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12 protocols using anti myc tag

1

Immunoprecipitation of Protein Complexes

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Cells were transiently transfected with the appropriated constructs and harvested 24 h later. Lysate preparation and subsequent immunoprecipitation were performed as described previously with minor changes (Tardat et al, 2015). Briefly, the lysates were cleared by centrifugation before pre‐clearing with 50 μl of mouse IgG agarose beads (Sigma) for at least 1 h at 4°C with rotation. After centrifugation, 25 μl of mouse anti‐Flag M2 agarose beads (Sigma) were added to the supernatant and allowed to precipitate overnight at 4°C with rotation. Beads were pelleted by centrifugation, washed three times, and resuspended in SDS buffer. For the analysis of immunoprecipitation, the proteins were separated by SDS–PAGE and detected with the following antibodies: anti‐Flag (Sigma, Cat#F1804), anti‐GFP (Roche, Cat#11814460001), anti‐Histone H3.3 (Millipore, Cat#09‐838), anti‐H3K27me3 (Cell Signaling, Cat#9733), anti‐Myc Tag (Abcam, Cat#Ab9132), and anti‐RNF2 (Active Motif, Cat#39663). For immunoblots, anti‐αTubulin (Sigma, Cat#T9026) was used as a loading control.
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2

Subcellular Protein Fractionation and Analysis

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Cytoplasmic and nuclear fractionation was achieved by first lysing the cells in buffer A (HEPES 10 mM (pH 8.0), KCl 10 mM, MgCl2 1.5 mM, DTT 1mM), centrifugation and recovering the supernatant. The cell pellet was re-suspended in buffer B (HEPES 20 mM (pH 8.0), MgCl2 1.5 mM, KCl 400 mM, NaCl 40 mM, EDTA 0.2 mM, DTT 1 mM, glycerol 25%) to lyse the nuclear envelope and nuclear proteins were extracted. Protein content was determined by a Bradford Assay (#500-0006; Bio-Rad) with BSA as a standard. 5μg of cytoplasmic and nuclear protein was analysed by electrophoresis on a mini protean TGX Precast gel (Bio-Rad). Primary antibodies used were anti-Myc-tag (AB13836; Abcam), anti-α-Tubulin (#3873; Cell Signaling) and anti-Histone H3 (06-599; Millipore). Secondary antibodies used were anti-rabbit and anti-mouse IgG HRP-linked (NA93IV; GE Healthcare). Chemiluminescence signal was detected using an ECL-kit (170-5060; Bio-Rad).
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3

Evaluating Mitochondrial and Epithelial Markers

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Metformin (cat# S5958), Gboxin (cat# S8828) and S‐Gboxin (cat# S0096) were purchased from Selleck; Protein A/G beads were purchased from GE (GE Healthcare, cat# 17‐0963‐03) or Millipore (Millipore, cat# 16‐266); Anti‐FLAG® M2 Affinity Gel (cat# A2220) was purchased from Sigma‐Aldrich. The antibodies used for immunoblotting or otherwise noted are listed as follows: anti‐β‐actin (cat# sc‐69879, 1:2,000 dilution) was purchased from Santa Cruz Biotechnology; anti‐TOMM34 (cat# ab230103, 1:1,000 dilution) was purchased from Abcam; anti‐Myc‐tag (cat# 2278, 1:1,000 dilution), anti‐ZO‐1 (cat# 9782, 1:1,000 dilution), anti‐E‐cadherin (cat# 9782, 1:1,000 dilution), anti‐Vimentin (cat# 9782, 1:2,000 dilution), anti‐Claudin‐1 (cat# 9782, 1:1,000 dilution), and anti‐FLAG‐tag (cat# 14793 S, 1:1,000 dilution) were purchased from Cell Signaling Technology; anti‐ATP5B (cat# A5769, 1:2,000 dilution), anti‐MT‐ND1 (cat# A18316, 1:2,000 dilution), anti‐MT‐ND2 (cat# A17968, 1:2,000 dilution), anti‐MT‐ND3 (cat# A17969, 1:2,000 dilution), anti‐MT‐ATP6 (cat# A17960, 1:2,000 dilution), anti‐MT‐ATP8 (cat# A17890, 1:2,000 dilution), and anti‐MT‐CO3 (cat# A17891, 1:2,000 dilution) were purchased from ABclonal Technology.
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4

