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19 protocols using signal enhancer hikari

1

Xenograft Tissue Histological Analysis

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Xenograft tissues were fixed with 4% paraformaldehyde for 4 h and then embedded in paraffin. Sections were then cut to 3–4 μm thickness. For hematoxylin-eosin (HE) staining, deparaffinized sections were stained with Carazzi’s hematoxylin for 10 min, followed by staining with eosin Y for 10 min. For immunofluorescent staining, deparaffinized sections were boiled in ImmunoSaver (Fujifilm Wako) at 98°C for 60 min for antigen retrieval. After blocking with Blocking One Histo (Nacalai Tesque, Inc.) for 60 min, sections were incubated with primary antibodies, including anti-human vimentin (Invitrogen, Carlsbad, CA, USA; cat. no. MA5-11883; 1:50 dilution) and anti-phospho-CREB (Cell Signaling Technology; 1:200 dilution), diluted in Signal Enhancer HIKARI (Immunostain Solution A; Nacalai Tesque, Inc.) overnight at 4°C. After washing, sections were incubated with secondary antibodies (AlexaFluor 568-conjugated goat anti-rabbit IgG [Thermo Fisher Scientific; 1:400 dilution] and AlexaFluor 488-conjugated goat anti-mouse IgG; 1:400 dilution]) and DAPI (5 μg/mL) diluted in Signal Enhancer HIKARI (Immunostain Solution B; Nacalai Tesque, Inc.) for 60 min at room temperature.
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2

Histological Analysis of Mouse Dorsal Skin

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Dorsal skin was excised and fixed with 20% formalin solution (Fujifilm Wako Pure Chemical Corporation). The skin samples were embedded in paraffin by a conventional method and stained with hematoxylin and eosin. Images were acquired using an Olympus virtual slide system VS110 (Olympus, Tokyo, Japan). The thickness of the epidermis was expressed as the mean values from five fields per mouse.
For immunohistochemistry, cryosections of mouse dorsal skin were fixed with 4% paraformaldehyde (Fujifilm Wako Pure Chemical Corporation) for 10 min, washed with 0.1% Triton X-100 in phosphate-buffered saline for 10 min, and incubated with Blocking One (Nacalai Tesque, Kyoto, Japan) for 30 min. Following overnight incubation at 4 °C with primary antibodies, the sections were incubated with Alexa Fluor-conjugated secondary antibodies at room temperature for 60 min in the dark and mounted in PLUS Antifade Mounting Medium (Vector Laboratories, Newark, CA, USA). Antibodies were diluted with Signal Enhancer HIKARI (Nacalai Tesque). Images were acquired using an LSM 700 confocal laser microscope (Carl Zeiss Co., Ltd., Oberkochen, Germany).
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3

Whole-cell Protein Extraction and Western Blot

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For whole-cell lysates, 3 OD600 cells were harvested and resuspended in 15% TCA overnight. About 500-μl 0.5-mm glass beads were added, and samples were vortexed for a total time of 15min, with intermittent cooling on ice. They were centrifuged at 15,000g for 10 min, and the obtained pellet was washed twice with 100% acetone, air-dried, and resuspended in 1× sample loading buffer and boiled for 10 min. Samples were separated on a sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and transferred to Immobilon-P (Merck).
For Supplementary Figs. 1c, 2d, e, and 6g, primary antibody and secondary antibody dilutions were made in skim milk. Proteins bound by antibodies were detected with Clarity western ECL (BioRad) and visualized with Versadoc (BioRad). For Fig. 7g and Supplementary Fig. 1a, 2b, 6a, b, d primary and secondary antibody dilution were prepared in Signal Enhancer Hikari (Nacalai tesque). ChemiDoc Touch (BioRad) was used to visualize proteins reacting with antibody in the presence of the substrate ECL Prime (GE Healthcare). ImageJ78 ,79 and Image lab v6.0.0 (BioRad) was used to visualize and process images. Antibodies used are tabulated in Supplementary Table 5. Uncropped blots are presented in the Source Data File.
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4

Western Blotting of DNA Damage Proteins

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The extraction of total cell lysates and Western blot analysis were performed as described previously [13 (link), 18 (link)] with the following modifications. The membranes were blocked in Blocking One (Nacalai Tesque, Kyoto, Japan) or ECL Prime
Blocking reagent (GE Healthcare Bio-Sci. Corp., Piscataway, NJ, U.S.A.) for 30 min at room temperature. The following antibodies were used: goat anti-XLF
polyclonal antibody (SAB2501119) (Sigma, St. Louis, MO, U.S.A.), rabbit anti-GFP polyclonal antibody (FL) (Santa Cruz Biotechnology, Santa Cruz, CA, U.S.A.),
mouse anti-γH2AX monoclonal antibody (JBW301) (Upstate Biotechnology Inc.) or mouse anti-β-actin monoclonal antibody (Sigma). The anti-XLF and anti-GFP
antibodies were diluted in Signal Enhancer HIKARI (Nacalai Tesque). In accordance with the manufacturer’s instructions, the binding to each protein was detected
using a Select Western blotting detection system (GE Healthcare Bio-Sci. Corp.) and visualized using the ChemiDoc XRS system (Bio-Rad, Hercules, CA,
U.S.A.).
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5

