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43 protocols using ipp 6

1

Quantification of Hepatocyte Proliferation

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Hepatocyte proliferation was analyzed by immunostaining with antiproliferating cell nuclear antigen (PCNA). The liver tissues were fixed in 10% formalin for 24 h, cut into 4 μm thick sections, and incubated with EDTA for antigen retrieval. The slides were then washed in PBS and incubated with 3% H2O2 for 10 min to quench endogenous peroxidases. After blocking with bovine serum albumin (BSA), the sections were incubated overnight with antiproliferating cell nuclear antigen (PCNA) antibody (Abcam, Cambridge, UK) overnight at 4°C, followed by HRP-conjugated goat anti-rabbit secondary antibody (Beijing ZSGB-Biotechnology Co., Ltd., Beijing, China) at room temperature for 30 min. Color was developed using DAB, and after counterstaining with hematoxylin, the sections were observed under a microscope and immunostaining was quantified with IPP 6.0 software (Media Cybernetics, USA).
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2

Immunohistochemical Analysis of EphB1 and EphrinB2

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The lumbosacral spinal cord sample was fixed in 4% formalin and embedded in paraffin. Sections 8 μm thick were incubated with polyclonal rabbit antibodies of anti-EphB1 (1 : 200, Santa), anti-ephrinB2 (1 : 200, Santa), anti-phosphorylated EphB1 (1 : 200, Santa), and anti-phosphorylated ephrinB2 (1 : 200, Santa). The anti-rabbit IgG antibody (1 : 200, Sigma) was used to incubate the tissue sections. After the tissue slides were incubated with ABC reagent (1 : 200, Thermo Fisher Scientific), they were strained with diaminobenzidine solution for 1 to 2 min and then rinsed in distilled H2O2. Next, the tissue slides were strained with hematoxylin solution for 1 to 2 min and were then rinsed in distilled H2O2 again. Normal goat serum was used as a negative background control. Finally, EphB1 and ephrinB2 immunopositive cells in the spinal dorsal horn were counted and the integrated optical density values were measured by the IPP 6.0 software (Media Cybernetics). Averaged optical (AO) values were calculated by the ratio of integrated optical density/area of tissue.
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3

Exosome Biodistribution Tracking in Mice

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Purified exosomes were labeled using PKH67 as previously described. PKH67-labeled exosomes from Panc02 and Panc02-H7 cells were injected intravenously into syngeneic C57B/L6 mice (20 μg exosomes/mouse). At 24 hpi, liver, lung, spleen, kidney, brain, and bone marrow tissues were harvested. Bone marrow cells were flushed from both the tibia and femurfor confocal microscopy. As controls, mice were injected with equivalent particle numbers of PKH67-labeled synthetic 100μm unilamellar liposomes. Fluorescence intensity was quantified using IPP6.0software (Media Cybernetics) to assess PKH67-labeled exosometissue distributions.
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4

Wound Healing Assay with Imaging

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The cell monolayer was scratched using a sterile 10-μL pipette tip and washed with PBS to remove detached cells. The remaining cells were cultured in serum-free medium, and photos were taken at 0 and 36 h. Gap widths were measured using IPP 6.0 software (Media Cybernetics, Bethesda, MD, USA), and data acquired from three areas of the wound on each plate were used to calculate the mean gap width at a given time.
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5

Western Blot Analysis of Inflammatory Proteins

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The total protein was extracted from placental tissues and HTR-8/SVneo cells using RIPA lysate (Beyotime, China) (with PMSF-protease and phosphatase inhibitor added), and then the protein concentration was measured by the BCA assay kit (Beyotime, China) according to the instructions of manufacturer. The protein samples of 30ug per well were added to 10% of the twelve-alkyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) slot to separate the protein and then electrotransferred onto the PVDF membranes. Next, the nonspecific site of the membranes were blocked with 5% skimmed milk for 1 h at room temperature and incubated overnight at 4 ℃ with first antibodies NLRP3 (1:1000, ab214185, Abcam), Caspase-1 (1:500, ab62698, Abcam), GSDMD (1:500, sc-81,868, Santa Cruz) and β-actin (1:1000, AF0003, Beyotime). On the second day, the membranes were incubated with the horseradish peroxidase (HRP) labeled secondary antibodies (1:1000, A0208/A0216, Beyotime) at room temperature for 1 h. Finally, under the action of ECL luminescent liquid, immunoreactive signals were detected by the Bio-Rad gel imaging system (MG8600 Thmorgan Biotechnology Co., Ltd., Beijing, China). The IPP6.0 software (Media Cybernetics, Singapore) was used to analyze the gray values and calculate the relative protein levels of NLRP3, Caspase-1 and GSDMD. The experiment was repeated at least three times.
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6

