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27 protocols using irdye 800 conjugated secondary antibody

1

Quantifying HA-DMT1 Phosphorylation

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To determine HA-DMT1 phosphorylation, cells transfected with HA-DMT1 or empty vector were scraped into ice-cold PBS and pelleted by centrifugation, then lysed in Nonidet-P40 (NP-40) buffer (40 mM HEPES, pH 7.4, 120 mM NaCl, 5% glycerol, 1% NP-40 and 1 mM EDTA, pH 8.0) containing phosphatase inhibitors (10 mM pyrophosphate, 10 mM β-glycerophosphate, 50 mM NaF and 0.5 mM orthovanadate) for 30 min at 4°C with rotation. Samples were centrifuged for 10 min at 15 000×g, and the protein concentration of the lysates was determined by the Bradford assay. The cell lysates were preincubated with anti-HA agarose (Pierce) overnight at 4°C with rotation and washed with TBS before protein elution at 95°C for 5 min. Eluates were electrophoresed on 4–20% gradient gels, transferred to PVDF membranes and the extent of HA-DMT1 phosphorylation was assessed by immunoblotting with mouse antiphosphoserine antibody (Millipore) followed by IRDye 800-conjugated secondary antibodies (Rockland Immunochemicals). Meanwhile, total cell lysates were immunoblotted with either anti-HA antibody or by antiactin antibody followed by IRDye800-conjugated secondary antibodies. After further washing, immunoreactivity was detected by an Odyssey Infrared Imaging System (Li-COR).
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2

Western Blot Analysis of CB1 and CB2

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Cells were washed twice with ice-cold PBS, and the total cell lysates were prepared in lysis buffer containing 150 mM NaCl, 1 mM EDTA, 50 mM Tris and 1% Triton containing a protease inhibitor cocktail (Complete Mini, Roche). Protein concentration was determined by the Bradford assay. Samples (25 µg) were separated by electrophoresis on 10% SDS–PAGE gels and transferred to PVDF membranes, and immunoblotted with rabbit anti-CB1 or -CB2 antibody (Cayman Chemical Company). The primary antibody was detected with IRDye 800-conjugated secondary antibodies (Rockland Immunochemicals, Inc.). After further washing, immunoreactivity was detected by an Odyssey Infrared Imaging System (Li-COR).
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3

Antibody-based Protein Expression Analysis

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The primary antibodies used were: anti-ITGA5 antibody (sc-136224) from Santa Cruz Biotechnology (Santa Cruz, CA, USA); anti-PARP antibody (#9532), anti-phospho(Ser473) and anti-total Akt antibody (#4060 and #9272, respectively), anti-phospho(Thr202/Tyr204) and anti-total Erk1/2 antibody (#9101 and #9102, respectively) from Cell Signaling Technology (Danvers, MA, USA); anti-beta-actin antibody (A5441) and Poly(2-hydroxyethyl methacrylate) (polyHEMA, P3932) from Sigma–Aldrich (St. Louis, MO, USA). The secondary antibodies were IR-Dye 800-conjugated secondary antibodies (Rockland, Gilbertsville, PA, USA). The Akt inhibitor (124005) and the ERK inhibitor (328007) were both from Calbiochem (La Jolla, CA, USA).
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4

Western Blot Analysis of Protein Extracts

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Protein from cultured cells and tumor tissues was extracted with radioimmunoprecipitation assay (RIPA) lysis buffer. Western blot analysis was performed as previously described.3 (link),12 (link) In brief, after nonspecific binding was blocked with 5% bovine serum albumin (BSA), membranes were incubated overnight at 4°C with primary antibodies against glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (sc-32233, Santa Cruz), Mincle (sc-390806, Santa Cruz), IL-6 (sc-32296, Santa Cruz), MMP13 (sc-30073, Santa Cruz), and CXCR4 (AB1848, Chemicon) and IRDye800-conjugated secondary antibodies (Rockland Immunochemicals). Signals were detected by the Odyssey imaging system (LI-COR Biosciences), and results were further quantified by ImageJ. The ratio of protein expression level was normalized against GAPDH expression.
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5

Quantitative Western Blot Analysis of APP and Reelin

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Immediately after harvest, one cerebral hemisphere per brain was lysed in 1% Nonidet P-40 (NP-40) STEN buffer [150 mM sodium chloride, 50 mM Tris, 2 mM EDTA, and 1.0% (v/v) NP-40]. Lysates were electrophoresed on 4–12% Bis-Tris Nu-Page gels (Invitrogen), transferred to nitrocellulose, and blocked using Odyssey blocking buffer (Licor) or 5% milk in phosphate buffered saline plus Tween. Samples were stored at −80 degrees Celsius with minimal freeze-thaw events. Western blotting was performed with anti-APP, C-terminal antibodies C7 and C9 (Rb; both 1:1,000; Selkoe Laboratory, Brigham and Women’s Hospital), N-terminal antibody APP597 (Rb; 1:1,000; IBL America, Minneapolis, MN) and the N-terminal Reelin monoclonal antibody G10 (Ms, 1:2,000, Abcam). GAPDH (Ms; 1:2,000, Millipore) was used as a protein loading control. IRDye680- and IRDye800-conjugated secondary antibodies (1:10,000; Rockland Immunochemicals) were used prior to analysis on the LiCor detection system. For Reelin, signal was detected using HRP-coupled goat anti-mouse antibodies followed by detection via enhanced chemiluminescence (SuperSignal West Dura Kit, LifeTechnologies).
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6

