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4 protocols using mu246 uc

1

Immunohistochemical Staining and Quantification

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Tissue slides were stained as previously described on the paraffin‐embedded slides (Damhofer et al., 2015). Antibodies and dilutions used were CK19 1 : 500 (MU246‐UC; Biogenex), CXCR4 1 : 400 (Ab124824; Abcam, Cambridge, UK), Ki67 1 : 2000 (SAB5500134; Sigma). For picrosirius red staining, slides were deparaffinized, stained in a 0.1% picrosirius red solution (Sigma) in saturated picric acid for 1 h, and washed three times with 0.1 m acetic acid solution. All slides were imaged on an Olympus BX51 (Tokyo, Japan). Quantification of Ki67 staining was performed with Fiji count particles (Schindelin et al., 2012), after DAB/H color deconvolution. For IF images, slides were cut at 10 μm, mounted in Prolong Gold (ThermoFisher), and imaged on an EVOS fluorescence microscope (ThermoFisher). For collagen staining in tissue culture vessels, cells were cultured as described and after 7 days of coculture washed with PBS three times prior to fixation in 4% paraformaldehyde for 15 min. Following three washes with PBS, cells were stained for their collagen deposition as described above for 18 h and were equally treated as the tissue slides. Cells were subsequently imaged on an Olympus BX51. Quantifications of the percentage of Ki67‐positive nuclei, width of HE staining, or percentage of Venus‐positive cells were performed using Fiji package of imagej.
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2

In Situ Hybridization of miR-34a in Urothelial Carcinoma

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We performed in situ hybridization (ISH) for miR-34a on a tissue microarray slide representing n=229 urothelial carcinoma cases, as previously described.35 (link) Briefly, 5′-,3′-fluorescein-tagged locked nucleic acid (LNA)-modified DNA probe complementary to entire miR-34a sequence (probe:5′FAM/A+CAA+CCA+GCT+AAG+ACA+CTG+CCA/3′FAM; +N denotes LNA modification) was added at 50 nM to 50% deionized formamide, 5× SSC, 500 μg/ml yeast tRNA, 1× Denhardt’s solution, 0.01% tween*20 solution and hybridized against tissue at 45°C for 75 min in Leica Bond-MAX automated staining station. miR-34a probe labeling was revealed by horseradish peroxidase (HRP)-mediated deposition of fluorescein-conjugated substrate. Then, expression of cytokeratin 19 protein levels was revealed with another round of HRP-mediated deposition of Dylight 594-conjugated substrate, after sequential incubations with primary anti-CK19 (50 μg/mL; MU246-UC, Biogenex) and secondary anti-mouse HRP conjugated antibody (1 μg/mL; 170–6516, Biorad). Tissue was counterstained with DAPI. RNA expression was assessed by fluorescence microscopy after manual selection of the cellular area of interest (i.e. urothelial carcinoma cells) using the ImagePro system. MiR-34a expression is presented as the miRNA fluorescence score (0,1+,2+,or 3+) within CK19-positive cancer cells (Figure 1).
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3

Immunohistochemical Profiling of Liver Markers

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Tissue sections (4 µm) on microscope slides (Thermo Fisher Scientific) were deparaffinized with xylene (JT Baker Avantor, Radnor, PA, USA) and ethanol (Merck, Darmstadt, Germany), and blocked with 3% endogenous hydrogen peroxide (Merck). The tissue was blocked using the Avidin/Biotin Blocking Kit (SP-2001, Vector Laboratories, Burlingame, CA, USA). Sections were incubated with 20% goat or horse serum (S-100/S-2000, Vector Laboratories), and incubated with the primary antibodies anti-ALG8 (rabbit, 1:50, HPA051898, Sigma-Aldrich, Burlington, MA, USA), anti-CK19 (mouse, 1:200, MU246-UC, BioGenex, Fremont, CA, USA), or anti-HNF4α (mouse, 1:200, Invitrogen MA1-199, Thermo Fisher Scientific) overnight at 4 °C. Tissue was incubated with the secondary biotinylated antibody goat anti-rabbit (1:200, BA-1000, Burlingame, CA, USA, Vector Laboratories) or horse anti-mouse (1:200, BA-2000, Vector Laboratories) for 30 min at room temperature. This was followed by incubation with avidin–biotin complex (ABC) (PK-6100, Vector Laboratories), 3,3′-diaminobenzidine (DAB) staining (1× (Sigma-Aldrich), 0.015% hydrogen peroxide (Merck)), Mayer’s hematoxylin staining (Sigma-Aldrich), and dehydration with ethanol and xylene. The protein expression and localization were visualized using the Zeiss Primovert microscope (Zeiss, Oberkochen, Germany), and analyzed using ZEN 2 blue (version 10, Zeiss).
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Immunofluorescent Staining of FFPE Tissues

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Formalin-fixed, paraffin-embedded tissue sections (4 µm) were blocked with a blocking buffer containing 1% normal swine serum blocking solution (Vector Laboratories, Burlingame, CA, USA), 1% bovine serum albumin (BSA) (Sigma-Aldrich, Burlington, MA, USA), and 0.1% gelatin from cold-water fish skin (Sigma-Aldrich) in 1× Gibco phosphate-buffered saline (PBS) (Thermo Fisher Scientific). Sections were incubated overnight with the primary antibodies anti-CK19 (mouse, 1:200, MU246-UC, BioGenex, Fremont, CA, USA) and anti-ALG9 (rabbit, 1:200, HPA038575, Sigma-Aldrich) at 4 °C. Secondary antibodies FITC 490 anti-rabbit (goat, 1:200, 111-005-003, Jackson ImmunoResearch, West Grove, PA, USA) and TexasRed 570 anti-mouse (goat, 1:200, 115-075-062, Jackson ImmunoResearch) were incubated for 45 min at room temperature. Protein expression and localization were visualized with the Zeiss Imager Z2 microscope combined with the ApoTome.2 (Zeiss, Oberkochen, Germany) and analyzed with ZEN 2 blue (version 10, Zeiss).
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