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29 protocols using ab6662

1

Immunostaining and Histological Analysis of Mouse Brain

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The histology and immunostaining were conducted as previously described (Xie et al., 2018 ; Tang et al., 2016a (link)). After pentobarbital overdose, mice were intracardially perfused with 0.9% saline solution followed by 4% paraformaldehyde in PBS. Mouse brains were removed immediately and placed in 4% paraformaldehyde solution overnight for post-fixation and then soaked in 30% sucrose solution for at least 48 h for cryoprotection. With a cryostat (Leica CM1950), the brains were sequentially cut into 40-μm-thick coronal sections from the olfactory bulb to the cerebellum (approximately +4.50 mm to −6.40 mm from the bregma). The sections were cleaned with PBS and mounted on chrome-gelatin subbed glass slides in sequence. To enhance the fluorescence intensity of the HSV-EGFP labeled slice, the sections were blocked with 3% BSA in PBS-0.3% Triton X-100 for 1 h at 37°C and subsequently incubated with anti-GFP antibody conjugation FITC (1:400, Abcam, ab6662) for 2 h at 37°C. After washing, brain sections were coverslipped with 70% DAPI-glycerol mounting medium.
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2

Immunostaining of Murine Brain Sections

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Mice were euthanized by cervical dislocation. Left hemispheres were removed and fixed for 72 h in 4% paraformaldehyde (PFA) in PBS. Forty-micrometer coronal sections were obtained using a Leica vibratome (Leica VT1000S). Next, free floating sections were washed three times in PBS, treated with NHCl for 30 min, and washed again three times with PBS. Floating sections were permeabilized and blocked with PBS containing 3% Triton X-100, 0.02% Azide, 2% BSA, and 3% NGS (Ab buffer) for 1 h at RT. After three washes in PBS, brain slices were incubated overnight at 4 °C with FITC-conjugated GFP primary antibody (AB6662; 1:500, Abcam) for signal enhancement. Sections were washed three times and incubated for 2 h at RT with fluorescent secondary antibody Alexa Fluor 488 goat anti-mouse (1:400; from Jackson Immuno Research, West Grove, PA, USA). Sections were analyzed using a two-photon confocal microscope (Leica SP5).
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3

Quantifying Fluorescent Protein Expression in Zebrafish

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To assess AR upregulation in Tg(gstp1:GFP) fish, larvae 4 hr post light illumination or bolus LDE treatment were dechorionated, washed twice in ice-cold PBS and fixed in 4% paraformaldehyde in 1 X PBS (Gibco 14190169) for at least overnight with gentle rocking at 4 °C. Fixed larvae were permeabilized with chilled methanol at –20 °C for 4 hr–overnight. Fish were then washed 2 times with PBS-0.1%Tween-1% DMSO for 30 min each with gentle rocking, then blocked in PBS-0.1%Tween containing 2% BSA and 10% FBS, then stained with anti-GFP FITC conjugated (Abcam, ab6662) primary antibody overnight at 4 °C in blocking buffer. Subsequently, the larvae were washed twice (30 min each wash), re-blocked for 1 hr at room temperature, and incubated with the AlexaFluor 568-conjugated fluorescent secondary antibodies (Abcam, ab175707) in blocking buffer for 1.5 hr at room temperature with gentle rocking, and then washed three times. Fish were imaged on 2% agarose plates on a Leica M205-FA equipped with a stereomicroscope. Quantitation of IF data was performed using ImageJ/FIJI (NIH).
To assess protein expression in zebrafish, larvae were fixed at 34 hours post fertilization (hpf) after dechorionation. Permeabilization and immunostaining protocols are as above except antibodies to the desired protein/tag and appropriate secondary antibodies were used.
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4

