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10 protocols using 4 6 diamidino 2 phenylindole dapi

1

In Situ Protein Interaction Assay

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About 20,000 cells were seeded per well in 8-well chamber slides (Millipore) and grown for 2 days with Dox (5 μg/mL) induction. After the indicated treatment, the cells were fixed with 4% PFA for 15 min in the dark at RT, permeabilized in 0.2% Triton X-100 (Sigma) in 1× PBS for 10 min at RT, washed with PBS, blocked with 100 mM glycine, and washed again with PBS. The in situ PLA experiment was performed using the DuoLink kit (Olink Biosciences, Uppsala, Sweden) following the manufacturer’s instructions. The following primary antibodies were used at the specified dilutions: mouse anti-FLAG at 1:1000; rabbit anti-α-Syn at 1:200, and rabbit anti-histone 3 at 1:200 dilution. The nuclear background of cells was visualized by staining with 4’,6-diamidino-2-phenylindole (DAPI; Agilent Technologies). After staining, cells were examined with a Zeiss Axio Observer 7 microscope.
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2

Immunofluorescence Visualization of Exogenous and Endogenous Proteins

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Transfected or drug-treated cells were fixed in 4% paraformaldehyde (PFA) in PBS for 20 min in the dark. For visualisation of exogenous TDP-43 and FUS, cells were then washed twice with DPBS and mounted using DAKO fluorescent mounting medium containing 4′,6-diamidino-2-phenylindole (DAPI; Agilent). For visualisation of endogenous TDP-43 and FUS, non-specific background staining was blocked after cell fixation using 1% bovine serum albumin (BSA) in PBS for 30 min. Cells were then incubated overnight at 4 °C with rabbit anti-TDP-43 (1:500; Proteintech #10782-2-AP) or rabbit anti-FUS (1:500, Proteintech #11570-1-AP) antibodies. The next day, cells underwent 2 × 5-min washes with DPBS, incubation with rabbit Alexa Fluor-647 secondary antibody (1:500; Invitrogen #A-21244) for 1 h, followed by 2 × 5-min washes and mounting as above. Cells were imaged for fluorescence intensity quantification with a 40 × objective on a Nikon A1R confocal microscope. Images of representative cells were obtained with a 100 × objective for figure preparation. Laser intensity, gain and offset settings were kept constant and at least five random fields of view were imaged for each experimental replicate.
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3

Immunofluorescence Staining of Endothelial Cells

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After been fixed with 4% (w/v) paraformaldehyde for 30 min, cells were permeabilized with 0.1% (v/v) Triton X-100 in PBS for 5 min. A total of 10% (v/v) goat serum was added, and the cells were incubated for 30 min to block unspecific antibody binding. Next, the cells were incubated with the following primary antibodies overnight at 4°C: anti-CD31 (Santa Cruz Biotechnology), anti-CD144 (eBioscience), anti–NRP-1 (Santa Cruz Biotechnology), and anti–α-SMA, (Chemicon). Then, the cells were washed with PBS three times and incubated with Alexa Fluor 488– or Alexa Fluor 565–conjugated secondary antibodies (Molecular Probe). The stained cultures were counterstaining with 4′,6-diamidino-2-phenylindole (DAPI) (DAKO). Confocal images were acquired with an Olympus FV1000MPE confocal microscope using an objective lens (UPlanSApo 60XW, NA 1.20, Olympus). Z-stack images were taken with 10-μm intervals. Images were analyzed using FV10-ASW 3.0 Viewer software (Olympus) and processed in ImageJ software.
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4

Histochemical Staining with DAB and DAPI

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Paraformaldehyde (PFA) was purchased from Merck (Darmstadt, Germany), and 3,3'-diaminobenzidine 4HCl (DAB) was purchased from Dojin Chemical Co. (Kumamoto, Japan). Bovine serum albumin (BSA) (essentially fatty acid and globulin-free), Trizma base and Brij-35 were from Sigma Chemical Co. (St. Louis, MO, USA). Biotin-16-dUTP, digoxigenin-11-dUTP and terminal deoxynucleotidyl transferase (TdT) were from Roche Diagnostics (Mannheim, Germany). Dideoxy ATP (ddATP) and dideoxy TTP (ddTTP) were from Jena Bioscience (Jena, Germany). Hpa II, Msp I, Sau3A I and Mbo I were purchased from Takara Bio Inc. (Shiga, Japan). 4',6-Diamidino-2-phenylindole (DAPI) was from DAKO (Glostrup, Denmark). Permount was purchased from Fisher Scientific Inc. (NJ, USA). All other reagents used in this study were from Wako Pure Chemicals (Osaka, Japan) and were of analytical grade.
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5