Estrogen Signaling and p38 MAPK Pathway

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17β-estradiol, SB203580 and MTT solution were purchased from Sigma-Aldrich (St. Louis, MO, USA). Resveratrol dimer was a kind gift of Professor X. Sun and coworkers (School of Pharmacy, Fudan University, Shanghai, China). The bicinchoninic acid (BCA) protein assay kit was obtained from Beyotime Institute of Biotechnology (Jiangsu, China). TRIzol reagent, expression vector kit with GFP and packaging mix were obtained from Invitrogen (Carlsbad, CA, USA). Lipofectamine 2000, Dulbecco's modified Eagle's medium (DMEM) and fetal bovine serum (FBS) were obtained from Gibco-BRL (Grand Island, NY, USA). Monoclonal anti-HIF-1α antibody, anti-ERα antibody and anti-ERβ antibody were from Santa Cruz Biotechnology, Inc. (Santa Cruz, CA, USA). Anti-p38 antibody and anti-p-p38 antibody were purchased from Cell Signaling Technology (Boston, MA, USA). IRDye800-conjugated secondary antibodies were procured from Rockland Immunochemicals (Gilbertsville, PA, USA).
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7

Western Blot Analysis of Inflammatory Proteins

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The proteins were extracted from the HRGECs using a RIPA lysis buffer and analyzed by western blot as described previously
[17 (link)]. Briefly, after blocking the nonspecific binding with 5% bovine serum albumin, the membranes were incubated with primary antibodies against TNF-α and transforming growth factor (TGF)-β1 overnight at 4°C. After washing, the membranes were incubated with IRDye 800-conjugated secondary antibodies (Rockland Immunochemicals, Inc., Gilbertsville, PA, USA), and the signals were detected using the Odyssey Infrared Imaging System (Li-COR Biosciences, Lincoln, NE, USA) and quantitated with Image J software (NIH). The protein ratio was normalized against the GAPDH and expressed as the mean ± standard errors of the mean (SEM).
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8

Immunoblotting Analysis of Connexin 43 and Myosin II

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Cultured BSMCs were lysed in detergent-based buffer (150 mM NaCl, 10 mM Tris/HCl, pH 7.4, 1 mM EDTA, 1 mM EGTA, 0.5% Nonidet P-40, 1% Triton X-100, 1 mM NaF, 1mM Na3VO4 and 1 Complete™ Mini protease inhibitor tablet, Roche). For each lane, 40 µg of protein was resolved by SDS/PAGE (10% gel). Resolved proteins were transferred on to nitrocellulose membranes, blocked in 3% BSA at room temperature and incubated with primary antibodies overnight at 4°C. Cx43 and NM-MHC-IIA (non-muscle myosin heavy chain II-A) were detected using polyclonal anti-Cx43 (1:5000 dilution; Sigma–Aldrich, C6219) and polyclonal anti-NM-MHC-IIA (1:1000 dilution; Covance PRB-440P) antibodies. The membranes were also probed for GAPDH (glyceraldehyde-3-phosphate dehydrogenase; anti-GAPDH antibody, 1:10000 dilution; Chemicon MAB374) as a protein loading control. Immunoreactive bands were revealed following a 1 h incubation with Alexa Fluor® 680 (red; 1:10000 dilution; Life Technologies) or IRDye 800-conjugated secondary antibodies (green; 1:10000 dilution; Rockland) and visualized using the Odyssey Infrared Imaging System (Li-Cor Biosciences). Band intensity was quantified using the Odyssey Infrared Imaging System.
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9

Protein extraction and Western blot analysis

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Protein from the renal cortex and mTEC was extracted using the radio-immunoprecipitation assay (RIPA) lysis buffer. The antibodies used were phospho-NK-kB p65 (Ser536) (#3033, CST), NF-κB p65 (#3034, CST), phospho-IKBα (Ser32) (#2859, CST), and IkBα (#9242, CST). IRDye800-conjugated secondary antibodies (Rockland Immunochemicals, Gilbertsville, PA) were used as secondary antibodies. Signals were detected using the LiCor/Odyssey infrared image system (LI-COR Biosciences, Lincoln, NE), and statistical analysis was performed using the Image J program.
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10

Quantitative Protein Expression Analysis

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Total proteins of tumour or normal (the skin of the same mouse) tissues were extracted by chilled RIPA lysis buffer (Pierce) and then subjected to the western blotting analysis with primary antibodies against CD31, VEGF, MMP-2, MMP-9, MMP-13, CXCR4, NKp46, p-Smad3, Smad3 (all from Santa Cruz Biotechnology) and E4BP4 (Cell Signaling) in 1:1,000, followed by incubation with the corresponding IRDyeTM800-conjugated secondary antibodies (1:10,000, Rockland Immunochemicals). β-Actin was used as an internal control. Expression levels of the proteins were detected by using LiCor/Odyssey infrared image system (LI-COR; Biosciences), and the band intensities were quantified with the Image J software (version 1.48, NIH, Bethesda). Images have been cropped for presentation; their full size images are presented in Supplementary Figs 15–20.
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