Quantitative Analysis of AAV-Transduced Neurons

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Based on the previous study (Lu and Yang, 2017 (link)), the AAV-infused mouse brains were sectioned at 60 μm of thickness. The sections were stained with GFP antibody (1:1000, ab6662; Abcam, Cambridge, UK) and Ctip2 antibody (1:500, ab18465, Abcam, Cambridge, UK). Afterward, the stained sections were imaged using a laser scanning confocal microscope (A1 confocal, Nikon Instruments [Shanghai]Co., Ltd.) under 40× objective lens. The MSNs were identified based on the positive staining of Ctip2. Neuronal structure reconstruction with neuTube (Feng et al., 2015 (link)) and Sholl analysis were performed with ImageJ (Longair et al., 2011 (link)).
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5

Immunostaining of Drosophila Eye Discs

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Wandering third-instar larval eye discs were dissected in 1× PBS and fixed in 4% formaldehyde+1× PBS for 15 min, permeabilized in 0.3% PBS-T (1× PBS, 0.3% Triton X-100) two times for 10 min and then incubated with antibodies overnight at 4 °C in 1× PBS+10% normal donkey serum (NDS, Jackson Immunoresearch)+0.1% Triton X-100 blocking serum. The following day, samples were washed in 0.1% PBS-T (1× PBS+0.1% Triton X-100) three times for 5 min. Samples were then incubated with appropriate fluorescently labeled secondary antibodies (Jackson Immunoresearch) for 1 h in 1× PBS+10% NDS+0.1% Triton X-100 followed by 4′,6-diamidino-2-phenylindole (DAPI) for 5 min. Finally, samples were washed five times for 5 min then mounted in FluorSave (EMD Millipore) on glass slides. All steps were carried out at RT and with gentle rocking, unless specified otherwise. Whenever fluorescent images have been compared, they have been obtained with the same acquisition and display settings.
Primary antibodies used were: anti-β-gal: DSHB 40-1a (1:200), anti-cleaved Drosophila Dcp-1: Cell Signaling Asp216 (1:500), anti-Dac DSHB mAbdac1-1 (1:100), anti-Elav: DSHB 7E8A10 (1:200), anti-GFP (FITC): Abcam ab6662 (1/1000), anti-Hairy: from T. Orenic (1:4), anti-Hth: from Richard Mann (1:2000), anti-Notch DSHB C458.2H (1:100), anti-Repo: DSHB 8D13 (1:500), anti-Senseless: from H. Bellen (1:100).
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6

Characterizing Smad7 in Infarct Macrophages

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In order to systematically characterize the time course of Smad7 expression in infarct macrophages, Smad7 (using an anti-Smad7 antibody by Thermo Fisher Scientific, #42-0400) and GFP staining (using an anti-GFP antibody, Abcam, #ab6662) was performed on the infarcted CSF1REGFP heart at baseline, 24h, 3-day, 7-day and 28-day timepoints (n=5-6/each time point). In order to identify myofibroblasts in the infarct, sections were stained with an anti-α-smooth muscle actin (SMA) antibody (Sigma, #F3777) as previously described41 . Myofibroblasts were identified as spindle-shaped α-SMA-positive cells located outside the vascular media. To determine the number of macrophages in the infarcted and remodeling myocardium, sections from infarcted Smad7 fl/fl and MyS7KO mice were stained with an anti-Mac2 (galectin-3) antibody (Cedarlane, #CL8942AP), as previously described42 (link),43 (link). Quantitative analysis was performed by counting the number of macrophages in 10 fields from 2 different levels for each animal.
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7

Immunofluorescence Staining of Retinal Sections

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Following PBS washing for 3 × 5 min, the retinal sections were incubated with 0.1% Triton for 10 min, subjected to normal rabbit serum (Invitrogen, CA, USA) to block non-specific binding sites, and then incubated at 37 °C for 30 min to discard serum. Then, primary antibody against Vimentin (NB300-223, 1:5000) or CHX10 (NBP1-84476, 1:1000) (Novus, St. Louis, MO, USA) was incubated with sections overnight in a humidified box at 4 °C (the NC group was treated with 0.01 mmol/L of PBS). Then, sections were washed thrice with PBS for 5 min, followed by incubation with the secondary antibody labeled with FITC fluorescence (ab6662, 1:1000, Abcam, USA) or Texas Red (ab6787, 1:1000, Abcam, USA) in a humidified box at 37 °C for 40 min. Following 5 min of PBS rinsing thrice, sections were sealed with water-soluble resin. Pictures were captured with a fluorescence microscope (Olympus IX71, Tokyo, Japan). Analyses of images were performed by using Fiji [16 (link)] and associated plugins as previously described [17 (link)].
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8

