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10 protocols using alexa 568 anti rabbit igg

1

Immunofluorescence Imaging of Mitochondrial Dynamics

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MEFs were fixed in pre-warmed 4% paraformaldehyde in PBS at room temperature for 20 minutes on an 8-well chambered cover glass.13 (link),62 (link),71 (link) They were then permeabilized using PBS containing 0.1% Triton X-100 at room temperature for 8 minutes. Following permeabilization, the cells were blocked in 0.5% BSA/PBS at room temperature for 30 minutes. Overnight incubation with primary antibodies in 0.5% BSA/PBS was conducted at 4°C, which was followed by a 1-hour incubation with fluorescently labeled secondary antibodies in PBS at room temperature. The primary antibodies used included pDrp1 S579 (1:200 dilution), pHistone H3 (1:200 dilution), Drp1 (Cell Signaling Technology, 8570; 1:200 dilution) for Figure 4E, Drp1 (BD Biosciences, 611113; 1:200 dilution) for Figure 5C, and TOM20 (Proteintech, 11802-1-AP; 1:300 dilution). The secondary antibodies (Invitrogen), used at a 1:400 dilution, were Alexa 488 anti-rabbit IgG, Alexa 568 anti-mouse IgG, Alexa 488 anti-mouse IgG (A21202), and Alexa 568 anti-Rabbit IgG (A10042). Imaging was performed using a Zeiss LSM800 GaAsP laser scanning confocal microscope with a 63× objective. NIH ImageJ software was used for image analysis.
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2

Immunohistochemical Analysis of Dopaminergic Neurons

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To determine whether neurons in the SS56699 split GAL4 line expressed TH, immunohistochemical processes was performed as described in Aso et al., 2014b (link). Briefly, 10 GFP-expressing brains were fixed (2% paraformaldehyde in Schneider’s medium), permeabilized in PBT (0.5% Triton X-100 in PBS), and blocked (5% normal goat serum for 90 min). Subsequently, brains were incubated in primary antibodies (diluted in 5% serum in PBT at 4°C for 2–4 days). Chicken anti-GFP (Abcam ab13970; 1:1000); anti-TH mouse monoclonal (Sigma MAB318; 1:200); anti-TH rabbit polyclonal (Sigma AB152; 1:200). After several washes (PBT for 30 min), brains were then incubated in secondary antibodies (diluted in 5% serum in PBT at 4°C for 2–4 days). Alexa 488 anti-chicken IgY (Invitrogen A11039; 1:400); Atto 647N anti-mouse IgG (Rockland 610-156-121; 1:400); Alexa 568 anti-rabbit IgG (Invitrogen A11036; 1:400). Finally, brains were washed thoroughly (PBT four times for 30 min or longer) and mounted on glass slides for confocal imaging.
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3

Immunofluorescence Staining of Stem Cells and Differentiated Cells

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For DPPSC analysis, the cells were fixed with Cytofix (BD Biosciences) for 1 h at room temperature and then incubated with 1% Tween-20 for 30 min at room temperature to increase cell permeability. The slides were sequentially incubated overnight at 4 °C with primary antibodies against SSEA-4 (1:50, BD Pharmingen) or OCT3/4 (1:50, BD Pharmingen) and then for 60 min at 37 °C with PE-coupled anti-rabbit IgG and FITC-coupled anti-mouse IgG (1:200, BD Pharmingen). For differentiated DPPSC at day 21, primary antibodies against osteocalcin (1:50, Millipore) and collagen IV (1:100, Abcam) were used. Alexa 568 anti-rabbit IgG (1:200, Life Technologies) and Alexa 488 anti-mouse IgG (1:200, Santa Cruz Biotechnology) were used as secondary antibodies, respectively. Between each step, the slides were washed with Perm/Wash 1X (1:200, BD Biosciences). The cells were examined by confocal fluorescence microscopy.
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4

