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36 protocols using ab125096

1

Immunofluorescence Staining of FFPE Tissue

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PFA-fixed paraffin-embedded (FFPE) sections were deparaffinised in xylene and gradually rehydrated through baths of ethanol of decreasing concentrations. Sections were bleached in 1% KOH/3% H2O2 solution for 15 min prior to being subjected to heat-mediated antigen retrieval in citrate buffer (0.01 M, pH 6). Sections were blocked in 10% goat serum for 1 h and incubated with the following primary antibodies: anti-mCherry (Abcam, ab125096, 1:3000 or 1:4000) (Kobayashi et al., 2014 (link)), anti-Mitfa (Sigma, SAB2702433, 1:1000) and anti-Sox10 (Abcam, ab125096, 1:4000) (Travnickova et al., 2019 (link)) overnight at 4°C. After PBS/0.1% Tween 20 washes, sections were incubated with Alexa Fluor 488 (#A11001) or 546 (#A11003) goat anti-mouse and/or Alexa Fluor 647 (#A31573) goat anti-rabbit secondary antibodies at 1:500 dilution (Invitrogen) and DAPI (Sigma, 1:500) for 30 min in the dark at room temperature and mounted in hydrophilic mounting medium prior to imaging. Sections were imaged using an Andor Dragonfly confocal microscope equipped with Andor Zyla sCMOS camera using 20× and 40× air objectives.
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2

Western Blot Analysis of Cellular Proteins

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Protein samples were extracted from cells and mitochondria, respectively, using RIPA lysis buffer (Chromotek) supplemented with protease inhibitors. Protein samples were diluted in LDS sample buffer (4×, Invitrogen) supplemented with sample reducing agent (10×, Invitrogen). Samples were heated at 95̊C for 5 min before loading on a 4–12% gradient Bis-Tris gel (Invitrogen). MOPS SDS running buffer (Invitrogen) was used and supplied with antioxidants (Invitrogen). The gel was soaked in running buffer and run at 160 V for 75 min. The gel was transferred to a 0.45 µm nitrocellulose membrane (Cytiva) and protein at 30 V for 150 min, 4̊C. The membrane was blocked for 1 h in 5% skimmed milk (Sigma) in PBS-Tween 20 (0.1%, Sigma). The membrane was probed for anti-GFP (ab183734, abcam), anti-mCherry (1C51, ab125096, abcam), anti-VDAC1 (ab15895, abcam) and anti-α tubulin (DM1α, T6199, Sigma), diluted 1 : 10 000, 1 : 3000, 1 : 1500, 1 : 1500, respectively, in 5% milk (PBS-Tween). Primary antibody signal was detected using goat anti-mouse IgG conjugated to IRDye 680RD (ab216776, abcam) and goat anti-rabbit IgG conjugated to IRDye 800CW (ab216773, abcam) secondary antibodies, diluted 1 : 15 000, imaged with an Odyssey CLx imaging system (LI-CO Biosciences).
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3

Oocyte Protein Extraction and Analysis

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Thirty oocytes were homogenized by 20 strokes in an Eppendorf Teflon-glass homogenizer in 10 μL/oocyte of buffer containing 1% TX-100, 150 mM NaCl, and phosphate-buffered saline plus protease inhibitors. The homogenate was centrifuged twice at 1000 × g for 10 min at 4°C to eliminate the yolk. The proteins in the supernatant were quantified by the BCA method. Sodium dodecyl sulfate polyacrylamide gel electrophoresis and Western blot experiments were performed as described (22 (link)), loading 100 μg of extract. We used the antibodies anti-GFP (ab290, AbCAM, Cambridge, United Kingdom), anti-Cherry (ab125096, AbCAM), and anti-tubulin (MMS-435P, Covance Antibody Products, Princeton, NJ) at 1:100 dilution.
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4

Immunoblotting of Exosomal Proteins

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Western blotting was performed as described in a previous study (20 (link)). Antibodies targeting the following proteins were used: IκBα (CST4812, Cell Signaling Technology, Danvers, MA, USA), p65 (CST6956S, Cell Signaling Technology), CD9 (NBP2-22187, Novus Biologicals, Centennial, CO, USA), CD63 (EXOAB-CD63A-1, SBI, Tokyo, Japan), TSG101 (ab228013, Abcam, Cambridge, UK), GM130 (ab52649, Abcam), glyceraldehyde-3-phosphate dehydrogenase (GAPDH; sc-47724, Santa Cruz Biotechnology, Santa Cruz, CA, USA), histone H3 (ab1791, Abcam), mCherry (ab125096, Abcam), and GFP (CST2555, Cell Signaling Technology).
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5

Retinal Immunohistochemistry in Mice

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Mice were anesthetized with isoflurane/oxygen and perfused transcardially with PBS followed by 4% paraformaldehyde in PBS. Longitudinal retinal sections were used for staining. The following antibodies were used: anti-Porin (ab15895 Abcam, 1:400, Waltham, MA), anti-mCherry [1C51] (ab125096, Abcam, 1:500), donkey anti-rabbit IgG 488 (A21206, Invitrogen, 1:600, Waltham, MA), and donkey anti-mouse IgG 546 (A10036, Invitrogen, 1:600). Images were taken with a Leica TCS SP5 confocal microscope (Leica Microsystems Inc, Buffalo Grove, IL).
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6

