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29 protocols using automated tissue processor

1

Histological Analysis of Adipose and Liver Tissues

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Adipose tissues and liver were fixed in 10% buffered formalin, dehydrated and processed using an automated tissue processor (Leica, Germany). Four micrometer-thick sections were stained with haematoxylin and eosin (H&E) to examine the morphology using an automated slide strainer (Leica, Germany). Images were obtained under bright field LEICA DM 2000 microscope with LEICA ICC50 HD camera (Leica Microsystems, Germany). The diameter of adipocytes was measured using the ImageJ software with Adiposoft plugin [53 (link)].
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2

Tissue Fixation and Processing

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Follicles and liver microtissues cultured in vitro were fixed for 4 h at 4 °C in 3.8% paraformaldehyde in PBS. Ovary, fallopian tube, endometrium and ectocervix were fixed in 10% formalin overnight. Tissues were dehydrated in ascending concentrations of ethanol (50–100%) before being embedded in paraffin using an automated tissue processor (Leica). Serial 5 μm sections were cut for haematoxylin and eosin, immunofluorescence and immunohistochemistry staining.
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3

Histological Analysis of Organ Pathology

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Brain and spleen tissue was collected from uninfected, infected-untreated, and combination treated groups and fixed in 10% buffered formalin (Sigma, USA) solution. The organ specimens were subjected to a tissue processor using an automated tissue processor (Leica, Germany) to remove the water from the tissues. The specimens were embedded into melted paraffin wax using a histoembedder (Leica, Germany), sectioned into a 4.0μm thick slice with a microtome (Leica, Germany) and stained with hematoxylin and eosin (H&E) using an autostainer. The morphological changes within the tissues of the different groups were observed under a light microscope (under 40×magnification).
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4

Histological Analysis of Aortic Remodeling

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Isolated aorta from each group was fixed in 10% formalin (v/v) for 24–48 h. The tissue was excised and processed using an automated tissue processor (Leica, Wetzlar, Germany) and subsequently embedded in Paraplast (Sigma-Aldrich, St. Louis, MO, USA). Afterward, the tissue was sectioned at 5 µm thickness using a microtome (Leica RM2235, Walldorf, Germany) before being stained with hematoxylin and eosin (H&E), and Verhoeff–Van Gieson’s (VVG) method, respectively [37 (link)]. H&E-stained aortic sections were used to measure the thicknesses of the aortic wall, tunica media, tunica adventitia (without the perivascular adipose tissue), and lumen diameter. Meanwhile, VVG staining was performed to compare the lining of internal lamella in the tunica media layer. For histomorphometry of the H&E-stained aorta, photographs were taken from five different non-overlapping fields (n = 10/group) using a 40 × objective. Each photograph was used for the morphometry analysis using the straight segmented or freehand lines tools of the cell sense system in Image analyzer (Olympus, Tokyo, Japan). The mean value of the five fields was used as a representative for each rat.
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5

Placental Histomorphology Analysis

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The placentas isolated from infected or uninfected mice were fixed in 4% paraformaldehyde overnight and then embedded in paraffin blocks using an automated tissue processor (Leica, Germany). After sections (5-μm thickness) were prepared, deparaffinized, and rehydrated, hematoxylin and eosin were used to stain the sections to observe histomorphology.
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6

Quantitative Analysis of Ovarian Follicles

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The dissected ovaries were fixed in 10% neutral buffered formalin (Sigma Aldrich) at room temperature overnight. The fixed ovaries were processed through serial ethanol, xylene, and paraffin baths in the automated tissue processor (Leica). The paraffin-embedded ovaries in blocks were cut serially into 6 µm sections, and every fifth section of the whole ovary was stained with H&E and analyzed for follicle counts. The follicles were categorized into primordial, primary, secondary, and antral follicles based on the follicle size as well as the shape and number of the surrounding layer(s) of granulosa cells (25 (link)). Only follicles with visible oocyte nuclei were counted. The total number of follicles counted for each category was then multiplied by a correction factor of 5 (the sampling rate) to be representative of the population of the entire ovary. The follicle counting was conducted independently by two experienced observers, and the average number was used for statistical analyses.
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7