Oocyte Maturation Analysis via Microscopy

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To detect oocyte maturation, ovaries were fixed and embedded in paraffin, and serial sections (5-µm) were stained with hematoxylin and eosin solutions (Sigma). Images were detected using a Zeiss Axioskop2 MAT microscope (Carl Zeiss MicroImaging), and the total number of follicles was determined. For immunofluorescence analysis, ovary tissues were embedding in a cryomold with compound (Sakura), frozen on dry ice and stored at −80 °C. For imaging, the samples were serially sectioned (5-µm) and fixed with 100% methanol. The sections were washed, blocked for 1 h at RT using Protein Block Serum-Free buffer, and then incubated overnight at 4 °C with a 1:100 dilution of primary antibodies as follows: anti-Nanos3 (Abcam), anti-Lhx8 (Santa Cruz Biotechnology), anti-Nobox (Abcam) and anti-stem121 (StemCells, Inc.) in Antibody Diluent with Background Reducing Components (Dako). After then, the sections were incubated for 90 min at RT with 1:200 dilutions of Alexa Fluor 594-conjugated goat anti-rabbit IgG and Alexa Fluor 488-conjugated mouse anti-goat IgG (Santa Cruz Biotechnology). The sections were counterstained with 4′,6-diamidino-2-phenylindole (DAPI, Dako). The number of follicles was determined, and follicles less than 100 µm in size in each rat were quantified. All experiments were performed in triplicate.
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6

Immunofluorescence Localization of TNF-α

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Double-immunofluorescence was performed using paraffin-embedded samples for cellular localization of TNF-α in periprosthetic tissue. Antigen retrieval was performed using 0.01 M citrate buffer and heat. Quenching of endogenous peroxidise activity was performed with 3% hydrogen peroxide (H2O2) in methanol. The sections were incubated with a mixture of primary antibodies (anti-TNF-α and anti-CD68 or anti-CD3) in a humidified chamber at 4°C overnight. Subsequently, the sections were incubated with the respective fluorescent-tagged secondary antibody for one hour. The sections were mounted using a fluorescent mounting medium containing the nuclear marker 4′,6’-diamidino-2-phenylindole (DAPI) (DAKO Cytomation, Glostrup, Denmark). To confirm the specificity of the antibodies, some sections were incubated with isotype control antibodies and processed in an identical manner. Cellular colocalization was examined by confocal microscopy using sequential mode to avoid cross-talk.
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7

Immunofluorescence Staining of Cultured Cells

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Cells (5×103) were seeded into chamber culture slides (BD Falcon, Franklin Lakes, NJ, USA) and fixed with 4% paraformaldehyde in PBS for 10 min at room temperature. After being washed with PBS, the fixed cells were incubated with primary antibodies overnight at 4℃. The cells were then washed three times with cold PBS and cultured with secondary antibody conjugated with goat anti-rabbit IgG-FITC (Santa Cruz Biotechnology, Santa Cruz, CA, USA) at room temperature for 1 h.
Nuclear staining was performed with 4′,6-diamidino-2-phenylindole (DAPI; DAKO, Glostrup, Denmark) for 10 min at room temperature in the dark. The cells were mounted on microscopic slides using EverBrite™ Hardset mounting medium (Biotium, Hayward, CA, USA). Immunolabeling was observed under confocal microscopy (Nikon, Tokyo, Japan).
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8

