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26 protocols using cy3 anti rabbit igg

1

Immunofluorescent Staining of Brain Sections

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Brain sections were washed four times for 5 min in KPBS and then blocked in KPBS containing 1% BSA, 4% NGS, and 0.4% Triton X-100. The tissues were incubated overnight at 4 °C with the primary Iba-1 antibody (1: 2,000; Wako Chemicals) and monoclonal anti-Aβ (6E10, 1: 3000; Covance). After washing four times for 5 min in KPBS, tissues were incubated in the appropriate secondary antibody (IgG anti-mouse Alexa 488; Thermofisher and IgG anti-rabbit CY3; Jackson Immunoresearch) for 2 h at room temperature. Following further washes in KPBS and incubation with DAPI, the sections were mounted onto Micro Slides Superfrost Plus glass slides and coverslipped with Fluoromount-G (Electron Microscopy Sciences).
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2

Immunostaining of Brain Sections

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Brain sections were washed four times for 5 min in KPBS and then blocked in KPBS containing 1% BSA, 4% NGS, and 0.4% Triton X-100. The tissues were incubated overnight at 4 • C with the primary Iba-1 antibody (1: 2,000; Wako Chemicals) and monoclonal anti-Aβ (6E10, 1: 3,000; Covance). After washing four times for 5 min in KPBS, tissues were incubated in the appropriate secondary antibody (IgG anti-mouse Alexa 488; Thermofisher and IgG anti-rabbit CY3; Jackson Immunoresearch) for 2 h at room temperature. Following further washes in KPBS and incubation with DAPI, the sections were mounted onto Micro Slides Superfrost Plus glass slides and coverslipped with Fluoromount-G (Electron Microscopy Sciences).
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3

Immunostaining of Cultured Neurons

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Neurons grown on glass coverslips were fixed with 4% (v/v, in PBS) paraformaldehyde for 30 min and immunostained with rabbit anti-cleaved caspase3 (Asp175) (1:300; Cell Signaling Techn, Inc.), mouse anti-MAP2 (1:500; SIGMA) [39 (link)], mouse anti-p53 (1:200; 554157, BD Biosciences) [30 (link)], and rabbit-COX IV (1:1000; ab16056, Abcam) antibodies. Immunolabeling was detected using anti-rabbit IgG–Cy3 (1:500) or anti-mouse IgG–Cy2 (1:500; Jackson ImmunoResearch). Coverslips were washed, mounted in SlowFade light anti-fade reagent (Invitrogen) on glass slides, and examined using a microscope (Nikon Inverted microscope Eclipse Ti-E) equipped with × 20 objective and a pre-centered fiber illuminator Nikon Intensilight C-HGFI and black and white charge-coupled device digital camera Hamamatsu ORCAER, or on a scanning laser confocal microscope (“Spinning disk” Roper Scientific Olympus IX81) with three lasers (405, 491, and 561 nm) and equipped with × 40 and × 63 PL Apo oil-immersion objective for high resolution imaging and device digital camera Evolve Photometrics.
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Immunohistochemical Analysis of Mouse Brain

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Immunohistochemical analysis was performed using mouse brains fixed in 4% paraformaldehyde for 12 to 16 hours. Mouse paraffin sections were deparaffinized in xylene followed by rehydration in ethanol diluted in serial dilutions and microwaved in 0.01 M citrate buffer, pH 6.0, at 120 °C for 15 min. The brain area was delimited using a DAKO pen (S2002, Agilent’s Dako, Glostrup, Denmark) and incubated overnight at 4 °C with primary antibodies. The next day, mouse brain sections were washed and incubated with secondary antibodies at room temperature for 1 hour. The antibodies and respective dilutions used included anti-γH2AX antibody, 1:200 (Ser139, #05-636, Millipore, MA, USA); rabbit anti-53BP1, 1:5000 (NB100-304, Novus Biologicals, CO, USA); anti-DARPP-32, 1:200 (Cell Signaling Technology, #2306, MA, USA); anti-Htt, 1:100 (EM48, #MAB5374, Millipore, MA, USA); anti-rabbit IgG Cy3, 1:1000 (711-165-152, Jackson Laboratory, Bar Harbor, ME, USA); anti-mouse IgG Alexa488, 1:1000 (A21202, Molecular Probes, OR, USA); anti-mouse IgG Cy3, 1:1000 (715-165-150, Jackson Laboratory, ME, USA); and anti-rabbit IgG Alexa488, 1:1000 (A21206, Molecular Probes, OR, USA).
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5

