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207 protocols using anti myc

1

Immunoprecipitation Methods for Protein Complexes

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Immunoprecipitations from TNT reactions were carried out using 4 μL of the reaction volume incubated with 2.5 μg anti-FLAG (Sigma, F1804), anti-ADAMTSL4 (Proteintech, 15304-1-AP), or anti-V5 (MBL, PM003) in 150 μl immunoprecipitation buffer (20 mM Tris-HCl [pH 7], 0.3 M NaCl, 2 mM EDTA, 1% NP-40 [IGEPAL® CA-630, Sigma] containing 0.2mM AEBSF Hydrochloride, (cat#101500, Calbiochem]) overnight at 4°C and then with 40 μl protein G Dynabeads for one hour. Protein complexes were washed three times in PBS and subsequently extracted with 1X SDS loading buffer for 3 minutes at 95°C.
Pull down of proteins from cell cultures was done by incubating 1 mg cell lysate with 5 μg anti-myc (Santa-Cruz, 9E10, sc-40), anti-V5 (MBL, PM003), or anti-His6 (Santa-Cruz, sc-803) in 1 ml immunoprecipitation buffer as described above.
Immunoprecipitation from conditioned medium was carried out by incubating 8 ml of medium with 5 μg anti-V5 (MBL, PM003), or anti-myc (Santa-Cruz, 9E10, sc-40) for 48 hours at 4°C and then with 40 μl protein G Dynabeads overnight. Protein complexes were washed three times in PBS and subsequently extracted with 1X SDS loading buffer for 3 minutes at 95°C.
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2

Protein Complex Identification via Co-IP

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Total cell lysate was collected with IP-lysis buffer (150 mM NaCl, 20 mM NaCl, 20 mM HEPES, pH 7.2, 10 mM NaF, 1 mM EDTA, 1% NP-40, 1 mM Na3V04, 1 mM PMSF, 1  DTT, and proteinase inhibitor cocktail) at 72 h, and subjected to immunoblotting with anti-myc (1:3000, Santa Cruz, CA, USA) and anti-HA (1:1000, Santa Cruz, CA, USA) monoclonal antibody. Co-immunoprecipitation was performed with 25 μl Protein A/G PLUS-Agarose (Santa Cruz, CA, USA) and anti-myc monoclonal antibody (1 μg) to pull-down the complex, which was then immunoblotted with anti-HA monoclonal antibody.
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3

Antibody Validation Protocols for Western Blotting

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Anti-ataxin-3: rabbit polyclonal, 1:10,000 [52 (link)]; mouse monoclonal 1H9, 1:1000, Millipore. Anti-HA: rabbit monoclonal, 1:1000, Cell Signaling Technology. Anti-MYC: mouse monoclonal 9E10, 1:1000, Santa Cruz Biotechnology; mouse monoclonal 9B11, 1:1000, Cell Signaling Technology. Anti-V5: rabbit monoclonal D3H8Q, 1:1000, Cell Signaling Technology.
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4

Immunofluorescence Staining of Phospho-Smad1/5/9

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Immunofluorescence was performed as described [61 (link)]. Generally, embryos were fixed in 4% Paraformaldehyde for overnight at 4 oC. Embryos were permeabilized by serial treatments with distilled water for 5 minutes at room temperature, cold acetone for 5 minutes at -20 oC, distilled water for 5 minutes at room temperature. For immunofluorescence of P-Smad1/5/9, all the steps before adding secondary antibody should be performed under 4 oC. Anti-Phospho-Smad1/5/9 (D5B10) Rabbit mAb (CST) was used at dilution 1:500. Anti-Myc (Santa Cruz) was used at dilution 1:500. Anti-rabbit Alexa Fluor 568 were used as secondary antibody (Molecular probes) at dilution 1:500. Embryos were counterstained with DAPI (5mg/ml in stock, 1:5000 diluted with PBS for working solution) for 1 hour. After immunofluorescence, the embryos were kept in 50% glycerol-50%PBS with 1mg/ml anti-fade reagent phenylenediamine (Sigma) avoid from light at 4 oC.
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5

Immunofluorescence Imaging of Protein Localization in Cells

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HeLa cells were seeded on coverslips and transfected with plasmids. After 48 h, cells were fixed with 4% formaldehyde, and incubated with anti-HA (Santa Cruz Biotechnology) or anti-Myc (Santa Cruz Biotechnology) antibody, followed by secondary goat anti-rabbit antibody coupled to Alexa488 (Invitrogen) and goat anti-mouse antibody coupled to Alexa546 (Invitrogen). The nucleus was stained with DAPI (Invitrogen). Coverslips were mounted and fluorescence was visualized with 40× magnification on a confocal laser scanning microscope (Carl Zeiss, Inc.), and pictures were analyzed with the ZEN 2009 software.
To count cells with mitotic defects, HeLa cells grown on coverslips were transfected with the indicated siRNA and plasmids for subsequent rescue. After fixation and permeabilization, cells were stained with monoclonal anti-β-tubulin-Cy3™ (Sigma) for 2 h, and the nucleus was counterstained with DAPI. Cells with mitotic defects were counted at 40× magnification with a fluorescence microscope (Nikon eclipse TE 2000-U).
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6