Quantifying Skeletal Muscle Morphology

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The tibialis anterior (TA) muscle was dissected from perfused mice, transferred into a 30 % sucrose solution for 2 days, and cut using a cryostat at 14-μm thickness. To visualize muscle fiber size and location of nuclei, the sections were stained by first blocking for 1 h at room temperature (0.1 % Triton X-100, 3 % BSA, 5 % goat serum in PBS) and then incubated with an antibody against laminin (L9393, Sigma; 1:100) for 24 h in blocking solution. The sections were washed three times in PBS and incubated for 3 h with secondary antibodies (Alexa-568 anti-rabbit IgG, Life Technologies; 1:1000). After washing with PBS, sections were incubated with 4′,6-diamidino-2-phenylindole (DAPI; Sigma; 1:1000), washed with PBS, and mounted using Vectashield. The area outlined by laminin was measured using ImageJ software. At least 300 muscle fibers per mouse were randomly selected and used for this analysis. Myonuclei located in the center of muscle fibers were counted. At least 1000 nuclei per mouse were counted.
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5

Neurochemical Mapping of Diencephalic Nuclei

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Mice were anesthetized with isoflurane and perfused transcardially with PBS. Brains were incubated in 4% paraformaldehyde overnight at 4 °C. The rostral to caudal extension of the DMH was cut in 50 μm coronal sections with a vibratome. Sections were blocked with 5% bovine serum albumin at room temperature and then incubated with anti-ChAT (1:1000; Millipore, AB144P), anti-c-fos (1:500; Abcam, ab7963), anti-dsRed (1:1000, Clontech, 632496), anti-cholera toxin subunit b (CTb) (1:500; Abcam, ab62429), and anti-5-HT (1:500; Immunostar, 20080) antibodies diluted in 0.5% Triton X-100 in PBS overnight at 4 °C. For ChAT staining, colchicine (1 μl of 10 mg/ml; Santa Cruz Biotech) was injected into the lateral ventricle of animals 1 day before sacrifice. After incubation in primary antibodies, sections were washed 3 times in PBS and then incubated with Alexa 488 anti-goat IgG (1:500, A11055), Alexa 568 anti-rabbit IgG (1:500, A10042), Alexa 488 anti-rabbit IgG (1:500, A11008), and Alexa 568 anti-mouse IgG for CTb staining (1:500, A11004; Life Technologies) diluted in 0.5% Triton X-100 in PBS for 3 h at room temperature. Tissues were then washed in PBS, dried and mounted with VECTASHIELD mounting media. Images were acquired using a scanning confocal microscope.
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6

Immunostaining of Mouse Brain Tissue

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Mice were anesthetized with isoflurane and transcardially perfused with preperfusion solution (9 g NaCl, 5 g sodium nitrate, 1,000 u heparin in 1 L distilled water). Brains were incubated in 4% paraformaldehyde overnight at cold room and sectioned with a vibratome in 50 μm on the following day. For immunofluorescence staining, sections were incubated in 10 mM sodium citrate solution (pH 9.0) for 30 min at 80 °C in a water bath. Following the antigen retrieval, the sections were blocked in 0.1 M PBS buffer containing 0.1% triton X-100, 5% normal goat serum or normal donkey serum, and 5% bovine serum albumin for 2 h at room temperature and then incubated with anti-TRPV1 (1:1,000, Alomone Labs, cat # ACC-030), anti-c-fos (1:500; Abcam, cat # ab7963), anti-GFP (1:1,000, Abcam, cat # ab13970), anti-mCherry (1:1,000, Novus Biologicals, cat # NBP2-25157), and anti-POMC (1:1,000, Phoenix, cat # H-029-30 [35 (link)]) antibodies for 72 h at cold room. And then sections were washed 3 times in PBS and incubated with Alexa 568 anti-rabbit IgG (1:500; Life Technologies, cat # A10042), Alexa 568 anti-mouse IgG (1:500; Life Technologies, cat # A11004), or Alexa 488 anti-chicken IgG (1:500, Abcam, cat # ab150169) for 2 h at room temperature. Tissues were washed, dried, and mounted with VECTASHIELD media containing DAPI. Images were acquired using a Leica SP2 confocal microscope.
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7

