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7 protocols using a32961

1

Protein Interactions via Coimmunoprecipitation

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Coimmunoprecipitation was performed as described previously.24 (link) Briefly, cells were lysed in immunoprecipitation buffer (50 mmol/L Tris-HCl, pH 7.5, 100 mmol/L NaCl, 2 mmol/L EDTA, 1% NP40) supplemented with protease and phosphatase inhibitors (A32961; Thermo Fisher). Proteins were incubated with antibodies for 3 hours at 4°C. After that, 30 µL of preequilibrated Dynabeads protein G (10003D; Bio-Rad) was added and incubated overnight at 4°C. The beads were washed 5 times with immunoprecipitation buffer before eluting with 2× Laemmli loading buffer and analyzed by Western blotting.
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2

Protein Expression Analysis in Cells

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Tissue or cell extracts were prepared in RIPA lysis buffer (89900, Thermo Fisher Scientific) supplemented with protease and phosphatase inhibitor (A32961, Thermo Fisher Scientific). Lysates were cleared by centrifugation. Supernatant proteins were mixed with LDS Sample Buffer (NP0007, Thermo Fisher Scientific), separated by SDS-PAGE and transferred to nitrocellulose membranes (1704270, BioRad, Hercules, CA, USA). Membranes were probed with the following primary antibodies: anti-SMYD2 (sc-393827, Santa Cruz Biotechnology, Dallas, TX, USA), anti-TMPRSS2 (ab109131, Abcam, Cambridge, UK), and HRP-linked β-actin (ab49900, Abcam).
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3

C2C12 Cell Protein Expression Analysis

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C2C12 cells were seeded at 2 × 105 cells/cm2 into a 6 cm dish, and cell lysates were collected after VV stimulation from days 1 to 3. RIPA Lysis and Extraction Buffer (89900, Thermo Fisher Scientific Inc., Waltham, MA, USA) containing protease and phosphatase inhibitor (1:100; A32961, Thermo Fisher Scientific Inc., Waltham, MA, USA) was used to extract the cell lysate. Western blot analysis was performed with primary antibodies against stathmin (1:1000), decorin (1:1000), Col-I (1:500), FGF7 (1:1000), TGFBr1 (1:500) and PAK3 (1:500) (Abcam Inc., Cambridge, MA, USA), pAKT (1:500), AKT (1:2000), MyoD (1:1000) and myogenin (1:500) (Cell Signaling Inc., Danvers, MA, USA), β-actin (1:10,000) (Arigo Biolaboratories Corp., TE Huissen, Netherlands), which were incubated with the membranes at 4 °C overnight. After being washed 3 times for 15 min each, the membranes were incubated with an HRP-conjugated goat antibody anti-mouse or anti-rabbit IgG secondary antibody (Arigo Biolaboratories Corp., TE Huissen, Netherlands) for 1 h at RT. The proteins were detected using an ECL substrate kit (Abcam Inc., Cambridge, MA, USA). Band intensity was quantified by using ImageJ software (National Institutes of Health, Bethesda, MD, USA). Intensity data were normalized to GAPDH and indicated controls for the target protein fold changes calculation.
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4

Protein Fractionation and Western Blot Analysis

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Proteins were prepared with radioimmunoprecipitation assay buffer (50 mmol/L Tris-HCl, pH 7.4, 150 mmol/L NaCl, 1 mmol/L EDTA, 0.25% sodium deoxycholate, 0.1% SDS) supplemented with protease and phosphatase inhibitors (A32961; Thermo Fisher). Nuclear and cytoplasmic fractions were isolated using a kit according to the manufacturer’s instructions (78835; Thermo Fisher). A total of 20 to 40 µg of proteins were separated using Criterion gels (Bio-Rad) and transferred to nitrocellulose membranes using the Trans-Blot Turbo Blotting System (Bio-Rad). The membranes were then blocked with 5% nonfat milk or bovine serum albumin, followed by incubation with primary antibodies overnight at 4°C. After 3 washes, the membranes were incubated with secondary antibody and scanned with an Odyssey CLx Imaging system (LI-COR Biosciences). The following antibodies were used: anti-ETS2 (sc-365666; Santa Cruz Biotechnology), anti-phospho-ETS2 (44-1105G; Thermo Fisher), anti-GAPDH (10R-G109a; Fitzgerald), anti-RCAN1.4 (D6694; Sigma), anti-MKP3 (sc-137246; Santa Cruz Biotechnology), anti-lamin A/C (2032; Cell Signaling), anti-NFATc1 (nuclear factor of activated T cells 1; MA3-024; Thermo Fisher), anti-GFP (green fluorescent protein; A-11120; Invitrogen), anti-FLAG (7425; Sigma), anti-Myc (2276; Cell Signaling), anti-Erk1/2 (9107; Cell Signaling), and anti-phospho-Erk1/2 (9101; Cell Signaling).
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5

