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81 protocols using sc 2005

1

Quantification of Amyloid-β and APOE

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Presence and relative levels of the amyloid-β peptides and APOE protein in each SDG fraction were assessed by dot-blot analysis on nitrocellulose membrane (Hybond P, Invitrogen), when the experiment was run on purified proteins in PBS. The blots were prepared by applying 2 µl of each fraction on the membrane. All fractions were applied on the same blot. The optical density of each dot was calculated by the ImageQuant™ TL software (v5, Invitrogen).
APOE protein was detected by the A1.4 antibody (1/8000, sc-13521, Santa Cruz Biotech.) and the secondary HRP-conjugated anti-mouse antibody (1/1000, sc-2005, Santa Cruz Biotech.) in
5%M-TBS-T
0.3%blocking solution (10 mM TBS containing 5% non-fat dry milk, 170-6404, Bio-Rad and 0.3% Tween-20). Amyloid-β peptides in the fractions were detected by the 6E10 mouse monoclonal antibody (1/1000, SIG-39320, Covance) and the secondary HRP-conjugated antibody (sc-2005, Santa Cruz Biotech.).
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2

Investigating Tat Protein Interactions

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J-Lat cells were cultured in the presence (P/I) or absence (CM) of mitogens for 6 h. Whole protein extracts were then digested with RIPA buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 1% Triton X-100, 1% sodium deoxycholate, 0.1% SDS, and 1 mM EDTA) supplemented with protease inhibitors (Sigma-Aldrich). Extracts before immunoprecipitation were used as controls to ensure that all samples contained the same starting material (input). Extracts were subjected to immunoprecipitation with a rabbit polyclonal anti-Tat antibody (ab43014, Abcam) (0.1 μg/mL) using magnetic protein G beads (Dynabeads, Invitrogen). Protein–protein interactions between the transcription factors NFAT2 and Tip60 and HIV-1 Tat were examined using Western immunoblotting with a mouse monoclonal antibody to NFAT2 (sc-7294, Santa Cruz) and a mouse monoclonal antibody to Tip60 (sc-166323, Santa Cruz). An extract of J-Lat cells expressing NFAT and Tip60 without antibody (-Ab) was used as a negative control. A goat anti-rabbit IgG HRP-conjugated antibody (sc-2004, Santa Cruz) and a goat anti-mouse IgG HRP-conjugated antibody (sc-2005, Santa Cruz) were used as secondary antibodies.
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3

Western Blot Analysis of Protein Expression

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Total protein was isolated from the cells and 20 μg of protein was dissolved in substrate-soluble buffer. The proteins were then separated by SDS-PAGE and transferred onto polyvinylidene difluoride (PVDF) membranes (IPFL00010; Millipore, Billerica, MA, USA). After blocking, the blots were probed with the primary antibodies overnight at 4°C. The antibodies used for western blot analysis included CK10 (1:1000, ab111447), CK14 (1:500, ab7800), CK19 (1:500, ab53119), integrin-β4 (1:500, ab128068), and mouse anti-human β-actin antibody (1:5000, ab6276) (all from Abcam). After washing, the membranes were incubated with secondary antibodies, which were goat anti-rabbit and goat anti-mouse IgG conjugated to horseradish peroxidase (sc-2004, 1:1000; sc-2005, 1:1000; Santa Cruz Biotechnology, Santa Cruz, CA, USA). Immunoreactive bands were detected by enhanced chemiluminescence (ECL) kit (PE-0010-100; Solarbio, Beijing, China) and imaged using the ImageQuant LAS 4000 system (GE Healthcare Bio-Sciences, Pittsburgh, USA).
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4

Western Blot Analysis of Lipid Metabolism Proteins

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Total cell lysates were prepared using radioimmunoprecipitation assay (RIPA) buffer (Sigma-Aldrich) supplemented with a protease inhibitor cocktail (Sigma-Aldrich) as well as Phosphatase Inhibitor Cocktails 2 and 3 (Sigma-Aldrich). Samples were separated on a 12% SDS-polyacrylamide gel and transferred to a nitrocellulose membrane. Membranes were hybridized with rabbit anti-adipose triglyceride lipase (ATGL; 2138, 1:1,000; Cell Signaling Technology), rabbit anti-phospho-hormone-sensitive lipase (HSL; Ser563; 4139, 1:1,000; Cell Signaling Technology), rabbit anti-HSL (4107, 1:1,000; Cell Signaling Technology), mouse anti-LXRα (ab41902, 1:1,000; Abcam), rabbit anti-LXRβ (ab28479, 1:500; Abcam), and mouse anti-GAPDH (MAB374, 1:80,000; Millipore) antibodies at 4°C overnight to detect expression, followed by 1-h incubation at room temperature with goat anti-mouse (sc-2005, 1:4,000; Santa Cruz Biotechnology) and goat anti-rabbit (P0448, 1:2,000; Dako) peroxidase-conjugated antibodies. Proteins were detected by chemiluminescence (Millipore).
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5