Antibody Reagents for Cell Biology

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Y-27632 and 4’,6-diamidino-2-phenylindol (DAPI) were purchased from Wako Pure Chemical Industries (Osaka, Japan) and Polysciences (Warrington, PA), respectively. Matrigel (growth factor-reduced) was purchased from Corning Incorporated (Corning, NY). Rabbit polyclonal antibodies against human Solo were prepared as previously described [14 (link)]. Other antibodies were purchased as follows: anti-FLAG (M2; Sigma-Aldrich, St. Louis, MO), anti-GFP (A6455; Life Technologies, Camarillo, CA), anti-β-actin (AC-15; Sigma-Aldrich), anti-K18 (DA-7; BioLegend, San Diego, CA), anti-GM130 (CSB-PA600856ESR1HU; Flarebio Biotech LLC, College Park, MD), anti-β4 (58XB4; BioLegend) for immunofluorescence, and anti-β4 (Clone 7; BD Biosciences, Franklin Lakes, NJ) for immunoblotting. Secondary antibodies, anti-mouse IgG-Alexa 488, anti-mouse IgG-Alexa 568, anti-rabbit IgG-Alexa 568, and anti-rat IgG-FITC, were purchased from Thermo Fisher Scientific (Waltham, MA).
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8

Immunofluorescence Staining of Cx26, p120, and GM130

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Indirect immunofluorescence was performed as described previously. Anti-Cx26 mAb clone CX-12H10 (Thermo Fisher Scientific) and anti-p120 Catenin pAb (Sigma-Aldrich, St. Louis, MO, USA), anti-GM130 pAb (Sigma-Aldrich) were diluted at 1:150, 1:200, and 1:3500, respectively. After fixation with acetone, cells are incubated with the diluted primary antibodies. Specific signals were revealed by anti-mouse IgG-Alexa 488 (Thermo Fisher Scientific) and anti-rabbit IgG-Alexa 568 (Thermo Fisher Scientific). Nuclei were stained with DAPI (KPL, Gaithersburg, MD, USA) at a concentration of 0.5 µg/mL.
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9

Ferroptosis-related Exosome Analysis

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EMEM (Wako, 051–07615), FBS (Biowest, S1810-500; Nuaillé, France), exosome-depleted FBS (Exo-FBS™, Gibco, A27208-03), erastin (Selleck Chemicals, S7242), RSL3 (MedChemExpress, HY-100218A), ferric ammonium citrate (FAC; Sigma Aldrich, F5879), RhoNox-4 (Goryo Chemical; FerroOrange, GC904-01), ExoSparkler Exosome Membrane Labeling kit-Deep Red (Dojindo, EX03), phorbol 12-myristate 13-acetate (PMA; Wako, 162–23591), polyethylene glycol 6000 (Wako, 167–22941), Autofluorescence Quenching Kit (Vector, SP-8400), Aurum™ Total RNA Mini Kit (BioRad, 64337836), NEBNext Ultra II Directional RNA Library prep kit for Illumina (BioLabs, E7760S), NEBNext Multiplex Oligos for Illumina (BioLabs, E6440S), desferal (DFO, Novartis), anti-CD63 (Thermo Fischer Scientific, #10628D), anti-mesothelin (IBL, #28127), anti-αSMA (Abcam, ab5694), anti-CD68 (CST, 97778S), anti-GFP (MBL life science, #598), anti-TfR1 (Thermo Fischer Scientific, #13–6800), anti-FtL (abcam, ab69090), anti-FtH (SantaCruz, sc-H53), anti-IRP1 (CST, #20272), anti-IRP2 (Novus, NB100-1798), Cell Cycle Regulation Antibody Sampler Kit (CST, #9932), anti-mouse IgG Alexa488 (Thermo Fischer Scientific, A11108) and anti-rabbit IgG Alexa 568 (Thermo Fischer Scientific, A-11011) were used.
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10

Drosophila Wing Imaginal Disc Analysis

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Pupae were fixed in 3.7% formaldehyde (Sigma-Aldrich) at 4 °C overnight, after which pupal wings were dissected. Larvae were fixed in 3.7% formaldehyde at room temperature for 20 min, after which wing imaginal discs were dissected. The following primary antibodies were used: mouse anti-DLG1 [1:50; Developmental Studies Hybridoma Bank (DSHB), University of Iowa], rabbit anti-phospho-SMAD1/5 (1:300; Cell Signaling Technologies), rabbit anti-phospho-Histone H3 (1:500; Millipore), rat anti-HA 3F10 (1:100; Roche). Alexa 488 conjugated phalloidin (1:200; Thermo Fisher Scientific). Secondary antibodies were anti-mouse IgG Alexa 488, anti-rabbit IgG Alexa 568, anti-mouse IgG Alexa 647, and-rat IgG Alexa 568 (1:200; Thermo Fisher Scientific).
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