Immunofluorescence analysis of iPSC-derived retinal organoids

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iPSC-derived retinal organoids were fixed in 4% paraformaldehyde at room temperature for 20 min. Post-fixation retinal organoids were incubated overnight with 30% sucrose in PBS, and then frozen and cryosectioned. The frozen sections were stained for a panel of retinal-specific antibodies. Antibodies against the following proteins were used at the indicated dilutions: RECOVERIN (Merck Millipore, AB5585, 1:800), NRL (Santa Cruz, sc-374277, 1:800), CRALBP (Abcam, ab15051, 1:500), HuC/D (ThermoFisher, A21271, 1:500), PKCα (BD Biosciences, 610107, 1:500), ARL13B (Proteintech, 17711-1-AP, 1:500), PRPF31 (Abnova, PAB7154, 1:500), SNRPB monoclonal antibody (Y12) (ThermoFisher, MA5-13449, 1:500). The following secondary antibodies were used: anti-mouse-IgG-FITC (Jackson Immuno Research, 715-095-151, 1:500), anti-mouse-IgG-Cy3 (Jackson Immuno Research/115-165-003, 1:500), anti-rabbit-IgG-Cy3 (Jackson Immuno Research/111-165-003, 1:500), anti-goat-IgG-FITC (Jackson Immuno Research/705-096-147, 1:500). Nuclei were labelled with blue-DAPI (ThermoFisher, 62248). All antibody details are shown in Supplementary Data 6.
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6

Immunofluorescent Labeling of Neuron Markers

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Explants were fixed in 4% PAF for 15 min at room temperature after 3 days of culture. Specimens were incubated overnight in a solution comprising anti-peripherin (polyclonal rabbit, 1:1000, Chemicon International Inc.) and anti-neurofilament −200 kDa (monoclonal mouse, 1:200, Thermo Fisher Scientific) primary antibodies. After PBS washing, sections were subjected to double immunolabeling by being incubated for 1 h with a solution containing the secondary antibodies: anti-mouse IgG Alexa Fluor 488-conjugated (Molecular Probes) and anti-rabbit IgG Cy3 (Jackson ImmunoResearch Laboratories Inc., West Grove, PA, USA). Following this, explants were mounted using a Dako fluorescent mounting medium.
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7

Immunostaining of Mitochondrial Proteins

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In brief, cells were fixed in 4% PFA (Sigma-Aldrich) for 15 min, followed by a 10-min permeabilization step (0.1% Triton X-100 in PBS for internal cell markers). The blocking step was performed by incubation in 2% BSA for 30 min. Cells were incubated with primary antibodies at 4°C overnight and further incubated with secondary antibodies for 1 h. For MitoTracker dye staining, cells were cultured in the normal media with 150 nM MitoTracker red (Invitrogen) for 30 min before further fixation and immunostaining. Antibodies against the following proteins were used at the indicated dilutions: CHCHD2 (HPA027407, 1:200; Sigma-Aldrich), SOX1 (4194S, 1:200; Cell Signaling Technology), NESTIN (MAB5326, 1:200; EMD Millipore), TUJ1 (MRB-435P, 1:500; Covance), mtTFA (ab119684, 1:500; Abcam), anti–mouse IgG-FITC (1:800; Sigma-Aldrich), and anti–rabbit IgG-Cy3 (1:1,000; Jackson ImmunoResearch Laboratories, Inc.). Nuclei were labeled with DAPI (Thermo Fisher Scientific). Colocalization coefficient studies were performed using ImageJ software by calculating Manders’ colocalization coefficient, which describes the amount of colocalizing pixels of GFP using pixels generated by RFP.
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8

