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9 protocols using rabbit anti tuj1

1

Immunofluorescence Staining Protocol for Neural Markers

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Immunofluorescence was performed on 4% paraformaldehyde (PFA)-fixed cells permeabilized with 0.25% Tween-20. Primary antibodies were mouse anti-Nestin (Millipore, Billerica, MA, USA), rabbit anti-Sox2 (Millipore), mouse anti-MAP2 (Covance, Princeton, NJ, USA), rabbit anti-GFAP (DAKO, Carpinteria, CA, USA), rabbit anti-Mushashi1 (Millipore), rabbit anti-Tuj1 (Millipore), mouse anti-NeuN (Millipore), mouse anti-Oct4 (Millipore), rabbit anti-Pax6 (Covance), rabbit anti-TUC4 (Millipore), mouse anti-Vglut1 (Synaptic Systems, Goettingen, Germany), mouse anti-BrdU (SBCT, Santa Cruz, CA, USA) and rabbit anti-Ki67 (Abcam, Cambridge, MA, USA). Species-specific Alexa-Fluor-labeled secondary antibodies was used for detection followed by mounting in Prolong gold anti-fade with DAPI (Life Technologies).
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2

Organotypic Slice Culture and Cell Transplantation

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All procedures were approved by the Institutional Animal Care and Use Committee of Seoul National University. The organotypic slice culture was performed as previously described27 (link)–29 (link). Cells (6 × 103 cells/μl) prepared in neurobasal medium were transplanted onto the slice using aspirator tube assembly for microcapillary pipette (Sigma). In 7 days, the slices were fixed with 4% PFA overnight at 4°C, permeabilized and blocked with 0.1% Triton X-100 in 3% BSA. They were incubated overnight at 4°C with mouse anti-SOX2, 1:500, rabbit anti-TuJ1, 1:1000 and mouse anti-human nuclei, 1:500 (Millipore). Incubation with the secondary antibodies was performed as described above. The z-stack images were captured using a laser-scanning confocal microscope at 3–4 µm intervals.
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3

Immunofluorescent Characterization of 3D iPSC-Derived Eyecups

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3D iPSC-derived eyecups were embedded in 4% agarose, sectioned at a
thickness of 100μm using a Leica VT1000 S vibratome (Leica Microsystems,
Wetzlar, Germany) and labeled with primary antibodies targeted against: mouse anti-SOX2
(#MAB2018; 1:1000; R&D Systems, Minneapolis, MN), rabbit anti-PAX6
(#901301; 1:1000; BioLegend, San Diego, CA), goat anti-biotinylated-OTX2
(#BAF1979; 1:500; R&D Systems, Minneapolis, MN), rabbit anti-Ki67
(#ab15580; 1:500; Abcam, Cambridge, MA), rabbit anti-TUJ1 (neuron-specific class
III beta-tubulin; #T2200; 1:500; Sigma-Aldrich; 1:500), goat
anti-biotinylated-NRL (#BAF2945; 1:500; R&D Systems), mouse anti-HuC/D
(#A-21271; 1:500; Thermo Fisher Scientific, Waltham, MA) and rabbit
anti-recoverin (#AB5585; 1:2000; EMD Millipore, Billerica, MA). To detect
F-actin, eyecups were stained with Alexa Fluor® 488 Phalloidin (Life
Technologies, Madison, WI; #A12379; 1:500). Primary antibodies were detected
using fluorescently-conjugated Alexa Fluor® secondary antibodies (Life
Technologies). Cell nuclei were counterstained using DAPI. Sectioned eyecups were imaged
using a Leica DM 2500 SPE confocal microscope (Leica Microsystems).
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4

