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9 protocols using aqua poly mount solution

1

Imaging S1R Localization in HEK293T Cells

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For imaging S1R localization in HEK293T cells, cells were cultured on glass coverslips in 24-well plates. Each well was transfected with 150 ng of S1R-GFP plasmid (WT or mutant) and 150 ng of mCherry-Sec61β using Lipofectamine LTX Plus (Thermo Fisher Scientific) according to the manufacturer’s instructions. Cells were fixed 48 hr post-transfection in 4% paraformaldehyde (PFA) in phosphate buffered saline (PBS) solution for 20 min, permeabilized and blocked with 5% bovine serum albumin (BSA), 0.1% Triton X-100 in PBS for 1 hr, and stained with anti-mCherry (16D7, 1:500, Invitrogen) and anti-TOM20 antibodies (FL-145, 1:500, Santa Cruz Biotechnology) overnight at 4°C. Next day, cells were washed and incubated with secondary antibodies (594 donkey anti-rat, A21209, 1:1000, Invitrogen; 647 goat anti-rabbit, A27040, 1:1000, Invitrogen) for 1 hr at room temperature. Cells were washed thrice with PBS and mounted using Aqua Polymount solution (Polysciences). Cells were visualized using fluorescent confocal microscope (Leica) with 63× oil immersion objective.
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2

Immunofluorescence Staining Protocol for Tissue Samples

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Dissections were performed in 1× PBS on ice and tissue collected within a maximum of 1 h. Fixation was performed with 4% paraformaldehyde (PFA) in 0.2% phosphate buffered saline with Tween (PBST) for 30 min at RT (wing discs, ovaries). Then the samples were blocked overnight with blocking buffer at 4°C. Primary antibodies (diluted in blocking buffer) were incubated with the samples for 8 h at RT. The samples were rinsed three times and washed three times (20 min/wash) with PBST. Secondary antibodies (diluted in PBST) were incubated overnight at 4°C. The samples were then rinsed three times and washed two times (20 min/wash) with PBST. Hoechst 33258 (2.5 μg/ml) was added in PBST before the last washing step and the samples were mounted with Aqua/Poly Mount solution (Polysciences, USA). Origins and dilutions of all antibodies are provided in Table S2.
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3

Immunofluorescent Analysis of DNA Damage Response

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Glass slides (ten-well, MP Biomedicals) were coated with poly-L-lysine after incubation for 20 min with a 1 mg/ml concentrated solution (Sigma-Aldrich). Afterward, slides were covered with 0.5/1 × 105 cells for 20′ then fixed with a 4% paraformaldehyde solution (Santa Cruz Biotechnology) for other 20′. After permeabilization with 0.2% Triton X100, a 0.5% BSA and 0.2% fish gelatin solution in DPBS was applied to block aspecific interactions, then cells were incubated 1 h at RT with the following primary antibodies: p16 antibody (1:100), 53BP1 antibody, (1:600), Anti-phospho ATM (Ser1981) antibody, (1:100). Slides were then washed with DPBS and incubated for 1 h at RT with either of the secondary antibodies: Donkey anti-Mouse IgG, Alexa Fluor 647 or Donkey anti-Rabbit IgG, Alexa Fluor 568 diluted 1:1000. Nuclei were stained using DAPI (Sigma-Aldrich) and, finally, Aqua-Poly/Mount solution (Polysciences. Inc.) was used to mount coverslips (Bio-Optica). Fluorescent images were obtained using Leica SP2 and Leica SP5 Confocal microscopes, DDR foci quantification was carried out using ImageJ64 (version 1.47).
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4

