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20 protocols using alexa fluor 488 goat anti rabbit

1

Quantitative Neuronal Peptide Immunostaining

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Larvae were dissected in PBS + 0.3% Triton X-100 and tissues were fixed in 4% paraformaldehyde for 30 min. Tissues were then washed with 1x PBST and incubated for 2 days in a 1:750 dilution of rabbit anti-NPF (Ray Biotech, Norcross, GA) in 1X PBST. Secondary antibodies (Alexa Fluor 488 goat anti-rabbit, Jackson ImmunoResearch, Burlington, Ontario) were diluted 1:750 in 1X PBST plus 5% normal goat serum. Stained samples were mounted in Vectashield anti-fade mounting medium for imaging and all images were collected on a Zeiss LSM 700 confocal microscope using a 20X objective.
Confocal images were quantitated using NIH Image J. For pixel area, thresholded pixels were counted for each image (threshold set to 90). For total fluorescence, the integrated density of pixels for entire images was measured. Images were then calibrated for background by calculating the average mean fluorescence of four circular regions of each image, multiplying that average by the total pixel area of the image, and subtracting that number from the integrated pixel density of the image.
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2

Immunostaining of NALCN in Brainstem

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Mice were anesthetized with ketamine/xylazine (60/10 mg/kg) and then transcardially perfused with 4% paraformaldehyde in 0.1 M PBS (pH 7.4). The perfused brains were removed and put into 4% paraformaldehyde solution overnight, followed by 30% sucrose for one day. Transverse sections of brain stem (−5.5 to −7.5 mm to Bregma) were cut (12 μm) using a freezing microtome (CM1850; Leica, Buffalo Grove, IL, USA). Sections were double-labeled by incubating at 4°C overnight with primary antibodies, including: NALCN (1:800, mouse, SMC-417, StressMarq Biosciences, Canada), NeuN (1:400, rabbit, ab104225, Abcam, Cambridge, MA, USA), NeuN (1:400, mouse, MAB377, Merck Millipore, Darmstadt, Germany) and Phox2b (1:500, rabbit, A92903N, Thermo Fisher, MA, USA). Then, the sections were incubated with secondary antibodies at room temperature for 2 h: Alexa Fluor 647 goat anti-mouse 1:200 (115-605-003), Alexa Fluor 488 goat anti-rabbit 1:200 (111-545-003) (Jackson ImmunoResearch, West Grove, PA, USA 19390). All photographs were captured using a Zeiss AxioImager Z.2. and prepared using Image J (NIH, Bethesda, MD).
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3

Immunofluorescence Analysis of Pancreatic Tissues

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After collection, pancreatic tissues were fixed in 4% phosphate-buffered formaldehyde for 24 h. Fixed tissues were then embedded in paraffin according to standard procedures [79 (link)]. Representative pancreatic slices (4 µm) were prepared and rehydrated before double immunofluorescence staining was carried out, using mouse monoclonal anti-insulin antibody (1:100,000; Sigma-Aldrich, Steinheim, Germany) and rabbit polyclonal anti-5-HT antibody (1:500; ImmunoStar, Hudson, NY, USA). Primary antibodies were detected with fluorophore-labeled secondary antibodies using Rhodamine Red-X goat anti-mouse (1:200; Jackson ImmunoResearch, West Grove, PA, USA) and Alexa Fluor488 goat anti-rabbit (1:400; Jackson ImmunoResearch, West Grove, PA, USA) as well as DAPI (1:1000; KPL, Gaithersburg, MD, USA). Images were recorded with an upright microscope Eclipse Ni-E (Nikon, Düsseldorf, Germany), equipped with a DS-Fi3 Color Camera (Nikon, Düsseldorf, Germany) and analysis software NIS elements AR 5 (Nikon, Düsseldorf, Germany).
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4

Immunofluorescence Assay for PKCε in ALS Model

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NSC-34 cells expressing human WT or SOD1-G93A were cultured on glass cover slips, fixed in 4% paraformaldehyde and processed in order to perform an immunofluorescence assay [12 (link),59 (link)]. The samples were probed with specific primary antibodies: anti-PKCε (sc-1681, Santa Cruz Biotechnology, Inc. Dallas, TX, USA, 1:200), anti-phosho-S729-PKCε (#44-977G, Thermo Fisher Scientific, Waltham, MA, USA, 1:200); Alexa Fluor 488 Goat anti-rabbit and Alexa Fluor 594 Goat anti-mouse were used as secondary antibodies (Jackson Immuno-research). The analyses were performed by using confocal microscopy, as reported elsewhere [60 (link)]. The fluorescence was quantified by extrapolating the mean intensity of each channel from multiple regions of interest (ROI) and normalized to the background [12 (link)] by using the NIS-Elements AR (Advanced Research) software.
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5

Immunofluorescence Imaging of Primary Neurons

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Primary neurons were fixed at DIV21 with 4% paraformaldehyde solution in PBS for 10 min and blocked in PBS-0.1 M glycine for 10 min. Then, cells were permeabilised in PBS-0.1% saponine 10 min, blocked with PBS-Normal Horse Serum 15% 30 min and incubated overnight at 4 °C in the presence of the following primary antibodies: rabbit TOM-20 (1:250, ProteinTech 11802-1-AP) and mouse MAP2 (1:500, Sigma-Aldrich M1406). Fluorescent secondary antibodies: AlexaFluor 488 goat anti-rabbit (1:100), Cy3 goat anti-mouse (1:100), and/or Cy3 goat anti-mouse (1:100; all three from Jackson ImmunoResearch, West Grove, PA, USA) were incubated for 1 h at RT. Nuclei were stained with DAPI-Fluoromount (SouthernBiotech, Birmingham, AL, USA). Immunofluorescence was analysed using a Leica Confocal SP5-II confocal microscope (Leica Microsystems CMS GmbH, Mannheim, Germany). Images were taken using a HCX PL APO lambda blue 63.0 × 1.40 OIL objective with a standard pinhole (1 AU), at 1024 × 1024-pixel resolution, 0.4 m thick and 3.0 digital zoom.
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6