Transwell Migration Assay for PMS Effects

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Cells were seeded at a density of 1x104 cells/well in the upper chamber of a transwell plate (8 µm pore-size filter; Merck KGaA) and received no treatment (control), were treated with sorafenib (positive control) or were treated with PMS at 25, 50 or 100 µg/ml at 37˚C for 48 h. Following addition of 100 µl FBS free medium and treatment with mitomycin C at 37˚C for 30 min, the upper chambers were placed in a 24-well plate. The lower chambers were filled with 500 µl medium supplemented with 10% FBS for 24 h. The cells that had migrated to the lower surface of the filter were stained with 0.1% crystal violet solution. Images were captured using a light microscope (magnification, x100; Olympus Corporation) and processed by IPP 6.0 software (Media Cybernetics, Inc.).
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7

TUNEL Apoptosis Detection in Liver and Pancreas

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TUNEL was used for in situ detection of apoptosis in the liver and pancreas. Tissues were paraffin dewaxed to water, washed in phosphate buffered saline (PBS), pH 7.4 twice for 5 min each time, then incubated in 3% hydrogen peroxide for 20 minutes. Samples were then PBS washed twice more and dried. Reaction solution (TUNEL kits, Roche Diagnostics GmbH, Germany) was added to each sample (50 µl), and the reactions were performed at 37°C for 60 min in the dark. After incubation, samples were again washed twice in PBS and 50 µl Converter-POD (TUNEL kits, Roche Diagnostics GmbH, Germany) was added to the sample and incubated at 37°C for 30 min. Samples were washed again in PBS and a DAB Horseradish Peroxidase Color Development Kit (Beyotime Institute of Biotechnology, Shanghai China) was used to stain the samples. Hematoxylin was used to stain the nuclei. Samples then underwent conventional dehydration and were transparently mounted with glycerol. Colored nuclei were read as positive cells. The specimens were analyzed using a computerized image analysis system (IPP6.0 software, Media Cybernetics Inc, USA), and the data were represented as the number of TUNEL-positive cells per field (at 400X).
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8

Quantifying CD68 Expression in Liver Samples

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Paraffin-embedded sections were stained with CD68 protein adducts using a polyclonal antibody (1:100 dilution; Zhong Shan-Golden Bridge Biological Technology Co. Beijing, China) to observe quantitative expression levels of CD68.
The specimens were analyzed using a computerized image analysis system (IPP6.0 software, Media Cybernetics Inc., USA). Two independent observers were blinded to treatment groups when analyzing CD68 staining. The cells where the cytoplasm stained brown, as observed under an optical microscope, were defined as positive cells. The hepatocytes and macrophages were calculated from 8-10 fields, and the percent of positive cells was calculated as followed: number of CD68 positive cells / number of total hepatocytes counted. (at 400X)
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9

Quantifying Pigmentation Patterns in Ducks

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Pigmentation spots on the body surface of all ducks were photographed under the same conditions. First, the digital camera was set to manual exposure, and each image was collected under identical exposure conditions, including exposure time and aperture. Then, the obtained images were imported into IPP 6.0 software (Media Cybernetics, USA) and magnified by the same multiplication factor. Using an irregular shape tool incorporated in the software, the area of interest (AOI) of each pigmentation spot was selected, and the geometric size of each region was measured. Pigmentation spot areas on the dorsal and ventral sides of ducks were measured. The proportion of pigmentation distribution on the body surface for each duck was calculated. Three replicates were made for each measurement, and the average values were taken as the final phenotype. A total of 300 ducks were selected to measure the pigmentation phenotypes at 4 and 8 weeks old.
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10

Aortic Valve Atherosclerosis Imaging

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Serial sections of the aortic valve were stained with oil red O and en face of the proximal aorta was stained with Sudan IV as previously reported (Luo et al., 2015b (link)). Briefly, obtained hearts were embedded with OCT, and serial 8-μm-thick frozen sections with 40-μm intervals were obtained and stained with oil red O. The images of plaque size and lesion area were analyzed using IPP 6.0 software (Media Cybernetics, Rockville, MD, United States).
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