMD Millipore, Billerica, MA) for macrophages and anti-mannose receptor (MR) (Abcam, Cambridge, MA) for mannose receptor. These were incubated with appropriate secondary antibodies and visualized using the DAB substrate kit or secondary antibodies conjugated with the appropriate immunofluorescence reporter. For visualization of MSA uptake, RITC-MSA was given during the secondary antibody incubation step in the tissue section. All images were taken with either a slide scanner (Leica SCN400, Leica microsystems, Wetzlar, Germany) for the immunohistochemical specimens or a confocal microscopy (LSM 710, Carl Zeiss, Jena, Germany) for the immunofluorescent staining.
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6

Immunohistochemical Localization of Oxidative Stress Markers

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Immunohistochemical localization was performed with paraffin-embedded tissue sections, deparaffinized and hydrated through xylene and graded alcohols using a standard protocol. Antibodies are used against Caspase 1 (Santa Cruz Biotechnology, Santa Cruz, CA), 8-oxo-dG (Abcam, Cambridge, MA), and Ogg1 (LSBio, Seattle, WA). Appropriate HRP-conjugated secondary antibodies and DAB incubation (Dako North America, Carpinteria, CA, USA) was used for visualization. All the slides were scanned on a Leica SCN400 (Leica Micro System, Buffalo Grove, IL) and analyzed by Tissue IA Optimizer (Leica). The values of positively stained cells were measured in an unbiased manner.
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7

Pancreatic Islet Morphology Analysis

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Pancreases were dissected from paired WT and Hid1-betaKO mice and fixed with 4% paraformaldehyde in PBS for 24 hr. After dehydration, the samples were embedded in paraffin. Continuous paraffin sections were obtained at 80 μm intervals from each pancreas. We studied islet morphology for each section using H&E staining, and the sections were scanned with a Leica SCN400 (Leica Microsystems, Wetzlar, Germany). Islet size and number of islets/mm2 were determined by ImageJ (National Institutes of Health, https://imagej.nih.gov/ij/ ).
For immunohistochemistry analysis, pancreas slices or cell samples were fixed with 4% paraformaldehyde in PBS for 15 min, followed by permeabilization in PBS containing 0.5% Triton X-100 (MERCK, Billerica, MA) for 10 min and blocking in PBS containing 5% goat serum for 60 min. The samples were incubated for 60 min in PBS containing primary antibodies and 2.5% goat serum and then exposed to fluorescent dye-conjugated secondary antibodies for 60 min at 37°C.
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8

Histological Evaluation of Ablation Depth

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The ablation area was measured using Image J software (version 1.8; National Institutes of Health, Bethesda, Maryland, USA). Adverse events were defined as extensive submucosal hemorrhage, muscularis propria damage, or perforation. Ablation depth was recorded as the deepest histological damaged layer. H&E- and TUNEL-stained tissue specimen slides were analyzed using a slide scanner (Leica SCN400; Leica Microsystems, Wetzlar, Germany) and an image viewer (Leica SCN400 Image Viewer; Leica Microsystems, Wetzlar, Germany).
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9

Tissue Microarray Analysis of NaPi2b Expression

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For the TMA, the whole biopsy was sectioned and stained with Hematoxylin (Histolab Products AB, Sweden). Three representative tumor areas were identified under the light microscope (Olympus BX45, Olympus Corporation, Tokyo, Japan), and three cores of 1,0 mm-diameter were punched with a manual tissue microarrayer (Beecher MTA-1, Estigen,Tartu, Estonia) and re-embedded into a predefined position on a new, empty, paraffin block. The TMA block was heated at 45 °C in 1 h, sectioned, 4 μm, and mounted onto slides.
For IHC analysis, the TMA slides were immunostained by UltraVision Quanto Detection System HRP DAB kit (Thermo Fisher Scientific, Wilmington, DE) and incubated overnight with the MX35 antibody at a concentration of 1:1000. All slides were counterstained with hematoxylin and mounted with Pertex (Histolab Products AB, Sweden). All TMAs were scanned by a Leica SCN400 (Leica Microsystems, Milton Keynes, UK). SlidePath Gateway LAN software was used for the evaluation of the NaPi2b distribution.
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10

Quantifying Spheroid Cell Staining

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Cryosections were analyzed using a laser scanning microscope (LSM 710, Carl Zeiss, Germany) and Zen 2010 black edition (Carl Zeiss, Germany). Alternatively, stained spheroids sections were imaged using a bright field slide scanner (Leica SCN400, Leica Microsystems, Wetzlar, Germany), and images were analyzed using Definiens Tissue Studio 64 software (Definiens AG, Munich, Germany). Photoshop Elements 10 software (Adobe Systems, San José, CA, USA) was used to determine percentages of stained cells and their intensities in spheroid layers.
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