Immunofluorescent Staining of CD31 and FLRT2

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The tissues were cryosectioned into 20 μm–thick sections, fixed with 3.7% formaldehyde, and permeabilized with 0.01% Triton X-100 for 15 minutes. The samples were then blocked with 3% BSA for 1 hour at room temperature and incubated with rat anti-CD31 (catalog MA3105, Thermo Fisher Scientific) and anti-FLRT2 (catalog ab154023, Abcam) diluted (1:50) in blocking solution overnight at 4°C. The sections were washed with PBS and incubated with Alexa Fluor 594 goat anti-hamster IgG (catalog 127-025-160, Jackson ImmunoResearch Laboratories) and Alexa Fluor 488 goat anti-rabbit (catalog 127-095-160, Jackson ImmunoResearch Laboratories) diluted (1:50) in blocking solution for 1 hour at room temperature. The sections were washed thrice with PBS and mounted on microscopy slides.
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7

Immunofluorescence Staining with Specific Antibodies

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Immunofluorescence was performed following the protocol described previously11 (link). Primary antibodies that we used include: rabbit anti-mouse LYVE-1 antibody (1:200, AngioBio), rat anti-mouse CD31 (1:100, BD Pharmingen), rabbit anti-phospho-Met (1:400, Cell Signaling), mouse anti-human PCNA (1:100, BD Pharmingen), mouse anti-human vimentin (1:50, Santa Cruz), and goat anti-mouse lectin FITC (1:100, Sigma). Secondary antibodies include: FITC-conjugated goat anti-rat, FITC-conjugated goat anti-rabbit, rhodamine-conjugated goat anti-mouse, Cy3-conjugated goat anti-rabbit, and Alexa Fluor 488 goat anti-rabbit (1:500, all from Jackson Immunoresearch). Fluorescent signals were visualized and digital images were obtained using the LSM-510 confocal microscope (Carl Zeiss). We quantified the images using ImageJ (NIH, Bethesda, MD), measuring the pixel number/10× frame of randomly selected 12 images in each sample. Each group included at least three different samples.
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8

Immunohistochemical Analysis of WDFY1 and NF-κB

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Mice were euthanized by cervical dislocation. Left hemispheres were removed and fixed for 72 h in paraformaldehyde solution (4% in a phosphate buffer 0.1M). 40 μm coronal sections were obtained using a Leica Vibratome (Leica VT1000S). Next, free-floating sections were washed three times in PBS, treated with NHCl for 30 min, and washed again three times with PBS. Floating sections were permeabilized in PBST (0.3%) with 0.02% Azide, 2% BSA, and 3% NGS (Ab buffer) for 1 h at room temperature. After three washes in PBS, brain slices were incubated overnight at 4°C with WDFY1 rabbit 1:100 (Bioss Abs, bs-13169R) or with NF-κB rabbit 1:200 (Santa Cruz Biotechnology Cat# sc-372, RRID:AB_632037). Sections were then washed three times and incubated for 2 h at room temperature with fluorescent secondary antibody AlexaFluor 488 goat anti-rabbit (1:400; from Jackson ImmunoResearch, West Grove, PA, United States). Immunofluorescence specificity was confirmed in slices without primary antibody. Sections were analyzed using a two-photon confocal microscope (Leica SP5).
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9

Immunofluorescence Imaging of PI16, α-Actinin, and HDAC1

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Paraffin sections were placed at 65 °C for 20 minutes and subsequently soaked in xylene and gradient ethanol for dewaxing. Then, the sections were permeabilized with 0.5% Triton for 20 minutes at room temperature and repaired in sodium citrate solution in 95 °C water for 10 hours. After naturally cooling to room temperature, sections were incubated with blocking buffer (5% BSA plus 10% goat serum and 0.05% Triton X‐100 in PBS) for 1 hour at room temperature. Then, the sections were incubated with primary antibodies at 4 °C overnight and secondary antibodies for 1 hour at room temperature. Finally, sections were dried and sealed with antifade mounting medium containing DAPI. A Carl Zeiss Axioskop microscope (Carl Zeiss) was used to capture fluorescent images. The primary antibodies used were anti‐PI16 (1:200, catalog number 121554; GeneTex), anti‐α‐actinin (1:200; catalog number A7811; Sigma‐Aldrich), and anti‐HDAC1 (1:200, catalog number 10197‐1‐AP; Proteintech). The secondary antibodies used were Cy3 goat anti‐rabbit, Cy3 goat anti‐mouse, Alexa Fluor 488 goat anti‐rabbit, and Alexa Fluor 488 goat anti‐mouse (1: 400, Jackson ImmunoResearch).
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10

Immunohistochemical Analysis of Apoptosis

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We carried out immunohistochemistry on heart cryostat sections (16 um) according to standard protocols [41] . In brief, zebrafish exposed to -asarone for 96 hrs were fixed in 4% PFA at 4 °C overnight. Fixed zebrafish were rinsed in PBS and equilibrated in 30% sucrose before embedding in Tissue-Tek OCT compound (Sakura Finetek Europe B.V.). The primary antibody used in this study is rabbit anti-Caspase 3 at 1:200 (Proteintech) and the secondary antibodies used (1:200) was Alexa Fluor 488 goat anti-rabbit (Jackson ImmunoResearch). We performed microscopy using a Zeiss LSM 510 confocal microscope.
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