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1

Quantitative Immunohistochemical Analysis of PPAR-α

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Immunohistochemistry was performed as described previously [26 (link)]. The tissue sections were incubated at room temperature for 2 h with the following primary antibody: HRP-labeled anti-PPAR-α antibody (1:200, Santa Cruz Biotechnology, catalog no. sc-398394). Slides were rinsed three times with PBS and then stained with DAB using the DAB substrate kit (Nichirei Biosciences). Sections were counterstained with Meyer's hematoxylin, dehydrated, cleared with 99% xylene, and then mounted in malinol. The expression of PPAR-α in cells was observed at 200x magnification using a light microscope (BX53; Olympus Corporation, Tokyo, Japan), and images were captured with a microscopic camera (DP20-5; Olympus Corporation). The classification of nuclear PPAR-α expression was assessed using the following scoring: no staining, 0; <25% positive cells, 1+; 25-50% positive cells, 2+; 50-75% positive cells, 3+; and >75% positive cells, 4+. The expression levels of PPAR-α  were grouped into negative (0, 1+, and 2+) and positive (3+ and 4+) groups.
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2

Immunocytochemical Assay for PPAR-α

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The cells were seeded on Nunc Lab-Tek chamber slides (Thermo Fisher Scientific) and incubated at 37°C until confluent. Cells were subsequently washed twice with PBS and fixed with 3.7% formalin at room temperature for 15 min. The cells were permeabilized with 0.25% triton in PBS for 10 min and blocked with 2% bovine serum albumin (Wako Pure Chemical Industries) in PBS for 1 h. Cells were incubated at room temperature for 2 h with HRP-labeled anti-PPAR-α antibody (1:200, Santa Cruz Biotechnology, catalog no. sc-398394). The cells were rinsed three times with PBS and then stained with 3,3′-diaminobenzidine tetrahydrochloride (DAB) using a DAB substrate kit (Nichirei Biosciences, Tokyo, Japan). The cells were counterstained with Meyer's hematoxylin, dehydrated, cleared with 99% xylene for 15 min, and mounted in malinol (Muto Pure Chemicals, Tokyo, Japan). The expression of PPAR-α in cells was observed at 200x magnification using a light microscope (BX53; Olympus Corporation, Tokyo, Japan), and images were captured with a microscopic camera (DP20-5; Olympus Corporation).
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3

Histological Analysis of Cartilage Micromass

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The cartilage-like micromass pellets were fixed with 4% PFA, dehydrated, and embedded in paraffin. Samples were sliced into 4-μm sections and stained with Toluidine Blue, Alcian Blue, and Safranin O. For aggrecan immunostaining, the sections were deparaffinized and incubated with 25 μg/ml hyaluronidase at 37 °C for 30 min and blocked with 10% goat serum and 1% BSA in Tris buffered saline (TBS) at room temperature for 1 h. The sections were incubated with rabbit anti-human aggrecan antibody (1:100 dilution, clone 13880-1-AP; Proteintech, Rocky Hill, NJ) at 4 °C overnight. After washing with TBS, the sections were incubated with peroxidase-conjugated anti-rabbit IgG antibody (1:200 dilution, DakoCytomation, Glostrup, Denmark) at room temperature for 30 min. For the peroxidase reaction, 0.3% 3,3′-diaminobenzidine tetrahydrochloride was used as the chromogenic substrate. The sample was observed with an upright microscope (BX51, Olympus, Tokyo, Japan) and photographed with a microscope digital camera (DP20-5, Olympus).
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Histological and Immunohistochemical Evaluation of Liver Pathology

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The liver sections were fixed with 10% formalin and embedded in paraffin. Subsequently, 5-µm-thick paraffin-embedded sections were stained with hematoxylin and eosin. Liver steatosis and inflammation were evaluated based on a previously described scoring system [32 (link)]. The liver sections were also stained with Sirius Red. For immunohistochemistry, the sections were pre-treated using heat mediated antigen retrieval with sodium citrate buffer (pH6.0) for 20 min. As the primary antibodies, alpha-smooth muscle actin (α-SMA) (ab5494; 1:200 dilution, Abcam, Cambridge, UK) and F4/80 (ab100790; 1:100 dilution, Abcam) were used with staining performed according to the suppliers’ recommendations. A goat anti-rabbit biotinylated secondary antibody was used to detect the primary, and visualized using an HRP conjugated ABC system (Vector Laboratories, Burlingame, CA, USA). DAB was used as the chromogen. Specimens for histology and immunohistochemistry were observed under an optical microscope (BX53; OLYMPUS, Tokyo, Japan) equipped with a digital microscope camera (DP20-5; OLYMPUS). The National Institutes of Health (NIH) ImageJ software (http://imagej.nih.gov/ij/) was used for quantitative analyses. All quantitative analyses were performed for 5 fields per each section in high-power fields (HPFs) at 400-fold magnification.
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5

In Vitro Tube Formation Assay

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HUVECs (passages < 12, 1.5 × 105/0.5 ml) were seeded in a 24-well plate and transfected with either microRNA mimics (10 nM), siRNAs (10 nM) or Tough Decoy (50 nM) on the next day. Forty-eight hours after transfection, tube formation assay was performed. HUVECs were plated (6.5 × 104 cells/0.5 ml) into Matrigel-coated wells in a 24-well plate to induce tube networking. BD matrigel matrix was purchased from BD Biosciences (Bedford, MA). Twenty-four hours later, the wells were examined with an Olympus CKX41 microscope and images were captured using an Olympus DP20–5 digital camera. The capillary tubes in those images were counted. For analysis of TuD transfection, images were taken eight hours after transfection instead of 24 hours after. For inhibitor assays, Ki8751 (Calbiochem, San Diego, CA) or N–[(3,5-difluorophenyl) acetyl]-L-alanyl-2-phenyl-1,1-dimethylethyl ester-glycine (DAPT; Peptide Institute) was added during tube formation on Matrigel at the indicated concentrations. To recover cells from Matrigel-coated wells, the cells were washed with PBS and incubated with 1 ml of ice-cold BD Cell Recovery Solution (BD Biosciences) with agitation on ice until the gel was resolved. Collected cells were washed with PBS twice and subjected to further analysis.
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