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4 protocols using thy 1

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Western Blot Analysis of Neuronal Signaling

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RGC-5 lysates of were prepared with a lysis buffer containing 50 mM Tris (pH 7.6), 150 mM NaCl, 1 mM EDTA, 10% glycerol, and 0.5% NP-40 and protease inhibitor cocktail (Invitrogen, USA). The total protein were then separated on 10% SDS-PAGE gel and transferred to the nitrocellulose membranes. We used primary antibodies against, Thy-1 (1:2000, Santa Cruz Biotechnology, USA), ERK1/2 (1:1000, Cell Signaling Technology, USA), phospho-ERK1/2 (pERK1/2, 1:2000, Cell Signaling Technology, USA), PI3k3 /serine-threonine kinase (AKT, 1:1000, Cell Signaling Technology, USA), phosphor-AKT (pAKT, 1:1000, Cell Signaling Technology, USA), TrkB (1:1000, Cell Signaling Technology, USA), phosphorylated TrkB (1:200, Cell Signaling Technology, USA) and IGF1R (1:200, Santa Cruz Biotechnology, USA). Horseradish peroxidase-conjugated secondary antibodies (Bio-Rad, USA) were used and Actin was used as internal control. The western blots were visualized with an enhanced chemiluminesence system (Amersham Biosciences, USA) according to the manufacturer’s protocol. Band intensities normalized to the total protein immuno-precipitation under each control condition and quantified with an ImageJ software (NIH, USA).
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2

Retinal Protein Expression Analysis

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The eye balls were enucleated after sacrifice and frozen at −80°C and cryosectioned (Leica Cryostat, Buffalo Grove, IL, USA). Immunohistochemistry was performed to analyze the protein expression changes in the retinal layers viz. rhodopsin (Santa Cruz Biotechnology, Dallas, TX, USA), Thy1 (Santa Cruz Biotechnology), brain-derived neurotrophic factor (BDNF; Santa Cruz Biotechnology), and ciliary neurotrophic factor (CNTF; Santa Cruz Biotechnology). The sections were fixed using HistoChoice (Sigma-Aldrich) and then incubated with primary antibody (1:100 dilution) at 4°C overnight. Next day, the sections were kept in Cy3 labeled secondary antibody solution (1:200 dilution) (Jackson Immunoresearch, West Grove, PA, USA) for half an hour and nuclei were counterstained with 4′,6-diamidino-2-phenylindole (Sigma-Aldrich) (1:1,000 dilution) (Table 1). The sections were subsequently imaged under a confocal microscope to analyze the protein expression.
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Immunohistochemical Analysis of FLC Samples

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Liver and tumor sections from patients with FLC were fixed in 4% paraformaldehyde, embedded in paraffin, and sectioned (7‐μm sections). Immunohistochemistry for PKAc, ph‐S675‐β‐catenin, ki67, and post‐GPI attachment to proteins (PGAP1) was performed on FLC samples from primary liver tumors and lung metastasis.
List of antibodies used in this study: ph‐S675‐β‐catenin (Cell Signaling Tech; #D2F1),TCF4 (Cell Signaling; #C48H11), p300 (Invitrogen; sc: PAI‐848), Col3A1 (Cell Signaling Tech; #30565), secreted protein acidic and cysteine rich (SPARC) (Abcam; ab203284), Thy1 (Santa Cruz; sc: H‐110), versican (VCAN) (Invitrogen; MA5‐34654), HDAC1 (EDM Millipore Corp.; 2E10), DNAJB1 (Abcam; ab69402), E2F1 (Santa Cruz; sc:C20), p21 (Santa Cruz; sc: F5), PGAP1 (Invitrogen; sc‐PA5 72,340), RUN domain‐containing 1 (RUNDC1) (Abcam; sc‐AB 151583), HECT‐type E3 ubiquitin transferase (HACE1) (Abcam; sc‐133,637), cyclin D1 (Santa Cruz; sc‐753), cdc2 (Santa Cruz; sc‐954), CYP3A4 (Santa Cruz; sc‐30,621), β‐actin (Sigma; A5316), ph‐Ser33/37/Thr41‐β‐catenin (Cell Signaling; #8561), and ph‐Tyr333‐β‐catenin (Bioss; #12856R‐CY3).
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Immunohistochemical Analysis of Retinal Cells

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Three eyes 1 week after intravitreal injection of NR or three normal eyes were collected and fixed by immersion in 4% paraformaldehyde, dehydrated, and embedded in paraffin. Sections were made through the optic disc and blocked with 1% bovine serum (Roche Diagnostics GmbH, Mannheim, Germany). The primary antibodies were against NRK1 (1:100; LifeSpan BioSciences), neurofilament-L (a marker of nerve fibers; 1:100; Dako, Tokyo, Japan), or Thy-1 (a marker of RGC; 1:50; Santa Cruz Biotechnology, TX). The secondary antibodies were FITC-labeled or rhodamine-labeled antibodies (1:100; Cappel, Aurora, OH). The sections were mounted on slides in DAPI-containing medium with cover glass.
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