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The TO-PRO is a nucleic acid stain used for labeling and detecting DNA in various applications. It functions by binding to nucleic acids and emitting fluorescence upon excitation, enabling visualization and analysis of DNA in biological samples.

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56 protocols using to pro

1

Immunohistochemical Analysis of Calretinin in Brain Slices

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Slice cultures were fixed in a solution of 4% (w/v) paraformaldehyde (PFA) in phosphate-buffered saline (PBS; 0.1 M, pH 7.4) and 4% (w/v) sucrose for 1 h, followed by 2% PFA and 30% sucrose in PBS overnight. After several washes with 0.1 M PBS (pH 7.4), cultures were re-sliced into 30 μm sections on a cryostat (CM3050S, Leica). Free-floating sections were washed several times in 0.1 M PBS. The sections were incubated thereafter for 1 h with 10% (v/v) normal goat serum (NGS) in 0.5% (v/v) Triton X-100 containing PBS to reduce unspecific staining. Some slices were also incubated for 48 h at 4°C with the primary antibody (rabbit anti-Calretinin, Swant, 1:500) in PBS with 5% NGS and 0.1% Triton X-100. The sections were washed several times and incubated for 4 h with appropriate Alexa488 or Alexa633-labeled secondary antibodies (Invitrogen; 1:1,000 or 1:500) in PBS with 5% NGS and 0.1% Triton X-100). TO-PRO (Invitrogen) nuclear stain was used to visualize cytoarchitecture (1:5,000; in PBS for 10 min). The sections were washed, transferred on glass slides, and mounted for visualization with an anti-fading mounting medium (Dako, Agilent Technologies).
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2

Quantifying Nitric Oxide in Tumor Slices

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C57BL/6, NOS2 KO, CD40L KO and CD40KO mice were inoculated s.c with 0.5 × 106 EG7-OVA cells. At day 7, tumors were dissected, embedded in 6% agarose (Invitrogen) and cut on vibratome (Leica, VT1000S) to obtain thick viable tumor slices (250 μm). Slices were loaded with the NO fluorescent probe (diaminorhodamine-4M AM; Sigma) for 1 hr at 37°C. CFSE-labeled CD8 + T cells (1.2 × 106) were added on the top of tumor slices. After 2 hr, tumor slices were fixed with 4% PFA for 30 min at RT. Nuclei were counterstained with 1 μg/ml ToPRO (Invitrogen). Slides were mounted with ProLong (Invitrogen) and analyzed by confocal microscopy (TCS SP5, Leica). For quantitative analysis of NO staining, different and noncontiguous regions of interest (50 ROIs) were randomly selected, and DAR-4M AM mean intensity was quantified for each ROI. Results were expressed as fold induction over control (no CD8+ T cells).
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3

Immunostaining of Imaginal Wing Discs

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Immunostaining of imaginal wing discs was performed according to standard protocols and using the following antibodies: rabbit anti-phospho-Histone 3 (1∶1000; Cell Signalling), rabbit anti-Emc (1∶50; kindly provided by Y.N. Jan), rabbit anti-Da (1∶100; kindly provided by C. Crominller), and mouse anti-ß-Gal (Promega). Mouse anti-Wg (1∶50) and mouse anti-CycB (1∶10) were obtained from the Developmental Studies Hybridoma Bank at the University of Iowa. Phalloidin-TRITC (Sigma) and TOPRO (Invitrogen) were also used to stain cell membranes and nuclei, respectively. All secondary antibodies (Molecular Probes) were used at dilutions of 1∶200.
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4

