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109 protocols using anti myc antibody

1

Investigating Integrin-Mediated Signaling Pathways

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Anti-UNC5C (cat. no. ab106949) and integrin α6 (cat. no. ab20142 for immunoprecipitation and ab181551 for western blotting) antibodies were purchased from Abcam. Anti-phosphorylated (p)-Akt (cat. no. 4060; Ser473), Akt (cat. no. 4685), p-p38 MAPK (clone D3F9; cat. no. 4511), p38 MAPK (clone D13E1; cat.no. 8690), p-ERK1/2 (Thr202/Tyr204; cat. no. 9101), ERK1/2 (cat. no. 9102), Src (cloneL4A1; cat. no. 2110), p-Src (Tyr416; cat. no. 2101), FAK (cat. no. 3285) and p-FAK (clone D20B1; Tyr397; cat. no. 8556) antibodies were purchased from Cell Signaling Technology, Inc. Anti-α-tubulin (cat. no. T6199) and Flag (cat. no. F3040) antibodies were purchased from Sigma-Aldrich; Merck KGaA. Anti-myc antibody (cat. no. HT101) was purchased from Transgene SA. Anti-integrin-linked kinase (ILK; clone E-2, cat. no. sc-137221) and p-ILK antibodies (Thr173; cat. no. sc-130196) were purchased from Santa Cruz Biotechnology, Inc. Goat anti-mouse horseradish peroxidase (HRP)-conjugated immunoglobulin G (IgG; cat. no. G-21040) and goat anti-rabbit HRP-conjugated IgG (cat. no. A16096) were purchased from Pierce; Thermo Fisher Scientific, Inc.
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2

ACBD3 and Dexras1 Interaction Analysis

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GST or GST-tagged ACBD3 constructs were cotransfected with Dexras1-Myc constructs into HEK293T cells using PolyFect (Qiagen, Valencia, CA), with a transfection efficiency of greater than 90%. Cells were lysed 48 hr after transfection in buffer A (100 mM Tris [pH 7.4], 150 mM NaCl, 1% Triton X-100, 15% glycerol, 1 mM PMSF, 25 mg/ml antipain, 50 mg/ml leupeptin, 50 mg/ml aprotinin, 25 mg/ml chymostatin, and 25 mg/ml pepstatin). Lysates were precleared with pansorbin cells (Calbiochem, Billerica, MA), then 1 mg of total protein was incubated with Glutathione-Sepharose beads overnight at 4 C. Beads were washed with wash buffer (50 mM Tris [pH 7.4], 500 mM NaCl, 10 mM b-glycerophosphate) twice, then once with buffer A. Beads were quenched in sample buffer (100 mM Tris [pH 6.8], 10% glycerol, 250 mM b-mercaptoethanol, 2% sodium dodecyl sulfate, and bromophenol blue). Total protein (50 mg) was loaded as input. Rhes-Myc binding was examined using an anti-myc antibody (EMD Millipore, Billerica, MA) followed by incubation with anti-mouse secondary conjugated to horseradish peroxidase (HRP) (Jackson Immunoresearch Laboratories, West Grove, PA); blots were then stripped and probed with an anti-GST antibody conjugated to HRP to detect ACBD3. Pierce Chemiluminescence (Life Technologies, Grand Island, NY) was used to detect bands on the Western blot.
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3

Immunoprecipitation and Immunoblot Analysis

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MPFMV:FLAG was immunoprecipitated from cell lysate of N. benthamiana leaves expressing MPFMV:FLAG with EZview red anti-FLAG M2 affinity gel (Sigma-Aldrich) [52 (link)]. Immunoblot analysis was performed [52 (link)] using anti-FLAG M2 antibody (Sigma-Aldrich), anti-myc antibody (EMD Millipore), anti-Bip antibody (Santa Cruz Biotechnology, Inc.), anti-H+ATPase antibody (Agrisera) or anti-MPFMV antibody. Anti-MPFMV antibody, a polyclonal antibody against the mature region of MPFMV, was generated as described previously [52 (link)].
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4

Colorimetric Assay of GLUT4myc Expression

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A colorimetric assay of surface GLUT4myc was performed using the anti-Myc antibody (1:100) as described previously30 (link). EVs (10 μg of total protein) were administrated to L6 myotubes for 4 h following 2 h of serum starvation. The cells were washed once with PBS and then incubated with anti-Myc antibody (EMD Millipore, Billerica, USA). After incubation with the primary antibody, peroxidase-conjugated rabbit anti-mouse IgG (1:1000) was added for 30 min at 4 °C. The cells were washed and 1 mL of OPD reagent was added. The colorimetric reaction was stopped by adding 0.25 mL of 3N HCl. After 10 min, the optical absorbance of the supernatant was measured at 492 nm.
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5

Antibody Inventory for Cellular Imaging

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The following antibodies were used: anti-PCNA (Rabbit), anti-LaminB1 antibodies (Abcam, Cambridge, UK); anti-FLAG, anti-HA antibodies (Merck, Darmstadt, Germany); anti-PCNA (mouse), anti-RFC4 antibodies (Santa Cruz, Dallas, TX, USA); anti-Myc antibody (Merck, Darmstadt, Germany). The anti-human ATAD5 antibody was raised in rabbits using the N-terminal 1–297 amino acid fragment and was then affinity-purified [12 (link)].
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6

