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6 protocols using alexa fluor 488 or alexa fluor 568 conjugated secondary antibody

1

Immunofluorescence Analysis of Ad-Fhit-Infected Cells

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Ad-Fhit-infected cells were seeded on coverslips, grown overnight, and fixed with 4% paraformaldehyde in PBS for 15 min. Following permeabilization with 0.5% Triton X-100 in PBS for 10 min at room temperature, cells were then blocked with 3% BSA in PBS for 30 min at room temperature and incubated overnight at 4°C with primary antibodies. After three 5-min washes in PBS, cells were incubated for 1 h at room temperature with Alexa Fluor 488- or Alexa Fluor 568-conjugated secondary antibodies (Invitrogen). Then, cells were counterstained with Hoechst 33342 for 5 min for nuclear staining, washed twice in PBS, and mounted on glass slides using Vectashield (Vector Laboratories; Burlingame, CA, USA). Cells were visualized using a Zeiss LSM 700 laser scanning microscope (Carl Zeiss; Oberkochen, Germany). Quantification of proteins in the acquired images was performed by using ImageJ software (NIH Image; Bethesda, MD, USA).
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2

Colocalization Analysis of PAR4-Venus and RGS-HA

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293T cells attached to poly-D-lysine- and collagen-coated coverslips were transfected with the indicated plasmids. After 48 h, cells were washed once with PBS and subsequently fixed with PBS containing 4% paraformaldehyde at room temperature for 20 min. Cells washed with PBS were blocked for 1 h at room temperature in blocking solution (PBS containing 0.1% Triton X-100, 10% normal goat serum, and 1% bovine serum albumin) and subsequently incubated with blocking solution containing antibodies against HA (1:150 dilution, Biolegend, San Diego, CA) and/or EE (EMD Millipore, Billerica, MA) at room temperature for 1 h. Cells were washed four times for 7 min each and incubated with Alexa Fluor 488- or Alexa Fluor 568-conjugated secondary antibodies (1500; Invitrogen) for 30 min. Following four additional washes for 7 min, cells were mounted with VECTASHIELD (Vector Laboratories, Burlingame, CA) and observed under a Zeiss LSM 700 confocal microscope with 40 × 1.2 numerical aperture objective (Carl Zeiss, Oberkochen, Germany). Pearson correlation coefficient (PCC) was calculated to quantify colocalization between PAR4-Venus and RGS-HA proteins in the presence of Gα. We assigned four square-shaped regions per cell to the cell membrane. PCC was calculated by IMAGE J software (National Institutes of Health, Bethesda, MD) between the stacks of images from two channels.
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3

Immunohistochemical Analysis of Embryonic Development

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Staged embryos were fixed in 4% paraformaldehyde overnight at 4°C, cryoprotected with 30% sucrose in phosphate-buffered saline (PBS) and embedded in Optimal Cutting Temperature tissue freezing medium (Triangle Biomedical Sciences, Durham, USA) for cryosectioning. 10 µm (immunohistochemistry) and 16 µm (in situ hybridization) transverse sections were collected. For immunohistochemistry, antigen retrieval was performed by boiling the slides in sodium citrate buffer (10 mM sodium citrate and 0.05% Tween 20, pH 6.0) for 20 min in a vegetable steamer. Furthermore, the sections were washed in PBS and incubated for 30 min with an Image iT™ FX signal enhancer (Molecular Probes, USA). Antigen was first recognized by primary antibodies during overnight incubation at 4°C and then visualized using Alexa Fluor 488- or Alexa Fluor 568-conjugated secondary antibodies (Molecular Probes, USA). Cell nuclei were counterstained with DAPI (1 : 1000) for 10 min (Sigma, USA). Slides were washed with PBS and mounted with Vectashield (Vector, USA). Images were taken with a Zeiss Axio Observer fluorescent microscope (Zeiss, Germany). The primary antibodies used: p27Kip1 (Santa Cruz Biotechnology, sc-528, 1 : 100), p57Kip2 (Abcam, ab75974, 1 : 100), H3K27me3 (Millipore, 07-449, 1 : 100) and SC-35 nuclear speckles (Abcam, ab11826, 1 : 200).
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4