Blastocyst Cell Counting Using Immunofluorescence

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The number of cells in each blastocyst in all groups was counted by first staining with anti-Oct3/4 antibody (Santa Cruz) to identify inner cell mass (ICM) cells and counterstained with 4′,6-diamidino-2-phenylindole (DAPI; Dako, USA) to label nuclei. Five days after IVF, the zona pellucida (ZP) was removed using an acid Tyrode solution (pH 2.5; Sigma-Aldrich). ZP-free blastocysts were fixed in 3.7% paraformaldehyde in 0.02% Triton X-100 in DPBS containing 0.1% BSA (DPBS-BSA) for 30 min at 4°C and permeabilized with 0.1% Triton X-100. Blastocysts were transferred to 5% normal goat serum for 2–4 h at 4°C and then incubated overnight at 4°C with anti-Oct3/4 antibody (Santa Cruz). Blastocysts were then incubated with secondary antibody and co-stained with Alexa Fluor 594 Phalloidin (Molecular Probes, USA) and DAPI. Blastocysts were mounted on a glass-bottomed dish in PBS and imaged using a Zeiss Axiovert 200M fluorescence microscope with Apotome and a 40× oil-immersion objective lens (Carl Zeiss, Germany). Z-stack images (15–20) of individual blastocysts were obtained and analyzed using Axiovision software 4.6 (Carl Zeiss). Oct3/4- and DAPI-positive cells were counted as ICMs; DAPI-only positive cells were counted as the total cell number. The number of trophectoderms (TEs) was calculated as total cell number minus ICM number.
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9

Immunocytochemical Analysis of PDGFR in Tissues

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Thick transverse cross-sections (8 µm) of tissues were obtained using a cryostat (2800 FrigocutN, Reichert Jung, Heidelberg, Germany) equilibrated at -30 and -20°C for adipose tissue and muscle, respectively. Sections were mounted on silane-coated slides for enhanced adhesion. Immunocyto-localization of PDGFR marker was carried out using a standard procedure. Briefly, after incubation in 2% bovine serum albumin (BSA; Sigma, Saint-Quentin Fallavier, France) to prevent non-specific binding, sections were incubated in PBS/0.1% BSA for 45 min at room temperature with the following primary mouse antibodies: anti-PDGFR and anti-laminin complex (Interchim, Montluçon, France). Nuclei were counterstained with 4'-6-diamidino-2-phenylindole (DAPI; Dako, Trappes, France). No significant staining was detected in slides incubated with control serum and/or goat IgG in the absence of the primary antibody. A Nikon DS-Ri1 epifluorescence microscope was used to acquire digital images using an Eclipse E400 digital camera and NIS-Elements software version 3.0 (Nikon).
Qualitative and quantitative analyses of stained cells were performed using a self-developed plugin for ImageJ (ImageJ 1.43, National Institutes of Health, Bethesda, MD, USA).
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10

Immunohistochemical Analysis of Epidermal Proteins

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Slides were incubated with primary antibodies for 1 h at room temperature following rinsing with PBS. Antigen retrieval was performed for 10 min in TEG buffer. Slides were washed in 50 mM NH4Cl in PBS for 30 min and blocked by 1% BSA, 0.2% gelatine, 0.05% Saponin in PBS at room temperature for 10 min, three times. Primary antibody was diluted in 0.1% BSA, 0.3% Triton X-100 in PBS, overnight at 4°C. Antibodies against involucrin, loricrin, and filaggrin were purchased from Covance (Denver, PA). Rabbit polyclonal antibody PAR2 (H-99; sc-5597) was provided by Santa Cruz Biotechnology (Dallas, TX). Slides were rinsed three times for 10 min in PBS containing 0.1% BSA, 0.2% gelatine, and 0.05% saponin at room temperature and the secondary biotinylated antibody (goat-anti rabbit; Vector Labs, Burlingame, CA) was diluted in 0.1% BSA, 0.3% Triton X-100 in PBS. Elite Standard Vectastain ABC kit and DAB kit (both Vector Labs) were finally applied according to the manufacturer's instructions. Nuclei were counterstained with 4,6-diamidino-2-phenylindole (DAPI) (Dako, Glostrup, Denmark).
For hematoxylin and eosin (HE)-staining, paraffin-embedded sections of 4 μm were used. Microscopic analyses were performed using an Axioskop2 (Zeiss, Oberkochen, Germany) microscope and the Axiovision software Rel4.7 (Zeiss).
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