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6 protocols using nbp1 40256

1

Western Blot Analysis of ER Stress

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Tissue lysates were separated by SDS-PAGE and transferred to 0.45 μm polyvinylidene difluoride membranes (Immobilon, Millipore. Merck KGaA, Darmstadt, Germany). Blots were incubated with antibodies directed against CD36 (NB400-144), ATF6 (NBP1-40256), and CHOP (NB600-1335) purchased from Novus Biologicals (Bio-Techne LD-R&D Systems Europe Ltd., Abingdon, UK). Equal loading of protein in each lane was verified by β-actin (A5441, Sigma–Aldrich, Merck KGaA, Darmstadt, Germany).
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2

Investigating Protein Homeostasis Regulators

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Livers were homogenized and lysed in a solution containing 20 mM Tris (pH 7.5) 150 mM NaCl, 1 mM EDTA, 1 mM EGTA, 1% Triton X-100, 2.5 mM sodium pyrophosphate, and 1 mM sodium orthovanadate. Subcellular fractions were obtained using Subcellular Protein Fractionation Kit for Tissues (Thermo Fisher Scientific). Immunoprecipitation was performed with each antibody using Capturem IP & Co-IP kit (Takara). Samples were separated by SDS-PAGE using 4 to 12% Bis-Tris gel (Bio-Rad) and transferred to a polyvinylidene difluoride membrane (Bio-Rad). Membranes were immunoblotted with each antibody. Amersham ECL prime (GE Healthcare Life Sciences) and ImageQuant LAS 4000mini (GE Healthcare Life Sciences) were used for the detection and quantification. Antibodies used in the present study are as follows: SREBP1 (ab3259; Abcam), VCP (ab11433; Abcam), S1P (ab140592; Abcam), SREBP2 (ab30682; Abcam), CHOP (2895; Cell Signaling Technology), BiP (3177; Cell Signaling Technology), β-actin (3700; Cell Signaling Technology), RHBDL4 (20869-1-AP; Proteintech), TBP (22006-1-AP; Proteintech), gp78 (16675-1-AP; Proteintech), HRD1 (13473-1-AP; Proteintech), Ubiquitin (10201-2-AP; Proteintech), carbohydrate-responsive element–binding protein (NB400-135; Novus Biologicals), ATF6 (NBP1-40256; Novus Biologicals), and normal mouse IgG (sc-2025; Santa Cruz Biotechnology).
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3

Antibody-Based Protein Expression Analysis

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Primary antibodies used in this study were ATF6 (100 ng/mL, NBP1‐40256, Novus Biologicals), CHOP (C/EBP‐homologous protein) (1:10.000, 2895, Cell Signaling, Danvers, MA), GRP78 (70 ng/mL, 11587‐1‐AP, Proteintech, Rosemont, IL), IRE1α phosphorylated at Ser724 (200 ng/mL, MBS9610512, MyBioSource, San Diego, CA), IRE1α (40 ng/mL, sc‐390960, Santa Cruz Biotechnology, Dallas, TX), eIF2α phosphorylated at Ser51 (1:10.000, 3398, Cell Signaling), eIF2α (1:10.000, 2103, Cell Signaling), GAPDH (100 ng/mL, MAB374; Sigma‐Aldrich, St. Louis, MO), and β‐actin (6.1 ng/mL, 4970; Cell Signaling Technology).
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4

Western Blot Analysis of EMC3, ATF6, and α-Tubulin

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Retinas were homogenized in radioimmunoprecipitation assay buffer (RIPA) lysis buffer. After ultrasound and adjustment of protein concentrations, equal amounts of protein were loaded into sodium dodecyl sulfate-polyacrylamide gels. Standard Western blotting procedures were performed. EMC3 antibody (mouse, 1:500; HPA042372; Sigma-Aldrich), cyclic AMP-dependent transcription factor ATF-6 alpha (ATF6) antibody (rabbit, 1:500; NBP1-40256; Novus Biologicals), and α-tubulin antibody (mouse, 1:1000; 660331-1-lg; ProteinTech Group, Rosemont, IL, USA) were incubated overnight at 4°C. The samples were then incubated with the IRDye Secondary Antibody (LI-COR; Biosciences, Lincoln, NE, USA), and signals were visualized using a near-infrared imaging system (Odyssey CLX, LI-COR; Biosciences) and quantified using the ImageJ software. The α-tubulin was used as a loading control. All the original Western blot bands were displayed (Supplementary Fig. S2).
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5

Studying ER Stress Signaling Pathways

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Murine recombinant insulin-like growth factor-1 (IGF-1) was purchased from PeproTech (Rocky Hill, NJ). Thapsigargin was obtained from Applichem (St Louis, MO), tunicamycin from Sigma (St Louis, MO) and brefeldin A from TOKU-E (Bellingham, WA). mTOR and PERK inhibitors were purchased from LC Labs (Woburn, MA) (rapamycin), Selleckchem (Houston, TX) (WYE125132, GSK2656157), Abcam (Cambridge, UK) (PP242) and from GlaskoSmith and Kline (Middlesex, UK) (GSK2126458). Antibodies against phospho-PERK (Thr980) (No.3179), PERK (No. 3192), phospho-eIF2α (Ser51) (No. 3597), eIF2α (No.2103), phospho-p70S6K1thr389 (No. 9234), p70S6K1 (No. 9202) and cleaved-caspase3 (No. 9664) were purchased from Cell Signaling Technology (Beverly, MA). Phospho-4E-BP1 (phosphorylation on Thr45; ab68187), and 4E-BP1 (ab2606) were from Abcam (Cambridge, UK). ATF6 clone 70B1413.1 were from Abcam (Cambridge, UK; ab11909) and Novus Biological (Littleton, CO; NBP1-40256). Antibodies against CHOP (SC-575), ATF4 (SC-200), GADD34 (SC-8327) and XBP1 (SC-7160) came from SantaCruz Biotechnology (Santa Cruz, CA) and BiP (610978) from BD Laboratories (Franklin Lakes, NJ). Antibody against α-tubulin was from Sigma-Aldrich (St. Louis, MO).
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6

Western Blot Analysis of UPR Markers

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Tissue lysates were separated by SDS-PAGE and transferred to 0.45 μm polyvinylidene difluoride membranes (Immobilon, Millipore. Merck KGaA, Darmstadt, Germany). Blots were incubated with antibodies directed against ATF6 (NBP1-40256), XBP-1 (NBP1-75514), CHOP (NB600-1335), dynamin related protein 1 (DRP-1; NB110-55288) and p62 (NBP1-48320) purchased from Novus Biologicals (Bio-Techne LD-R&D Systems Europe Ltd, Abingdon, UK); rabbit polyclonal antibodies against Beclin 1 (PA1-16857) and LC3A/LC3B (PA1-16931)
were obtained from Pierce (ThermoFisher Scientific). Equal loading of protein in each lane was verified by β-actin (A5441, Sigma Aldrich).
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