In Situ Hybridization and Immunostaining of Embryonic Tissues

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Embryos were fixed with 4% paraformaldehyde in phosphate-buffered saline (PBS, pH 7.4) overnight and submerged in 12.5%, 25% sucrose, and 25% sucrose/OCT solutions sequentially. Fixed embryos were embedded in OCT compound (Tissue-Tek) and sectioned at 12 μm thickness using a cryostat (Fisher Scientific). Tissue slides were kept at -20°C. In situ hybridization was performed with digoxygenin-labeled Myh9, Myh10, Myh14, and Myl9 antisense or sense probes according to standard methods. Immunostaining was performed using the following primary antibodies: anti-rabbit NMHCIIA (Covance, 1:500), Phalloidin-conjugated Alexa 488 (1:200), anti-rat E-cadherin (Invitrogen, 1:300), anti-rabbit p63 (Abcam, 1:200), anti-rabbit Ki67 (Thermo Scientific, 1:200), and anti-rabbit cleaved caspase-3 (Asp175) (Cell signaling, 1:200). Anti-rabbit IgG-Cy3, anti-rat Cy2, or Dylight 649 (Jackson Immunoresearch Lab) were used as secondary antibodies to visualize the signals. Images were captured using a Zeiss Axio Imager Z2 microscope or a Zeiss Cell Observer spinning disk confocal microscope.
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9

Antibody validation for neuroscience research

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The following antibodies were used: homemade anti-Myo1b polyclonal antibodies (Almeida et al., 2011 (link)), 1:1,000 for Western blot and 1:50 for immunofluorescence; mouse monoclonal antibodies against Tau-1 (1:100) purchased from EMD Millipore and β-3 tubulin (1:150) purchased from Abcam; and rabbit polyclonal anti-GAPDH (1:20,000 for Western blot) purchased from Sigma-Aldrich. We also used Alexa Fluor 488–, 546–, or 647–coupled secondary antibodies against mouse or rabbit IgG (1:400) and horseradish peroxidase–conjugated secondary antibodies against mouse or rabbit IgG (1:5,000; Invitrogen); and anti–rabbit IgG Cy3 (1:400; Jackson ImmunoResearch Laboratories, Inc.; or 1:500; Molecular Probes). Alexa Fluor 488– or 546–conjugated phalloidin was used to detect F-actin (1:400; Invitrogen).
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10

Immunohistochemical Analysis of Post-Ischemic Cardiac Tissue

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6 µm cryosections were prepared for LV staining. H&E staining was carried out as previously described [19 (link)]. Infiltration by immune cells 14 days after I/R was determined by immunohistochemical staining for CD45 (#550539, BD Biosciences) combined with a counterstain with eosin as previously described [22 (link)]. The following antibodies were used for immunostaining: anti-α-actinin (A7811, Sigma-Aldrich), anti-CD68 (ab53444), anti-CX43 (Cell Signaling 3512), anti-F4/80 (Cell Signaling 30325), anti-GSL I IsolectinB4 (Vector B-1205), anti-NEU1 (sc-32936, Santa Cruz Biotechnology), Fluorescein-labelled anti-wheat germ agglutinin (WGA) (Vector Laboratories Inc. FL-1021), Fluorescein-labelled Avidin D (Vector A-2001) and anti-mouse IgG-Alexa Fluor® 488 and anti-rabbit IgG-Cy3 (both from Jackson ImmunoResearch). For nuclear staining, Hoechst (Thermo Fisher Scientific Inc.) was used.
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