Immunohistochemistry and Western Blot Antibodies

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The following primary antibodies and dilutions were used for immunohistochemistry (IHC) staining and western blotting: rabbit polyclonal anti-UTX (1:1,000; Millipore, #ABE409); mouse monoclonal anti-SOX2 (1:500; R & D, #MAB2018); rabbit anti-PAX6 (1:1,000; Millipore, #AB2237); rabbit anti-TBR2 (1:1,000; Abcam, #AB23345); mouse monoclonal anti-β-ACTIN (1:20,000; Proteintech, #60008-1-Ig); rat monoclonal anti-BrdU (1:1,000; Abcam, #AB6362); rabbit monoclonal anti-Ki67 (1:1,000; Abcam, #AB15580); rabbit anti-PCNA (1:500; Santa Cruz Biotechnology, #SC7907), rabbit anti-TUJ1 (1:1,000; Sigma, #T2200); rabbit monoclonal anti-PTEN (1:1,000; Cell Signaling Technology, #9188); rabbit monoclonal anti-AKT (1:1,000; Cell Signaling, #4685); rabbit monoclonal anti-phospho-AKT (1:1,000; Cell Signaling, #3787); rabbit monoclonal anti-mTOR (1:1,000; Cell Signaling, #2983); rabbit monoclonal anti-phospho-mTOR (1:1,000; Cell Signaling, #5536); rabbit monoclonal anti-H3 (1:4,000; Cell Signaling, #4499S); rabbit polyclonal anti-trimethyl-histone H3 (Lys27) (1:2,000; Cell Signaling, #3377S); and rabbit anti-FLAG (1:1,000; Sigma, #7425).
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5

Antibody Characterization for Western Blot and Immunostaining

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The following primary antibodies were used for Western blotting and immunostaining in this study: mouse anti-Flag (Sigma-Aldrich, F3165), rabbit anti-Flag (Proteintech, 20543-1-AP), rabbit anti-Vps4B (Proteintech, 17673-1-AP), mouse anti-P62 (Abcam, ab56416), rabbit anti-LC3B (Abcam, ab48394), mouse anti-V5 (Proteintech, 66007-1-Ig), mouse anti–glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (Proteintech, 60004-1-Ig), mouse anti–β-tubulin class III (Tuj 1; Abcam, ab78078), rabbit anti–Tuj 1 (Sigma-Aldrich, T2200), and mouse anti–β-actin (Cell Signaling Technology, 3700). The horseradish peroxidase–conjugated secondary antibodies were as follows: goat anti-mouse (Sigma-Aldrich, A4416) and goat anti-rabbit (Sigma-Aldrich, A9169). The fluorophore-conjugated secondary antibodies were as follows: goat anti-rabbit Alexa Fluor 488 (Life Technologies, A11036), goat anti-mouse Alexa Fluor 488 (Life Technologies, A11029), goat anti-mouse Alexa Fluor 568 (Life Technologies, A11031), goat anti-rabbit Cy5 (Life Technologies, A10523), and goat anti-mouse Cy5 (Life Technologies, A105234).
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6

Examining Innervation of Mouse Footpads

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Adult mice were euthanized with CO2. Hairy skin from the top of each foot was removed and fixed in 100% acetone for 8 hours at room temperature, followed by immersion in 1mg/ml X-gal in staining solution (0.1 M Phosphate Buffer pH 7.5, 5 mM potassium ferricyanide, 5 mM potassium ferrocyanide, 20 mM Tris-HCL, 0.02% NP-40, 0.01% sodium deoxycholate) for 48 hours at 4°C. Tissues were then rinsed, post-fixed in 4% paraformaldehyde/1xPBS overnight, washed in PBS, submerged in 30% sucrose/1xPBS, and embedded in O.C.T. media. Sections of 15–20 μm thickness were cut and collected on glass slides and kept frozen until use. Antibodies on these sections included Rat anti-CD3 epsilon (1:100, NBP1-26685, Novus Bio) and Rabbit anti-C-Kit (1:100, D13A2, Cell Signaling Tech). For DRG neurons, whole ganglia were briefly fixed in 4% paraformaldehyde for 5 minutes, followed by X-gal staining as above for 1.5–2 hours, and embedded for cryosections as above. Sections (10 μm thickness) were counterstained with Rabbit anti-Tuj1 (1:1000, Sigma T2200) and DAPI. Brightfield and fluorescence images were acquired on a Zeiss Observer V1. Tuj1-positive neurons with nuclei in the plane of sectioning were counted manually, and percent overlay with X-gal staining were calculated.
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7

Hypothalamic Protein Expression in Food-Restricted Offspring

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Separate litters (Controls, N=6; food-restricted, N=5) were used for determining offspring hypothalamic protein expression (Western Blot) at two ages (1 and 21 days). Excess 1 day old male pups during litter culling were euthanized by decapitation and brains collected. At 21 days of age, one male offspring per litter was anesthetized by 5 % isoflurane/2 % oxygen by mask, subsequently euthanized by an overdose of pentobarbital (200 mg/kg i.p.) and brain collected. Hypothalami were obtained by dissecting semi-spheres adjunct to two sides of hypothalamus, the dorsal part removed, and the ventral part (~2 mm) used.
Western Blot was performed as previously reported by our group (Desai et al, 2008). Data were normalized to GAPDH (1:10,000, Chemicon). Primary antibodies used were DNMT1 (1:500, Santa Cruz), rabbit anti-Hes1 (1:1000, Santa Cruz), rabbit anti-Tuj1 (1:5000, Sigma) and rabbit anti-GFAP (1:10,000, DAKO).
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8

Immunofluorescence Staining of Brain Slices

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Brain slices or cells cultured in vitro were washed with phosphate-buffered saline (PBS) for 5 min, fixed in 4% paraformaldehyde for 20 min, and blocked in 5% bovine serum albumin (Sangon)/PBS containing 1% Triton X-100 (1% PBST) for 1 hour. Subsequently, the primary antibody was diluted with 1% PBST, added, and then incubated at 4°C overnight. The following day, the samples to be visualized were rinsed with PBS three times and incubated with secondary antibodies at room temperature for nearly 1.5 hours. The primary antibodies used for immunofluorescence are listed here: rabbit anti-TRPM2 (1:1000; Bethyl Laboratories), rabbit anti-TUJ1 (1:1000; Sigma), mouse anti-BrdU (1:1000; Millipore), rat anti-BrdU (1:1000; Abcam), rabbit anti-CUX1 (1:100; Santa Cruz Biotechnology), rabbit anti–cleaved caspase-3 (1:1000; Cell Signaling Technology), rabbit anti-PAX6 (1:1000; Millipore), mouse anti-MAP2 (1:1000; Millipore), mouse anti-NESTIN (1:1000; Millipore), rabbit anti-KI67 (1:1000; Abcam), mouse anti-SATB2 (1:300; Abcam), rabbit anti-SP5 (1:200; Bioss), rabbit anti-TBR2 (1:1000; Abcam), rat anti-CTIP2 (1:1000; Abcam), and mouse anti-SOX2 (1:1000; R&D Systems). Secondary antibodies applied were conjugates of Alexa Fluor Cy3, Cy5, or 488 (1:1000; Jackson ImmunoResearch). 4′,6-Diamidino-2-phenylindole (DAPI) (2 mg/ml; Sigma) was used for nuclear staining.
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9

Neuronal and Glial Differentiation Assay

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Disassociated Control NPCs in differentiating medium were seeded in 24 well plates with pre-placed cover glasses (Fisher, catalogue number: 12-545-84 18CIR-1D). Following 5 day treatments with DNMT siRNA and 5-Aza, cells were fixed in 4% paraformaldehyde in PBS for 30 min and stained using rabbit anti-Tuj1 (1:500, Sigma), rabbit anti-GFAP (1:500, DAKO) and secondary antibody donkey anti-rabbit IgG-Alexa 488 (1:250). Secondary antibodies were donkey anti-rabbit IgG-Alexa 488 (1:250) or donkey antimouse IgG-Alexa 568 (1:250).
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