Western Blot Analysis of Oxidative Stress Markers

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Cell or tissue lysates with equal amounts of protein (40 μg) were mixed with loading dye, boiled for 5 min, separated on a denaturing 12.5-% SDS-polyacrylamide gel and transferred to Amersham™ Hybond™ 0.45 μm PVDF membrane (GE Healthcare, UK). The membrane was blocked in 5% dry milk or BSA in TBS buffer with 0.1% Tween (TBS-T) for 1 h and incubated overnight with antibodies against glutathione-S-transferase A3 (ab175246, Abcam), glutathione-S-transferase P1 (PA5-29601, Invitrogen), glutathione reductase (ab16801, Abcam), superoxide dismutase 2 (PA5-30604, Invitrogen), NAD(P)H quinone oxidoreductase 1 (PA5-19624, Invitrogen), pro-caspase 3 and active caspase 3 (ab13847, Abcam), or β-actin (4967, Cell Signaling) as a reference. Then, the membrane was washed twice with TBS-T and incubated with HRP-conjugated secondary antibody (ab6721, Abcam or sc-2005, Santa Cruz Biotechnology) at room temperature for 1 h, followed by several washings with TBS-T and deionized water. Protein bands were visualized by ChemiDoc XRS+ imaging system (Bio-Rad Laboratories, Hercules, CA) using chemiluminescence mode.
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6

Quantification of Adenosine A2B and HIF-1α Proteins

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We extracted protein samples from ~2.0×106 cells or 70 mg of frozen liver tissues. The samples were homogenized in lysis buffer (RIPA; Biosesang), quantified with BCA protein assay kit (Thermo Fisher Scientific, Inc.), and immunoblotted with anti-adenosine A2B receptor antibody (1:1,000 dilution; ab40002, Abcam) followed by rabbit anti-goat IgG HRP (1:20,000 dilution; A5420, Sigma-Aldrich); or anti-HIF-1α antibody (1:1,000 dilution; cat no. 610959, BD Biosciences) followed by goat anti-mouse IgG HRP (1;5,000; sc-2005, Santa Cruz Biotechnology). We also probed the nitrocellulose membranes with actin-peroxidase conjugate (1:20,000 dilution; A3854, Sigma-Aldrich). The protein signals were detected using an enhanced chemiluminescence solution (SuperSignal™ West Femto; Thermo Fisher Scientific, Inc.), and images were obtained using the ImageQuant LAS 4000 system (GE Healthcare Biosciences).
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7

Western Blot Analysis of EMT Markers

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Cells (please see below) were lysed by using lysis buffer for western blotting (P00l3, Beyotime) and loaded onto 10% sodium dodecyl sulphate-polyacrylamide gels and were then transferred onto polyvinylidene difluoride membranes (Millipore). The quantification of total protein was performed using a Pierce BCA Protein Assay kit (Thermo Fisher Scientific), and equal amounts of protein (30 μg) were used for analysis. Blots were blocked with 5% milk/TBST and incubated with primary antibodies (Twist1: 1:500, sc-15393, Santa Cruz Biotechnology; Slug: 1:1,000, 6591, Cell Signaling Technology; Snail: 1:1,000, ab53519, Abcam; Vimentin: 1:1,000, 2707-1, Epitomis; EphA2: 1:500, sc-924, Santa Cruz Biotechnology; VE-cadherin: 1:500, ab33168, Abcam; MMP2: 1:500, ab37150, Abcam; E-cadherin: 1:200, SC-8426, Santa Cruz Biotechnology; p-smad2/3: 1:500, sc-11769, Santa Cruz Biotechnology) at 4°C overnight, followed by incubation with secondary antibodies (goat anti-mouse IgG-HRP and goat anti-rabbit IgG-HRP, 1:2,000; sc-2005 and sc-2030; Santa Cruz Biotechnology) for 2 h at room temperature. Blots were developed using an enhanced chemiluminescence detection kit (Amersham Pharmacia Biotech). For protein loading analyses, p-actin antibody (1:1,000, P30002, Abmart) or GAPDH (1:2,000, ab9485, Abcam) was used.
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8