Brain Tissue Fixation and Fluorescence Imaging

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After the conclusion of experiments, mice were deeply anesthetized with sodium pentobarbital (120 mg/kg) and then perfused transcardially with 20 mL 0.9% NaCl solution followed by 20 mL paraformaldehyde PBS solution (PFA, 4%, w/v). The brains were fixed in PFA solution overnight and sectioned. Slices were washed with PBS, fluorescence-enhanced with the anti-GFP antibody (FITC, ab6662, Abcam, Cambridge, MA) or c-Fos antibody (226003, Synaptic Systems, Germany) then Cy5 goat-anti-rabbit IgG (111-175-144, Jackson), incubated with DAPI (C1002, 1:1000, Beyotime, Shanghai, China), and later mounted with DAPI. Fluorescence images were then obtained with an epifluorescence microscope (Eclipse 80i, Nikon, Tokyo, Japan) with a 10X (CFI Plan Apo Lambda, 0.45 N.A.) or a 20X (CFI Plan Apo Lambda, 0.75 N.A.) objective lens, and were analyzed with ImageJ software (NIH, U.S.).
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9

Viral Tracing and Immunohistochemistry in Mice

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Mice were deeply anesthetized with a ketamine/xylazine mix (400 mg ketamine + 20 mg xylazine kg body weight−1 I.P.). All animals were perfused with filtered saline, followed by 4% paraformaldehyde. Following perfusion, brains were placed in 4% paraformaldehyde for 24 hours and then moved to a 20% sucrose solution in 0.02 M potassium phosphatebuffer (KPBS, pH 7.4) for 2 days. Brains were then frozen and cut into four series 40μm sections with a sliding microtome equipped with a freezing stage. To identify fiber and electrode locations, relevant sections were identified and mounted on slides. Sections were then photographed under bright field and fluorescence. For Herpes Simplex Viruses visualization, 3 or 4 or 5 days after viral injection, mice were perfused, and brains cut at 40μm. The mCherry signal was amplified with Rabbit-anti-mCherry (Abcam, ab167453,1:500) followed by TRITC-conjugated affinipure Goat anti-Rabbit (IgG (H+L) 111–025-144, Jackson Immuno, 1:200). The EYFP signal was amplified with Goat anti-GFP antibody (FITC), (ab6662, Abcam, 1:500) followed by Alexa Fluor® 594 AffiniPure Goat anti-Rabbit (IgG (H+L), 111–585-103, Jackson Immuno, 1:200).
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10

Quantifying Autophagy Markers in Cancer Cells

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AGS and HGC27 cells (105 cells/well) were seeded into a 24-well plate (Thermo Fisher, CA, USA), fixed with 4% paraformaldehyde (Solarbio, Beijing, China) for 20 min, permeabilized with 0.1% Triton X-100 (Solarbio, Beijing, China) for 20 min, and then blocked with 4% bovine serum albumin (Gibco, CA, USA) for 1 h. AGS and HGC27 cells were incubated with anti-LC3 antibody (ab192890; Abcam, Cambridge, UK) at for 2 h, followed by a 30 min incubation with fluorescein isothiocyanate (FITC)-conjugated secondary antibody (ab6662; Abcam, Cambridge, UK) [31 (link)]. Subsequently, the cells were washed three times with PBS and fixed with a mounting medium (Solarbio, Beijing, China). Fluorescent images were acquired using a laser scanning confocal microscope (FV3000; Olympus, Beijing, China). ImageJ (National Institutes of Health, CA, USA) was used to establish methods to quantify the average number of LC3 puncta per cell in each group.
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