Protein Extraction and Western Blot Analysis of SKNBE(2) Xenograft Tissue

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SKNBE(2) xenograft tissue (20–30 mg) was homogenized with an Ultra-Turrax homogenizer (IKA) in 300 µL of RIPA lysis buffer (MFCD02100484, Sigma-Aldrich, St. Louis, MO, USA) supplemented with protease/phosphatase inhibitors (A32961, Thermo Scientific, Rockford, IL, USA) and 1 mM EDTA. The homogenates were centrifuged at 4 °C for 10 min, and the supernatant was collected. A total of 15 µg of protein was used for Western blot analysis. The primary antibodies were diluted in tris-buffered saline 0.5% Tween-20 (TBS-T) and 10% blocking reagent (11921673001, Roche, Mannheim, Germany). The following antibodies were used: heat shock protein A6 (HSPA6) (1:1000, 13616-1-AP, Proteintech, Wuhan, China), carnitine palmitoyltransferase 1A (CPT1A) (1:1000, 12252, Cell Signaling, Danvers, MA, USA), voltage-dependent anion channel (VDAC) (1:1000, ab15895, Abcam, Cambridge, UK), and β-actin (1:2000, ab8227, Abcam, Cambridge, UK). Horseradish peroxidase-labelled secondary antibodies were used (K400311-2, Dako, Glostrup, Denmark). The band densitometry was calculated using Image Lab Software 5.2.1 (Bio-Rad, Hercules, CA, USA) and normalized to β-actin.
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6

Immunoblotting for NOTCH3 in Meningioma

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Meningioma cells for immunoblotting were lysed in 1% SDS in 100mM pH 6.8 Tris-HCL containing protease and phosphatase inhibitor (A32961, Thermo Scientific), vortexed at maximum speed for 1min, rocked at 4°C for 5min, and centrifuged at 4°C for 15min at 15000×g. Supernatant protein quantification was performed using BCA assays (23225, Pierce). 20μg of lysate from each cell line was boiled for 15 min in Laemmli reducing buffer. Proteins were separated on 4–15% TGX precast gels (5671084, Bio-Rad), and transferred onto ImmunBlot PVDF membrane (1620177, Bio-Rad). Membranes were blocked in 5% TBST-milk, incubated in primary antibodies, washed, and incubated in secondary antibodies. Membranes were subjected to immunoblot analysis using Pierce ECL substrate (32209, Thermo Fischer Scientific). Primary antibodies recognizing NOTCH3 (5276, Cell Signaling, 1:1000) or GAPDH (8245, Abcam, 1:5000) and secondary antibodies recognizing mouse (7076, Cell Signaling, 1:2000) or rabbit (7074, Cell Signaling, 1:2000) epitope were used.
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7

Quantifying Aortic Plaque Cytokines

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Plaques from Ldlr-/- mice fed WD for 20 weeks and treated or not with ApoB ASO for 3 weeks were carefully scraped out from the aortic wall, placed in a tube containing 100 μL PBS and protease/phosphatase inhibitor (A32961, Thermo Fisher Scientific) and weighed. Plaques were manually homogenized until no pieces were apparent (~2 min). Concentrations of CCL2, IL-4, and IL-13 in suspensions were measured using a custom mouse LEGENDplex assay (Biolegend).
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