Western Blot Analysis of Protein Lysates

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Total cell lysates were electrophoresed on 5–20% SDS-polyacrylamide gels, and the fractionated products were electroblotted onto Hybond-P membranes (GE Healthcare Bio-Sci. Corp., Piscataway, NJ). The membranes were blocked in Blocking One (Nacalai Tesque, Kyoto, Japan) or ECL Prime Blocking reagent (GE Healthcare Bio-Sciences, Piscataway, NJ, USA) for 30 min at RT55 (link),56 (link). The following antibodies were then applied: mouse anti-XLF monoclonal antibody (D-1, 1:500) (Santa Cruz Biotechnology, Santa Cruz, CA, USA), rabbit anti-GFP polyclonal antibody (FL, 1:4000) (Santa Cruz Biotechnology), or mouse β-actin monoclonal antibody (AC-15, 1:500) (Sigma-Aldrich). The antibodies were diluted in Signal Enhancer HIKARI (Nacalai Tesque). Binding to each protein was detected using the Select Western blotting detection system (GE Healthcare Bio-Sciences) and visualized using the ChemiDoc XRS system (Bio-Rad, Hercules, CA, USA).
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6

Western Blot Analysis of Brain Injury

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Tissues for western blot analyses were collected on 6 days post-injury. The injured brain tissues from the ipsilateral hemisphere were carefully dissected under a dissecting microscope, and then homogenized in a buffer solution containing M-PER Mammalian protein extraction reagent 5 mM Na3VO4, 1 mM NaF, 1 mM Na2P2O7, 1 mM Benzamidine, 5 mM EDTA, and HALT Protease Inhibitor Cocktail (Thermo Fisher Scientific, Waltham, MA). Total protein concentration was estimated using a BCA kit (Thermo Fisher Scientific, Waltham, MA). Protein samples were separated by 4–20% SDS-PAGE and transferred to PVDF membrane (BioRad, Hercules, CA). The blots were incubated in Signal Enhancer HIKARI (Nacalai Tesque INC, Japan) containing primary antibodies against alpha II spectrin (Santa Cruz Biotechnology, Dallas, TX), MMP9 (NeuroMab, San Diego, CA), IgG (Thermo Fisher Scientific, Waltham, MA) or GAPDH (Cell Signaling, Danvers, MA). Molecular mass was estimated with a pre-stained protein marker with a standard molecular weight range (BioRad, Hercules, CA). Blots were developed using an ECL kit (Thermo Fisher Scientific, Waltham, MA) and visualized by LAS-3000 Imaging System (Fuji, Cambridge, MA). Densitometric analyses were performed using ImageJ.
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7

Cell Lysis and Immunoblotting Protocol

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Preparation of cell lysates and immunoblotting was performed as described previously.32 The antibodies were diluted in Signal Enhancer HIKARI (Nacalai Tesque). Band signals were visualized using Western Lightning Plus‐ECL (PerkinElmer Japan) and captured using an Amersham Imager 600 (GE Healthcare). Immunoblotting combined with in vitro protein linking was performed as described previously, with minor modifications.33 Briefly, the collected cells were lysed in lysis buffer (0.5 mol/L Tris–HCl [pH 6.8], 10% glycerol, 2% sodium dodecyl sulfate containing 1/100 protease (#25955‐11), and phosphatase (#07575‐51) inhibitor cocktail (Nacalai Tesque), followed by sonication. The lysates were then centrifuged at 15,000 g at 4℃ for 15 minutes. The supernatants were collected and analyzed by immunoblotting using a primary antibody at a protein dose of 50 μg.
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8

Quantifying Astrocyte Protein Expression

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Proteins of cultured astrocytes were separated by 10% SDS-PAGE and transferred onto a PVDF membrane (Pierce, Rockford, IL). The primary and secondary antibodies (Pierce, Rockford, IL) were incubated using the Signal Enhancer HIKARI (Nacalai Tesque, INC, Japan) and the protein bands were detected with the SuperSignal® West Femto (Pierce, Rockford, IL). Molecular mass was estimated with pre-stained markers (BioRad, Hercules, CA). Protein bands were analyzed using the ImageJ software. To evaluate the changes of protein expression in astrocytes cultures treated with a siRNA designed to target rat Calhm1 mRNA, blots were developed for of CALHM1, Cx43 or Panx-1, and then, stripped, and re-probed for ß-actin to express the changes as the ratio of the protein over ß-actin.
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9

Immunofluorescence Staining of Astrocytes

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Astrocyte monolayers were fixed with 2% paraformaldehyde in PBS, blocked with 0.5% BSA in PBS and incubated with the corresponding rabbit polyclonal primary antibody, mouse monoclonal primary antibody or both in the case of co-immunofluorescence analysis, and then, with the appropriate Alexa-568-labeled goat anti-rabbit or anti-mouse secondary antibody (Invitrogen Molecular Probes, USA, Cat. #A11011 or Cat. #A11004, respectively), or Alexa-488-labeled goat anti-rabbit or anti-mouse secondary antibody (Invitrogen Molecular Probes, USA, Cat. #A11008 or Cat. #A10680, respectively) using the Signal Enhancer HIKARI (Nacalai Tesque, INC, Japan) as indicated by the manufacturer. The fluorescent signal was examined using an Olympus BX41 WI microscope and a CCD camera (Jenoptik ProgRes C5).
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10

Ku80 Immunoblot Analysis Protocol

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The extraction of total cell proteins and western blot analysis were carried out as described previously 14, 15, 18 with the following modifications. The following antibodies were used: rabbit anti‐Ku80 polyclonal antibody against human Ku80 (AHP317; Serotec, Oxford, UK), rabbit anti‐Ku80 polyclonal antibody against canine Ku80 (583V AP), rabbit anti‐GFP polyclonal antibody (FL, Santa Cruz Biotechnology, Santa Cruz, CA, USA), and mouse anti‐β‐actin monoclonal antibody (Sigma, St. Louis, MO, USA). The anti‐Ku80 antibody (583V AP) was raised for this study against corresponding to the amino acids: 277–290 of canine Ku80, characterized and affinity‐purified. The two anti‐Ku80 and anti‐GFP antibodies were diluted in Signal Enhancer HIKARI (Nacalai Tesque, Kyoto, Japan).
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