Fixation and Histological Processing of Implants

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IP implants were kept intact within the peritoneum. The overlying skin was removed to isolate the entire peritoneal cavity, fixed for 48 hours in Bouin’s Solution, then dissected into three 1 cm sections before being fixed for another 24 hours. Bouin’s solution was rinsed out with successive rinses of 1xPBS before being placed in 70% ethanol for FFPE processing.
SQ implants were dissected from the underlying muscle with overlying skin attached to the implant. Samples were fixed overnight in 10% neutral buffered formalin (NBF) overnight, and then rinsed in distilled water before being placed in 70% ethanol for formalin-fixed paraffin-embedded (FFPE) processing.
VML implants were dissected and collected similarly to those previously described for flow cytometry. Samples were incubated in 10% NBF for 48 hours before rinsing in distilled water and placing in 70% ethanol for FFPE processing. All models were dehydrated in a graded ethanol series and cleared in xylenes before paraffin infiltration using an automated tissue processor (Leica). Samples were mounted on paraffin blocks, and 5 μm sections were taken before being baked for 3 hours at 60°C and stained with hematoxylin and eosin (H&E, Sigma) or Masson’s trichrome (Sigma) as per manufacturer’s instructions. Slides were imaged on an EVOS microscope.
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8

Histological Analysis of Cryopreserved Tissues

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The fresh and cryopreserved/thawed tissues were either fixed in 4% paraformaldehyde (PFA) for TUNEL staining analysis or Bouin’s solution for follicle counting for 24 hrs at 4°C. Tissues were washed after fixation and placed in 70% ethanol, dehydrated through a graded series of ethanol concentrations, and processed for paraffin embedding using a standard protocol and an automated tissue processor (Leica, Manheim, Germany), and 5 μm serial sections were cut for histological analysis, with 4 sections sequentially placed on each slide. After deparaffination, every 4 out of 8 sections were stained with hematoxylin and eosin. An additional set of histological sections from donors 3, 4, and 5 were stained with picrosirius red stain for collagen assessment of the cortex stromal tissue. The details are reported in Supplemental Figure 2.
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9

Liver Histopathological Assessment Protocol

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Liver tissue samples collected at necropsy were processed for histopathology using an automated tissue processor (Leica, Germany) and paraffinized tissue blocks were prepared. Thin paraffin sections were cut at 4μm thickness using a semi-automated microtome (Leica, Germany). Tissue sections were then stained with Hematoxylin and eosin (H&E) and were examined under Olympus microscope BX57 and images were captured at 10× and 40× magnifications using DP71 digital camera system.
Histopathology was evaluated both qualitatively and quantitatively under the supervision of a qualified veterinary pathologist. The extents of vacuolar degeneration and necrosis were assessed by semi quantitative scoring criteria (Grade 0; for absence or less than 5% area affected, Grade 1; mild/minimal or less than 25% area affected, Grade 2; moderate or about 50% area affected and Grade 3; severe or more than 50% area affected). In addition, the number of mitotic figures was counted in the entire histology section and was expressed as number per unit area.
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10

Immunohistochemical Staining of Ocular Tissues

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Globes were enucleated and fixed by emersion (2% formaldehyde in phosphate buffered saline pH 7.5, overnight at 4°C). Fixed globes were then opened with a razor blade and processed through a sucrose gradient prior to embedding in OCT media (cryosections) or dehydrated and embedded in paraffin using an automated tissue processor (Leica). 7 μm cryosections or 5μm paraffin sections were then used for immunostaining using standard methods. Paraffin sections were dewaxed and subjected to heat induced antigen retrieval (10 mM TRIS, 1 mM EDTA, 0.05% Tween20, pH 9, autoclaved 121°C 30 min liquid cycle) prior to staining. For staining, all sections were first blocked and permeabilized (5% donkey serum, 2.5% BSA, 0.5% Triton X100 in TBS, pH 7.5, 1 hr at room temperature) and then incubated overnight with appropriate primary antibodies diluted in additional blocking buffer. Slides were then washed (6 × 5 minutes, 0.05% Tween 20 in TBS, pH 7.5) and incubated for an additional 1hr at room temperature with appropriate Alexafluor-conjugated secondary antibodies (Invitrogen, Carlsbad CA, USA). Primary antibodies used: Goat anti PODXL, 1:250 (R&D systems AF1556), Goat anti CD31, 1:250 (R&D systems AF3628), Chicken anti GFP 1:5000 (Abcam, AB13970), Goat anti PDGFRB 1:100 (R&D systems AF1042). Slides were mounted and imaged using a Nikon A1R confocal microscope.
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