Characterization of hiPSC-derived Cardiomyocytes

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hiPSC-derived CMs were detached from the plate by incubating with 1 ml of TrypLE (Thermo Fisher Scientific, 12604013) for 5 min at 37°C. A double volume of PBS was added to stop the reaction, and the cells were passed through a 100 μm cell strainer. hiPSC-derived CMs were centrifuged at 200 g for 5 min, fixed with 1% PFA for 20 min and washed 3x with PBS. hiPSC-derived CMs were incubated with primary antibodies against mVenus (Biorbyt, orb334993, 1:800) and mCherry (Abcam, ab125096, 1:250) and anti-cardiac troponin T-APC (Miltenyi Biotec, 130-120-403, 1:50) in blocking buffer (PBS, 4% donkey serum, 0.1% Triton X-100 in PBS, 2 mM EDTA) for 2 h at RT. After washing, the cells were incubated with the secondary antibodies anti-goat Alexa Fluor® 488 (Jackson ImmunoResearch, 705-546-147, 1:500), anti-rabbit Alexa Fluor® 555 (Abcam, ab150062, 1:500) and Hoechst 33342 (Thermo Fisher Scientific, H21492) for 1 h at 4°C. Cells were then washed 3x with PBS and centrifuged at 200 g for 5 min. Finally, 5 million cells were resuspended in 500 μl of FACS buffer (PBS, 2% FBS, EDTA) and kept on ice until further analysis. Cells were analyzed on Amnis ImageStream-X MkII (Luminex, United States).
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7

Antibody Sources for Protein Detection

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Commercially available antibodies against DNAJA2 (rabbit monoclonal), DNAJB1 (mouse monoclonal), V5 tag (mouse monoclonal), GAPDH (mouse monoclonal), Pgk1 (mouse monoclonal) and mCherry (mouse monoclonal) were obtained from Abcam (UK)(ab157216; RRID:AB_2650527, Enzo life sciences (NY, USA) (ADI-SPA-450-E; RRID:AB_10621843), Invitrogen (CA, USA)(R960-25; RRID:AB_2556564), Sigma (G8795; RRID:AB_1078991), Invitrogen (459250; RRID:AB_2532235) and Abcam (ab125096; RRID:AB_11133266), respectively. Anti-mouse Ydj1 (SMC-150; RRID:AB_2570364) and anti-rabbit Sis1 (COP-080051; RRID:AB_10709957) were obtained from StressMarq Biosciences Inc. (Canada), and Cosmo Bio Co. (Japan), respectively. Antibody against YFP (rabbit polyclonal; RRID: AB_2650530) was generated in the laboratory. Anti-DnaK (rabbit polyclonal; RRID:AB_2650528) and anti-human Hsp/Hsc70 (rabbit polyclonal; RRID:AB_2650529) antibodies were a kind gift from Matthias Mayer (University of Heidelberg).
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8

Viral Diffusion Imaging in Rat Brains

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Upon completion of experiments, rats were deeply anaesthetized and perfused intracardially with 4% PFA in order to examine the diffusion of the virus. The brains were dissected, stored overnight at 4 °C, and finally transferred to 30% sucrose. Coronal sections (50 μm) were cut on a cryostat and collected in PBS. Free-floating sections were incubated in a blocking solution (4% bovine serum albumin (BSA), 10% normal goat serum and 0.5% Triton X-100) for 1 h at RT. Then, they were incubated in primary monoclonal mouse antibody to mCherry (1: 500 dilution, Abcam, ab125096) in the blocking solution overnight at 4°. Subsequently, sections were washed with PBS and incubated for 1 h at RT with secondary fluorescent labels AlexaFluor-568-labeled anti-mouse antibody (1:400 dilution, Lifetechnologies, A11036) diluted in PBS for 1 h on a shaker at room temperature. Sections were washed in PBS, mounted with mounting media containing DAPI (Vector, H1200) and coverslipped.
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9

Embryonic Neuron Culture and Protein Analysis

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Embryonic hippocampal and cortical neurons were cultured as described previously.24 (link) Briefly, neurons were seeded at a density of 200,000 cells/well in 6-well tissue culture dishes (Falcon, Glendale, AZ, USA) precoated with poly-D-lysine (0.1 mg/mL; Sigma-Aldrich) and cultured in defined medium of Neurobasal, l-glutamine (2 mm), penicillin-streptomycin, and B27 supplement (1:50; all from Thermo Fisher Scientific). On day 3, adeno-associated viruses (AAVs) were transduced at a multiplicity of infection of 100,000. On day 7, cultures were rinsed with Dulbecco's phosphate-buffered saline (DPBS) and subsequently lysed in 500 µL RIPA with protease inhibitor cocktail followed by sonication. Lysate was clarified with centrifugation at 10,000 × g for 10 minutes. Samples were boiled for 5 minutes in SDS sample buffer and run on 4% to 20% TGX gels (Bio-Rad). Then, 0.2-µm nitrocellulose membranes were probed with rabbit anti-Kif5a (ab5628, 1:2000; Abcam, Cambridge, MA, USA), mouse anti-FLAG (F1804, 1:1000; Sigma-Aldrich), mouse anti-mCherry (ab125096, 1:5000; Abcam), or mouse anti-GFP (ab1218, 1:5000; Abcam) diluted in 5% milk with 0.2% Tween-20 in tris-buffered saline (TBST).
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10

Western Blot Analysis of GFP and mCherry

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Use 6% SDS-PAGE gel, and the separated proteins were transferred by electro blotting to NC membranes. The membranes were blocked with 5% non-fat dry milk in TBST and incubated with the primary antibody including anti-GFP antibody (Abcam, ab6658) and anti-mCherry antibody (Abcam, ab125096) overnight at 4 °C. Then washing three times, the second antibody including anti-Goat HRP (Proteintech, SA00001-3) and anti-mouse HRP (Proteintech, SA00001-8) for about 2 h Immunolabelling was detected using SuperSignal West Femto (Thermo Fisher Scientific, 34096).
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