Characterizing Androgen Receptor Binding

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ChIP was performed using the chromatin immunoprecipitation linked PCR assay with the EZ-ChIP kit (Merck Millipore, Germany). Cross-linked chromatin was extracted from HeLa cells and EAhy926 endothelial cells transfected with the Myc-tagged AR expression plasmid pCMV-Myc-AR and immunoprecipitated using an anti-Myc antibody (Merck Millipore, Germany). Rabbit IgG was used as a negative control, whereas an anti-RNA polymerase II antibody (Merck Millipore, Germany) was used as a positive control. The precipitated DNA was used for PCR detection of the ARE bound by the AR and the promoter bound the RNA polymerase II. The PCR primers for the ARE include forward primer 5′-GCATATACCACTTCCTTGTTCTGAGCTG-3′ and reverse primer 5′-TCATATATTTCCACCTTGCACCATTTG-3′. The negative control for PCR was performed for a distal, non-ARE site using forward primer 5′-CTTCCCAGTTTACAGTATGTTGTTATAGCA-3′ and reverse primer 5′-GAGTTCTGCATTGTAACCATGTTTTTTT-3′. The PCR primers for the promoter (RNA polymerase II) included the forward primer 5′-GCAACTTCCTTGTTATATGCAAATGAAAAG-3′ and reverse primer 5′-CTGTTTCACTAGGGCCTGGGGCA-3′. Each ChIP assay was replicated at least three times.
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7

Gastric Cancer Cell Lines Cultivation

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The human GC cell lines AGS, MGC80-3, BGC-823, HGC-27, and MKN28 were obtained from the Cell Bank of Type Culture Collection of Chinese Academy of Sciences (Shanghai, China), and cultured in RPMI-1640 or Dulbecco’s modified Eagle medium (Sigma-Aldrich, St Louis, MO, USA) supplemented with 10% fetal bovine serum (Gibco, Grand Island, NY, USA) at 37 °C in a humidified atmosphere containing 5% CO2. Rabbit anti-human LOX-1 polyclonal antibody and horseradish peroxidase (HRP)-conjugated anti-GAPDH antibody were purchased from Proteintech (Chicago, IN, USA). Anti-Myc antibody was obtained from Merck Millipore (Billerica, MA, USA). Anti-ZO-1, -E-cadherin, -Vimentin, -Snail, -Akt, -GSK3β, -phospho-Akt (Ser473/Thr308) and -phospho-GSK3β (Ser9) antibodies were obtained from Cell Signaling Technology (Beverly, MA, USA). Anti-Twist antibody was from Santa Cruz Biotechnology (Santa Cruz, Dallas, TX, USA). The PI3K inhibitor, LY294002 was purchased from Selleck Chemicals (Houston, TX, USA).
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8

Detecting Protein Interactions via Co-IP

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Agrobacterium tumefaciens (GV3101) containing the 35S::mBES1-GFP-Flag expression vector was infiltrated alone or together with A. tumefaciens (GV3101) harboring 35S::AGB1-Myc-HA into the leaves of tobacco plants (Nicotiana benthamiana). About 48 h after infiltration, the transformed tobacco leaves were collected for the co-immunoprecipitation (Co-IP) assay (Gampala et al., 2007 (link)). Samples were homogenized in lysis buffer. After centrifugation, protein supernatant was incubated with 10 μl protein G magnetic beads (Invitrogen), which were previously incubated with 1 μl of anti-Myc antibody (Millipore) overnight at 4°C, for 1 h at 4°C. Then the beads were washed three times with lysis buffer and eluted into 1× SDS loading buffer, boiled for 5 min, and analyzed by Western blot. The mBES1–GFP–Flag pulled down by AGB1–Myc-HA was detected with anti-Flag antibody (Sigma) and AGB1–Myc-HA was detected with anti-HA antibody (Sigma). The primers used for plasmid construction for the Co-IP experiment are listed in Supplementary Table S1.
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9

ChIP-qPCR Analysis of SOG1-Myc Fusion

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ChIP was performed as described previously (Gendrel et al., 2005 (link)). pSOG1:SOG1-MYC seeds were germinated in 100 ml of liquid MS medium, and cultured under continuous light at 23°C with gentle shaking (50 rpm). After a 2 week culture period, bleomycin was added to the medium to a final concentration of 0.6 µg/ml, and the seedlings were cultured for 12 hr. Chromatin bound to the SOG1-Myc fusion protein was precipitated with anti-Myc antibody (Millipore). ChIP-qPCR was performed using immunoprecipitated DNA. Three independent ChIP experiments were conducted. To quantify the precipitated chromatin, gene-specific primers listed in Supplementary file 1 were used for real-time qPCR. PCR reactions were conducted with the Light Cycler 480 Real-Time PCR System (Roche) under the following conditions: 95°C for 5 min; 60 cycles at 95°C for 10 s, 60°C for 20 s and 72°C for 30 s.
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10

ChIP Protocol for C. albicans Transcriptome Analysis

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The Chromatin immunoprecipitation (ChIP) protocol was adapted from Nobile et al. (2012) [54 (link)]. C. albicans cells were grown in liquid YPD to stationary phase at 30°C, and then collected and washed with PBS twice. 5 x 106 cells were inoculated into 200 mL of YPD and cultured to OD600 = 0.4. Cells (10 mL) were transferred to a 9 mm-dish and treated in 5% CO2 at 37°C with shaking for 6 hours, and then fixed and cross-linked with 1% formaldehyde at room temperature. The cross-linking reaction was quenched after 20 min by adding glycine to a final concentration of 125 mM. The cells were harvested, resuspended in ice-cold lysis buffer, and homogenized with a bead beater. Sonication was performed with a Diagenode Biorupter (15 min, high setting, 30 sec on, 1 min off) to obtain chromatin fragments of an average size of 500–1000 bp. The chromatin was immunoprecipitated with 2 μg of anti-Myc antibody (Millipore, Inc.) and protein A-Sepharose beads (GE Healthcare). ChIP DNA was analyzed by quantitative real-time PCR assays.
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