Puromycin Labeling of Nascent Proteins

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For puromycin labeling experiments, tissues were dissected in Schneider's insect medium (Sigma-Aldrich, USA) supplemented with 10% fetal calf serum (FCS; Sigma-Aldrich) at 25°C. They were then incubated with Schneider's insect medium containing puromycin (5 μg/ml, Sigma-Aldrich) and cycloheximine (100 µg/ml, Sigma-Aldrich) for 2 h at RT. Then the samples were fixed with 4% PFA in PBST 0.2% at RT and blocked overnight with blocking buffer at 4°C. Primary anti-puromycin antibody (diluted in PBST) was incubated with the samples for 8 h at RT. The samples were rinsed three times and washed three times (20 min/wash) with PBST. Secondary antibodies (diluted in PBST) were incubated overnight at 4°C. The samples were then rinsed three times and washed two times (20 min/wash) with PBST. Hoechst 33258 (2.5 μg/ml) was added in PBST before the last washing step and the samples were mounted with Aqua/Poly Mount solution (Polysciences). See Table S2 for antibody details.
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5

Immunofluorescence Staining Protocol

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Samples were permeabilized and blocked in incubation buffer (0.25 % Triton X-100 and 1% bovine serum albumin in PBS) for 60 minutes. Samples were then treated with primary antibodies (see Table S1) in incubation buffer either at 4°C overnight or four hours at room temperature. Samples were rinsed with wash buffer (0.05% Triton X-100 in PBS; 2 x 60 minutes) and treated with incubation buffer at least 60 additional minutes at room temperature. Samples were treated with 1:200 secondary antibodies (Alexa-conjugated, Thermo Fisher Scientific, USA) and 5μg/mL DAPI (4′6-Diamidino-2-Phenylindole Dihydrochloride, MP Biomedicals, 157574) in incubation buffer overnight at 4°C or at least two hours at room temperature. Samples were mounted by adding a drop of Aqua Polymount solution (Polysciences, Inc.) to the well and placing a round glass coverslip over the top. The mounted samples were stored overnight at 4°C and then sealed around the edges with fingernail sealant until imaging.
Confocal immunofluorescence microscopy images were collected using a Nikon A1R laser scanning confocal microscope with Plan Apo 10x, Plan Fluor 20x Ph1 DLL, or Plan Apo 20x DIC M objectives. Images were processed using NIS Elements and ImageJ. Some z-stacks were aligned using the “Align Current ND Document” (NIS Elements) before creating maximum projection images.
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6

Immunofluorescent Localization of CCK Receptors

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Panc-02 cells were grown on glass coverslips and fixed in ice-cold methanol and acetone for 20 min each. After 3 washes in PBS, cells were permeabilized with 0.2 % Triton X-100 in PBS for 1 h at room temperature. Nonspecific binding was blocked in PBS containing 5 % goat serum and 0.1 % Triton X-100 for 1 h. Cells were subsequently incubated in PBS with 5 % FBS, 0.05 % Triton X-100 with either a rabbit polyclonal CCK-A receptor antibody (PA-3116, Pierce, Rockford, IL, USA) or a CCK-B receptor antibody (#9491, CURE, Los Angeles, CA, USA) at a titers of 1:400 overnight at 4 °C. After three PBS washes, the cells were incubated in PBS containing 1 % FBS, 0.05 % Triton X-100, and a secondary goat anti-rabbit AlexaFluor 488-labeled antibody (Amersham Biosciences, Waltham, MA, USA) at a titer of 1:2,000 for 1 h at 4 °C in the dark. The slides were washed thrice with PBS, counterstained with Hoechst 33342 (0.5 μg/mL; AnaSpec, Fremont, CA, USA), and mounted with Aqua Poly/Mount solution (Polysciences, Warington, PA, USA). Images were captured on a Leica DM IRE2 confocal microscope.
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7