Immunofluorescence Assay for TMEM225 in Mouse Testis

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Testes and epididymides from ICR mice were collected, fixed in Bouin's solution, embedded in paraffin, and cut into 4 m-thick sections. The sections were mounted on poly-L-lysine-coated glass slides, deparaffinized, and rehydrated. The antigen was retrieved by heating in 1 mM EDTA (pH 8.0) using a pressure cooker for 5 min. These sections or smeared sperm samples were then blocked for 1 h with 5% skim milk in phosphate buffered saline (PBS), followed by incubation with primary antibody for 1.5 h. After washing with PBS, the samples were incubated with Alexa Fluor 488-or Alexa Fluor 568-conjugated secondary antibodies (Molecular Probes). Antibody dilutions were as follows: rabbit anti-TMEM225 #63, 10 g/ml; rabbit anti-TMEM225 #64, 10 g/ml; mouse anti-sp56 antibody, 1:500; Alexa Fluor-conjugated secondary antibody, 1:500. When necessary, DAPI and Alexa 488-conjugated lectin PNA (Molecular Probes) were used to stain the nuclei and acrosomes, respectively. The images were captured with a BX50 microscope (OLYMPUS) equipped with a DP50 CCD camera (OLYMPUS). For confocal microscopic analysis, the sections were stained similarly, but Alexa Fluor 633-conjugated goat anti-rabbit IgG (Molecular Probes, 1:500) was used to detect TMEM225.
The images were scanned with a Leica TCL SL confocal microscope.
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5

Quantifying Nucleolar Size and Pre-mRNA Foci

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For immunofluorescent staining, cells were fixed with 3.7% formaldehyde for 10 min and permeabilized with 0.2% Triton X-100 for 10 min. After blocking with 2% bovine serum albumin (BSA) in PBS (PBA) for 30 min, the samples were incubated with the appropriate primary antibody in 2% PBA at room temperature for 1 h or at 4 °C for overnight. Bound antibody was visualized with an Alexa Fluor 488- or Alexa Fluor 568-conjugated secondary antibody (Invitrogen). DAPI (4’, 6-diamidino-2-phenylindole, Sigma-Aldrich) was used as a nuclear counterstain. All images were collected using a LSM 900 confocal microscope (Carl Zeiss) and the nucleolar size and the intensity profiles of each cell on the microscopic images were analyzed by the ZEN blue software. For details on measurement of the volume of nucleoli, we calculated nucleolar volume assuming an ellipsoid shape, V = 4πabc/3, where a, b, and c are the lengths of all three semi-axes of the ellipsoid. 3D image stacks reconstructed from a 2D stack of confocal images by Zen blue were used to measure each length of ellipsoid. To quantify the fluorescence of intensity of pre-mRNA foci (RNA-FISH) and nucleolar enrichment (Rrp proteins), different fluorescence signal bandwidth images were combined and then the fluorescence intensity profile in the cross-sectional lines were plotted as a function of X–Y distance across the cell.
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6

Immunofluorescence Imaging of Murine Pancreatic Cells

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Murine pancreatic frozen sections and pancreatic β cells from C57BL/6N were fixed with 3% paraformaldehyde in phosphate-buffered saline (PBS) for 30 min and permeabilized with 0.1% Triton X-100 in PBS for 30 min. The cells were then treated with 50 mM NH4Cl-PBS for 10 min at room temperature and blocked with PBS containing 1% bovine serum albumin for 15 min. The coverslips were incubated with primary antibody overnight, washed three times with PBS, and incubated with Alexa Fluor 488– or Alexa Fluor 568–conjugated secondary antibody (Invitrogen; 1:500 dilution) for 60 min. Samples were washed five times and mounted using SlowFade Gold (Invitrogen). The microscopic images were obtained with an A1 (Nikon) confocal laser scanning microscope equipped with a 100× oil immersion objective lens (1.49 NA) and NIS elements. The images were adjusted using NIS elements and ImageJ software.
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