Western Blotting of Xenograft Proteins

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Western blotting was performed as previously described22 (link), 23 (link), 46 (link). The lysates from the xenografts or cell lines with different treatments were homogenized in RIPA lysis buffer using a homogenizer. The supernatants were collected by centrifugation (12,000 rpm at 4 °C for 25 min; Beckman GS-6R). Protein was resolved by electrophoresis and transferred onto polyvinylidene fluoride (PVDF) membranes (Millipore, Bedford, MA, USA). The membranes were probed with monoclonal HIF-1α (NB100–105, Novus biological, Littleton, CO, USA), Bax (2772 S, Cell signaling, Boston, MA, USA), Bcl-2 (3498S, Cell signaling), caspase-3 (9661S, Cell signaling), PARP (5625, Cell signaling), and PCNA (18197, Abcam, Cambridge, MA, USA), as well as p21 (Sc817, Santa Cruz, CA, USA), CDK4 (Sc70831, Santa Cruz), SP1 (ab27595, Abcam), HK2 (2772S, Cell signaling), PKM2 (4053S, Cell signaling), LDH-A (3582S, Cell signaling), and PDK1 (3820 S, Cell signaling). Following incubation with the primary antibody overnight at 4 °C, membranes were washed with Tris-buffered saline (pH 7.2) containing 0.05% Tween-20 and subsequently incubated with horse radish peroxidase (HRP)-conjugated anti-mouse (Sc-2005, Santa Cruz) or anti-rabbit (Sc-2357, Santa Cruz) secondary antibody for 1 h at room temperature. Bands of interest were analyzed using the ChemiDocTM Touch Imaging System (BIO-RAD, Hercules, CA, USA).
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9

Western Blot Analysis of Protein Targets

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Total proteins were isolated using RIPA lysis buffer (Beyotime, Shanghai, P.R. China). The protein concentration was measured using a BCA protein concentration determination kit (Beyotime). Samples with the same amount of protein were separated using sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (10%) and transferred onto polyvinylidene difluoride (PVDF) membranes (Millipore, Billerica, MA, USA). The membranes were then incubated with 5% skimmed milk at room temperature for 1 h to block the nonspecific sites. The membranes were incubated with antibody against IRF2 (1:1,000; SC-374327; Santa Cruz Biotechnology, Santa Cruz, CA, USA), CBX7 (1:1,000; SC-376274; Santa Cruz Biotechnology), and GAPDH (1:1,000; SC-47724; Santa Cruz Biotechnology) at 4°C overnight. The goat anti-mouse IgG–horseradish peroxidase-conjugated antibody (1:2,000; SC-2005; Santa Cruz Biotechnology) was then used to incubate with the membranes at room temperature for 1 h. Then the band signals were developed using an enhanced chemiluminescence detection kit (Beyotime). GAPDH was selected as the endogenous standard.
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10

Immunoblotting of Aortic Protein Expression

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Protein expression in thoracic aortas was determined by immunoblotting, as described previously [23 (link)]. Briefly, thoracic aortas were homogenized with T-PER tissue protein extraction reagent (Thermo-Pierce, 78510, Rockford, IL, USA) containing protease inhibitor cocktails (Sigma-Aldrich, P8340) and protein concentrations were determined by BCA Protein Assay Kit (Bio-Rad, 5000001, Hercules, CA, USA). Proteins from each sample (20 μg) were separated by 8%–12% Tris SDS-PAGE gel electrophoresis and transferred to polyvinylidene difluoride membranes (Bio-Rad Laboratories, Inc., 1620256, CA, USA). After blocking with 5% non-fat dry milk, membranes were incubated with anti-p-Akt (Ser473), anti-p-S6 Ribosomal Protein (Ser235/236), anti-Akt (C73H10), anti-S6 Ribosomal Protein (Cell Signaling Technology, 4058; 4856; 2938; 2217, Beverly, MA, USA), or anti-β-actin (AC-15) (Sigma-Aldrich, A5441) antibodies overnight at 4 °C, and incubated with the secondary antibodies (Santa Cruz, sc-2004; sc-2005, Santa Cruz, CA, USA) at room temperature for 1 h. Proteins were visualized with enhanced chemiluminescence reagents (Thermo-Pierce, Rockford, IL, USA) and the blots were exposed to hyper film. Results were quantified by using Quantity-one software (Bio-Rad).
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