Tyrosine Hydroxylase Immunohistochemistry in Mouse Brain

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P10 pups were deeply anesthetized with isoflurane and then perfused transcardially, first with PBS (pH 7.4) and with 4% paraformaldehyde (PFA) dissolved in PBS. The brains were removed and postfixed in 4% PFA overnight at 4°C, and then were coronally sectioned (40 μm thick) using a vibratome (Leica Biosystems). Tyrosine hydroxylase (TH) staining was accomplished as follows: (1) rinse 40 μm-thick slices in PBS (pH 7.4) three time; (2) block slices in 10% normal goat serum (Thermo Fisher, Cat. #: 50062Z) with 0.1% Triton X-100 (Sigma-Aldrich, Cat. #: T8787) in PBS for 1 h at room temperature; (3) incubate slices in rabbit polyclonal anti-TH primary antibody (1:700 in PBS; Sigma-Aldrich, Cat. #: T8700) for 24 h at 4°C (4) rinse slices in PBS three times; (5) incubate slices in Cy3-conjugated goat anti-rabbit IgG (1:100 in PBS, Jackson ImmunoResearch Laboratories, Cat. #: 111-165-003) and DAPI (1:1000) for 2 h at room temperature on a rotary shaker; (6) rinse slices in PBS three times and mount with an Aqua-Poly/Mount solution (Polysciences). TH-positive fibers in the cortex were imaged using a confocal microscope (Zeiss LSM800) and quantified by measuring the optical density of TH-immunofluorescence using MATLAB (Mathworks).
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8

Immunofluorescence Assay for DNA Damage Response

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Multitest slides (10 well, MP Biomedicals) were treated for 20’ with Poly-L-lysine solution (Sigma-Aldrich) at 1mg/ml concentration. After two washes with DPBS solution, approximately 0.5/1x105 cells were seeded on covers for 20’ and fixed with 4% paraformaldehyde (Santa Cruz Biotechnology) for other 20’. Cells were then permeabilized with 0.1% Triton X-100. After blocking with 0.5% BSA and 0.2% fish gelatin in DPBS, cells were probed with the indicated primary antibodies. After primary antibodies incubation (53BP1 Antibody, Bethyl Laboratories; Anti-phospho Histone H2A.X (Ser139) Antibody, clone JBW301, Merck), cells were washed three times with DPBS and incubate with Alexa 488-, 568- and/or 647-labeled secondary antibodies (Invitrogen). Nuclear DNA was stained with DAPI at 0.2 μg/ml concentration (Sigma-Aldrich) and covers were mounted with Aqua-Poly/Mount solution (Polysciences. Inc.) on glass slides (Bio-Optica). Fluorescent images were acquired using Leica SP2 and Leica SP5 Confocal microscopes. Quantification of DDR foci in immunofluorescence images was conducted using Cell Profiler (version 2.1.1, revision 6c2d896) in Figures 1D and 4G.
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9

Tau Isoforms Immunohistochemistry in Frozen Brain

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Frozen human brain sections were used for histological analysis. Antibodies used were mouse anti-phospho-tau (clone AT8; Thermo Fisher #MN1020), mouse anti-3R-tau (clone 8E6/C11, Millipore #05–803), mouse anti-4R-tau (hybridoma supernatant of clone ET-3, kindly provided by Peter Davies, Northwell, USA), and biotin-conjugated donkey anti-mouse IgG (Polyclonal, Jackson #715–065-151). Sections were washed with TBS for 5 min, blocked with TBS including 3% donkey serum for 30 min and stained with primary antibodies at 4 °C in a humidified chamber overnight. Thereafter, slides were washed three times in TBS for 5 min, blocked with TBS including 3% donkey serum, and incubated with secondary antibody at RT for 1 h. Upon washing (3 × 5 min in TBS), slides were incubated with peroxidase conjugated streptavidin (Jackson #016–030-084) at RT for 30 min and subsequently washed (3 × 5 min TBS) and stained with AEC Single/Plus (abcam #103742) for 15 min. Staining was stopped by incubation in deionized water for 2 min. Slides were mounted in Aqua-Poly/Mount solution (Polysciences #18606), scanned (VMscope, Germany) and analyzed using CaseViewer 2.1 software.
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