Immunohistochemical Analysis of Embryonic Patterning

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Tissue preparation and immunohistochemistry were carried out as previously described [20 (link)]. Briefly, the trunk region of fixed embryos (between 20 and 24 somite pair) was dissected out, cryo-preserved and frozen, and then cryo-sectioned at 12 μm. Immunohistochemistry was performed with primary antibodies against the following proteins: Islet-1 [Developmental Studies Hybridoma Bank (DSHB), Iowa City, IA, USA; 1:100 dilution], Lim-1/2 (DSHB; 1:100 dilution), AP-2 (DSHB; 1:100 dilution), HNK-1 (hybridoma-producing primary monoclonal antibody supernatant from the American Type Culture Collection, Manassas, VA, USA; 1:50 dilution), and Laminin (Sigma, MO, St. Louis, USA; 1:500 dilution). The following secondary antibodies (AlexaFluor; Invitrogen, Carlsbad, Calif., USA) were used at a 1:1000 dilution: anti-rabbit IgG-Alexa 546, anti-rabbit IgG-Alexa 633, anti-mouse IgG-Alexa 546, anti-mouse IgG2b-Alexa 546, anti-mouse IgG1-Alexa 633, and anti-mouse IgM-Alexa 546. When necessary, TO-PRO (Invitrogen) was used for nucleus staining. Images were collected with a Nikon Eclipse TE2000 confocal microscope.
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5

Immunofluorescence Analysis of Submandibular Gland Tissue

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Paraffin embedded submandibular gland tissue sections were processed for immunofluorescence analysis as previously described [22 (link)]. Primary antibodies used at the indicated dilutions include ΔNp63 (1:50, Cell Signaling Technology, D2K8X), K5 (1:100, gift from Dr. Julie Segre), K14 (1:100 [45 ]), alpha-smooth muscle actin (Sma) (1:200, Sigma, 1A4), Aqp5 (1:100, Alomone Labs), K7 (1:50, Abcam), Mist1 (1:100, Abcam), Troma-III (K19, 1:50, Development Studies Hybridoma Bank), Ki67 (1:100, Leica Biosystems, MM1), and Cleaved Caspase-3 (1:100, Cell Signaling Technology, D175). Sections were stained with TOPRO (Invitrogen) and mounted using VECTASHIELD Antifade Mounting Medium (Vector Laboratories) and imaged using an Andor Dragonfly Spinning Disk Confocal Microscope with Fiji [46 (link)]. Microscopy data in this study was acquired at the Optical Imaging and Analysis Facility, School of Dental Medicine, State University of New York at Buffalo.
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6

Tissue Microarray Analysis of Immune Cell Infiltration

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For IHC assessment, a tissue micro-array was constructed using cores of 0.6 mm in diameter. Three zones were used for each tumor: intratumoral, invasion front, and peritumoral. Three cores were used for each zone. Peritumoral zones were not obtained for two tumors. Sequential 3-μm sections were cut and colored by HES or used for immunohistochemistry.
IHC was also performed on tissue sections from formalin-fixed paraffin-embedded tissue blocks from WT and OSM-KO mice. Serial sections of 3 μm were cut. Immunohistochemistry was performed using a BenchMark automated staining system (Ventana Medical System, Tucson, AZ) for CD3 (Dako, A0452, 1:200), CD68 (Ventana, 790-2931, ready to use), and MPO (Dako, IS511, ready to use). Images were taken using a camera fixed to the microscope (Leica Application suite, version 4.4). Quantification of inflammatory cells was performed using assisted counting software (Visilog Noesis).
For immunofluorescence studies, tumor sections were fixed in acetone/methanol (20/80) and stained with anti-OSM (R&D system, MAB4951, 1:50), followed by staining with a goat anti-rat-IgGAF555 secondary antibody (Thermofisher, A-21434, 1:100). Cell nuclei were stained with TOPRO (Invitrogen). Image acquisition was performed with an Olympus FV1000 confocal microscope using FlowView software (ImageUP platform, University of Poitiers).
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7