Western Blot Analysis of Transfected HEK293 Cells

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HEK293 cells were transfected in 6-well plates and cultured for 48 h. Cells were lysed for 10 min at 4 °C with 100 mM Tris pH 7.5, 150 mM NaCl, 10 mM EDTA, 0.2% Triton X-100, 1% PMSF, and protease inhibitor cocktail. Cell lysates were cleared by centrifugation at 10,000×g for 3 min at 4 °C. Proteins were resolved on 10% SDS-polyacrylamide gels and transferred to PVDF membranes using a TransBlot Turbo Blotting apparatus (Bio-Rad). Membranes were blocked in PBS containing 5% milk and 0.1% Tween-20 and incubated overnight at 4 °C with primary antibody. The following antibodies were used: anti-GFP (Clontech cat. no. 632380, 1:8000, for YFP constructs); anti-Myc tag (Abcam cat. no. ab9106, 1:1000); and anti-β-actin (Sigma cat. no. A5441, 1:10,000). After washing, membranes were incubated with horseradish peroxidase-conjugated goat anti-mouse or anti-rabbit IgG for 45 min at room temperature. Proteins were visualized using Novex ECL Chemiluminescent Substrate Reagent Kit (Invitrogen) and a ChemiDoc XRS+ imaging system (Bio-Rad).
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5

Western Blotting of Protein Extracts

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Total protein extracts were obtained using the lysis buffer (120 mM NaCl, 20 mM Tris-HCl pH 7.5, 2% Nonidet P40) completed with a mix of proteases and phosphatases inhibitors. 80 μg of extracted proteins were separated by SDS-PAGE and then transferred onto PVDF membranes (Merck Millipore, Darmstadt, Germany). Membranes were blocked with BSA or 5% not-fat milk and then incubated with the following antibodies: anti-myc tag (ab9132, Abcam, Cambridge, UK), anti-MPPED2 (H00000744-D01P, Abnova, Taipei City, Taiwan), anti-PTEN (ab32199, Abcam), anti-pospho-Akt (Ser473) (#4051, Cell Signaling, Danvers, MA, USA), anti-Akt (#92725, Cell Signaling). To normalize the amount of protein loaded, the membranes were incubated with anti-GAPDH (Santa Cruz Biotechnology Inc., Santa Cruz, CA, USA) and anti-β-Actin protein (Sigma-Aldrich). Filters were then incubated with horseradish peroxidase-conjugated secondary antibody (1:3000) for 1 h at room temperature and the signals were detected by western blotting detection system (ECL).
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6

Immunoprecipitation and Immunoblot Analysis

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HEK293T cells were seeded in 6-well plates and transfected with the indicated plasmids. After 24-h incubation, cells were scraped and resuspended in Pierce IP Lysis Buffer (Thermo Fisher Scientific, USA) supplemented with protease inhibitor cocktail (Roche). Cell debris was removed by centrifugation (16,000 ×g, 4°C, 15 min). Antibodies were added and incubated with 50 μl protein A magnetic beads (SureBeads, Bio-Rad, USA) with rotation. The beads were washed extensively with PBS supplemented with 0.1% Tween 20. Beads probed with appropriate antibodies were incubated with 300 μg proteins 4°C with rotation. Proteins were analyzed by immunoblot analysis. Protein samples were probed with the following primary antibodies: anti-FLAG tag (1:2000; Fujifilm Wako Pure Chemical Corporation, Japan), anti-MYC tag (1:2000; Abcam, UK)
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7

Western Blot Analysis of Protein Targets

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RIPA buffer (Sigma-Aldrich) plus a protease and phosphatase inhibitor cocktail (Roche, Basel, Switzerland) was used to lyse cells as previously described [18 (link)]. Proteins were loaded onto SDS-PAGE gels, transferred onto polyvinylidene difluoride membranes, and blocked with 5% skim milk in Tris-buffered saline supplemented with 0.1% Tween-20 (TBS-T) for 1 h at room temperature. The membranes were incubated overnight with primary antibodies at 4 °C. The following antibodies were used; Anti-FLAG tag (Wako), Anti-MYC tag (Abcam), Anti-GFP (Santa Cruz), Anti-Tubulin or β-actin antibodies (Abgent). Anti-pSTAT1/STAT1, Anti-HA tag, Anti-HIS tag, Anti-MYC tag, