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6 protocols using alexa 488 conjugated anti rabbit igg secondary antibody

1

GFP Immunohistochemistry in Medaka Larvae

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Medaka larvae at 10 dpf were fixed in 4% paraformaldehyde in 0.85X PBS at 4 °C overnight. After fixation, the specimens were embedded in paraffin and sectioned serially at 5 μm. The deparaffinized sections were treated with anti-GFP antibody (1:500, Invitrogen, A11122) at room temperature for 3 h. After several washes with PBS, sections were incubated with Alexa 488-conjugated anti-rabbit IgG secondary antibody (1:500, Invitrogen, A21206) for 1 h. The sections were counterstained with DAPI.
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2

Quantitative Phospho-S6 Ribosomal Protein Imaging

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System; PerkinElmer) for 1 hat RT. The cells were incubated with anti-digoxigenin-POD (1 : 200 in TNB, Roche) and rabbit anti-Phospho-S6 Ribosomal Protein antibody (1 : 400 in TNB, #4858S, Cell Signaling) in a humidified chamber overnight in 4°C, next they were washed with PBS-T, and incubated with Alexa 488-conjugated anti-rabbit IgG secondary antibody (1 : 1000; Invitrogen). The hybridization signal was amplified with TSA Cy3 System (Perkin Elmer). The imaging was performed using confocal microscope LSM 700, Axio Imager Z2 (Zeiss) in a stack of 0.4 μm thick Z section, using a 40× objective (oil immersion; 1.3 NA) with 1.2 zoom factor. The obtained stack was "flattened" into a single image using a maximum intensity projection. Quantification of fluorescence signal intensity was performed in ImageJ software. Signal intensity was averaged on the cell area.
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3

Autophagy-Related Protein Detection

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Anti-LC3-I&II antibody was purchased from MBL International corporation (Woburn, MA). Anti-LC3-II and anti-ATG5 antibodies were purchased from Cell Signaling Technology (Danvers, MA). Peroxidase-conjugated secondary antibodies were purchased from Santa Cruz Biotechnology (Santa Cruz, CA). Alexa 488-conjugated anti-rabbit IgG secondary antibody, LysoTracker® Red DND-99 and DRAQ5 were purchased form Life Technologies (Grand Island, NY). BCA protein assay reagent was purchased from Pierce (Rockford, IL). Super signal enhanced chemiluminescence (ECL) reagent was obtained from Amersham Bioscience (Piscataway, NJ) and PVDF membranes were purchased from Millipore (Bedford, MA). HRP-labeled secondary antibody and DAB for immunohistochemical staining were purchased from Vector Laboratories (Burlingame, CA).
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4

Immunofluorescence Staining of Tubulin and γH2AX

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Cells were cultured on cover glasses in well plates. The prepared cover glasses were fixed in 4% paraformaldehyde/phosphate-buffered saline (PBS) at 25 °C for 15 min and washed three times with PBS. The cells were permeabilized and blocked with 0.3% Triton X-100 (Agilent Technologies, Santa Clara, CA, USA) and blocked with 5% FBS at room temperature for 60 min. The cells were then washed three times with PBS and incubated with anti-α-tubulin (1:1000 #T6199 Sigma Aldrich, St Luis, Missouri, USA) and anti-γH2AX (1:500 #2578 Cell signaling Technology, Danvers, MA, USA) at 4 °C overnight. After extensive washing with PBS, the samples were incubated with Alexa-594-conjugated goat anti-mouse IgG secondary antibody (1:500 #A11001 Life technologies,) and Alexa-488-conjugated anti-rabbit IgG secondary antibody (1:500 #A11072 Life technologies) at 25 °C for 60 min. The cover glasses were washed three times with PBS, mounted in in VECRASHELD Mounting medium for fluorescence (Vector Laboratories, Inc Burlingame, CA), and sealed with nail polish. Images were acquired using OLYMPUS FSX 100 fluorescence microscope (OLYMPUS, Tokyo, Japan).
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5

Immunohistochemistry of Neuronal Cell Types

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Mice were deeply anesthetized (150 mg/kg) and transcardially perfused with 4% PFA in PBS. Brains were removed and post fixed in the same fixative for 2h at 4°C and equilibrated with 30% sucrose in PBS at 4°C overnight. Coronal sections (50 μm thickness) were generated using a sliding microtome (SM2020R, Leica). Sections were blocked for 1h at room temperature with blocking buffer (0.1% Triton X-100 and 5% normal goat serum in PBS) and incubated with rabbit polyclonal anti-RFP antibody (Abcam, Cat#ab62341, RRID: AB_945213), rabbit polyclonal anti-GFP antibody (MBL International, Cat#598, RRID: AB_591819) and/or rat-monoclonal anti-Ctip2 antibody (Abcam, Cat#ab18465, RRID: AB_2064130) at 1:200 in blocking buffer at 4°C overnight. After washing three times in PBS for 10 min, sections were incubated with Alexa-594-conjugated anti-rabbit IgG secondary antibody (Thermo Fisher Scientific, Cat# A11037, RRID: AB_2534095), Alexa-488-conjugated anti-rabbit IgG secondary antibody (Thermo Fisher Scientific, Cat#A11034, RRID: AB_2576217) and/or Alexa-488-conjugated anti-rat IgG secondary antibody (Thermo Fisher Scientific, Cat#A11006, RRID: AB_2534074) at 1:400 in blocking buffer for 2 h at room temperature. After washing three times in PBS for 10 min, sections were counterstained with 1 μg/mL of 4’, 6-diamidino-2-phenylindole (DAPI) (11034-56, Nacalai Tesque).
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6

Quantifying Neurite Outgrowth from Thawed Neurospheres

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Neurospheres frozen on day 27 were thawed, seeded in 24-well plates coated with iMatrix511 for three days, and fixed with 4% paraformaldehyde. The neurospheres were stained with an anti-tubulin beta III (TUBB3) antibody (BioLegend, Inc., San Diego, CA, USA) and an Alexa 488-conjugated anti-rabbit IgG secondary antibody (Thermo Fisher Scientific), followed by counterstaining of the nucleus with 4’,6-diamidino-2-phenylindole (DAPI) (Biotium Inc., Fremont, USA). A fluorescence microscope (BZ-X710; KEYENCE CORPORATION, Osaka, Japan) was used for visualization, and the area covered by neurites was defined as the TUBB3-positive area minus the DAPI-positive area using the BZ-H3M measurement module (KEYENCE CORPORATION).
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