Western Blot and Immunofluorescence Analysis

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Cells were seeded at a density of 2 × 105 cells/well in six‐well tissue culture plates. Cells were lysed in lysis buffer (20 mM Tris–HCl [pH 7.5], 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Nonidet P‐40, and protease and phosphatase inhibitors). After measurement of protein concentration with a BCA protein assay kit (Pierce, Rockford, IL, USA), equal amounts of total proteins per lane were subjected to SDS‐PAGE, followed by semi‐dry transfer of proteins to Fluoro Trans W membrane (Pall, Glen Cove, NY, USA). Immunodetection was undertaken with the ECL blotting system (Amersham Bioscience, Piscataway, NJ) on a Luminescent Image Analyzer (LAS400; Fujifilm, Tokyo, Japan). For immunofluorescence labeling, cells were fixed in 3.7% formaldehyde in PBS for 15 min, permealized with 0.2% Triton X‐100 in PBS for 5 min, and incubated with primary antibodies diluted with Blocking One solution (Nacalai Tesque) overnight at 4°C. The cells were then incubated with secondary antibodies for 1 h and TOPRO (Invitrogen) for 5 min. Fluorescence was examined by a confocal laser scanning microscopy (Olympus, Tokyo Japan).
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8

Astrocyte Characterization in Cultures

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Precursor or mature astrocyte cultures were fixed at 2, 14, 19, 21 and 28 DIV with 4% paraformaldehyde (Sigma-Aldrich, Cat. #P6148), and immunostained with antibodies against CD44, GFAP, S100β, ALDH1L1, Cx43, EAAT2, AQP4, Islet-1, MAP2, Nestin and Iba1, as described in Table 1. Antibody binding was visualized with the appropriate fluorescent secondary antibodies as described in Table 2. Immunolabeled APCs or astrocytes were documented on an inverted Nikon Eclipse Ti-U microscope equipped with a SPOT Pursuit™ USB Camera CCD (14-bit), Epi-FL illuminator, mercury lamp, and Sutter Smart-Shutter with a lambda SC controller. Cells were photographed using a ×40 objective; positive cells were counted offline within five randomly chosen fields, and the percentage of positive cells compared to the total number of TO-PRO (Invitrogen, Cat. #T3605) positive cells was calculated.
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9

Claudin-5 Expression and Localization in Aβ-Treated CMEC

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Evaluation of the expression and localization of the TJ protein claudin‐5 after Aβ peptide treatment in CMEC cells was evaluated by immunocytochemistry (ICC) as previously described (Fossati et al., 2010). Briefly, cells were plated on collagen‐coated glass chamber slides (Thermo Fisher Scientific) and were grown in EBM‐2 0.25% FBS +bFGF 1:2000 to facilitate the development of tight junctions. After cells were confluent for 5 days, cells were treated for 24 h with 10 μM of Aβ42 oligomers, Aβ42 fibrils, or freshly solubilized Aβ42, washed with PBS, and subsequently fixed for with 4% paraformaldehyde at room temperature. Claudin‐5 was visualized by incubation with anti‐claudin‐5 mouse monoclonal antibody (Invitrogen), followed by an incubation with Alexa Fluor 488‐conjugated anti‐mouse IgG (Invitrogen) and nuclei visualized by counterstaining with To‐pro (Invitrogen). Images were then acquired using Nikon Eclipse Ti inverted fluorescence microscope with deconvolution. Specificity of the antibody detection was assessed by omission of the primary antibody during the ICC procedure.
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10

Dysferlin Expression in Human Myotubes

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Primary human myotubes nascently differentiated for 3 d to induce dysferlin expression were trypsinized and replated 3 h before damage. Cells were washed twice with PBS ± Ca2+ ± calpeptin (Tocris Bioscience, Bristol, UK), depending on scrape conditions. Cells were scraped in PBS containing 1:2500 TOPRO (Invitrogen) for 15 s and then transferred into a fluorescence-activated cell sorting tube (BD Bioscience) and incubated at 23–26°C for 10 min. After recovery, cells were pelleted at 300 × g for 1 min at 23–26°C, the supernatant discarded, and the cell pellet resuspended in PBS containing 1:200 propidium iodide (Invitrogen). Cells were analyzed on a BD FACSDiva flow cytometer to assess damaged and repaired cells.
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