Protein Extraction and Analysis

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The clinical tissues were homogenized with tissue homogenization treatment and centrifuged at 12000 g/min at 4°C for purification of protein. The cells were lysed with RIPA lysis buffer containing the protease inhibitor cocktail (Yeasen, Shanghai, China) on ice for 30 min. The lysis was centrifuged at 4°C for 15 min, and the supernatant was collected and subjected to BCA assay for protein concentration evaluation. A total of 30 μg protein was subjected to SDS-PAGE and transferred to the PVDF membrane. The membrane was incubated with primary antibody overnight and subjected to the second antibody at room temperature for 1 h. The antibodies are as follows: anti-RORγ (Abcam, Cambridge, USA, ab78007), anti-GAPDH (Proteintech, USA, 60004-1-Ig), anti-Myc (Santa Cruz, CA, USA, 9E10), anti-HBx (Abcam, Cambridge, USA, ab203540), and anti-β-actin (Proteintech, USA, 23660-1-AP). The enhanced chemiluminescence (ECL) system (Yeasen, Shanghai, China) was used to visualize the protein band. The Quantity One software (Bio-Rad, CA, USA) was used to quantify protein expression.
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7

Immunocytochemistry of Transfected Neurons

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Transfected neurons were fixed at 3 days post-transfection. Immunocytochemistry was performed as described previously11 (link),51 (link). First, hippocampal neurons were fixed in 2% formaldehyde/1 × PBS/4% sucrose for 10 min followed by incubation in cold methanol (−20 °C) for 10 min. Fixed neurons were incubated with primary antibodies diluted in 1 × GDB (0.1% gelatin, 0.3% Triton X-100, 0.45 M NaCl, 17.7 mM sodium phosphate buffer, pH 7.4) in a humidified container overnight at 4 °C. Antibodies used and their dilution factors are: anti-GABAAR γ2 (1:250; Synaptic Systems), anti-GABAAR α2 (1:250; Synaptic Systems), anti-vGAT (1:800; Synaptic Systems), anti-NL2 (1:500; Synaptic Systems), anti-gephyrin (1:1000; Synaptic Systems), anti-β-Gal (Promega), and anti-myc (1:100; Santa Cruz Biotechnology).
Alexa 488, Cy3- or Cy5 conjugated secondary antibodies were used to visualize bound primary antibodies.
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8

Investigating SYK and NF-κB Signaling

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Unless stated otherwise, all chemicals were purchased from MilliporeSigma. Antibodies were obtained from the following sources: anti–p-Tyr (catalog 9411), anti–p-SRC (Y416) (catalog 2101), anti-SRC (catalog 2109), anti–p-SYK (Y525/526) (catalog 2710), anti-SYK (catalog 2712), anti–p-IκBα (catalog 2859), anti-IκBα (catalog 9242), anti-GAPDH (catalog 2118), anti-TLR2 (catalog 12276 for human and 13744 for mouse), anti–NF-κB (catalog 3033), and anti–NF-κB (catalog 8242) from Cell Signaling Technology; anti-MyD88 (catalog SAB3500472) and anti-FLAG M2 (catalog F3165) from MilliporeSigma; anti-Myc (catalog sc-40) and anti-actin (catalog sc-47778) from Santa Cruz Biotechnology; anti-HA (M180-3) from MBL International; anti–p-Tyr (4G10) (catalog 05-321) from Millipore; anti-PPP1R11 (ab171960) from Abcam; and anti-3BP2 (catalog H00006452-M01) from Abnova. Halt Protease and Phosphatase Inhibitor Cocktail was from Thermo Fisher Scientific. SYK inhibitor was from Millipore. PP2 and BMS 345541 were from Selleckchem.
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9

Antibody Characterization in Cell Lines

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GGTI-2133, FTI-277, and zaragozic acid were purchased from Sigma. Antibodies (Abs) used in this study were: anti-β-tubulin III (Tuj-1, Covance, MMS-435P), anti-sarcomeric α-actinin (Abcam, ab9465), anti-GAPDH (Millipore, MAB374), anti-synaptophysin (Invitrogen, 18–0130), anti-NF68 (Sigma, N5139), anti-Lamin B1 (Abcam, ab16048) and anti-MYC (Santa Cruz, sc-40). All antibodies were used in 1:1000 dilution.
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10

Western Blot Analysis of Signaling Proteins

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Western blot analysis was performed as described.[21 (link)] The primary antibodies used in this study were anti-pMTOR (Ser2448), anti-E2F2, anti-SLC2A2, anti-SLC2A3, and anti-SLC2A4 (Abcam, Cambridge, UK), anti-YY1, and anti-CCNA2 (Santa Cruz Biotechnology), anti-MYC, anti-CCNE1, anti-EIF4EBP1, anti-pEIF4EBP1 (Thr37/46), anti-RPS6KB1, and anti-pRPS6KB1 (Thr389) (Cell Signaling Technology, Danvers, MA), anti-SLC2A1 (Novus Biologicals, Littleton, CO), anti-HA-tag (Zymed Laboratories, South San Francisco, CA), and anti-ACTB (actin, beta) (Chemicon, Temecula, CA). The plasma membrane proteins were prepared with the Qproteome Plasma Membrane Protein Kit (Qiagen, Valencia, CA) following the manufacturer’s instructions.
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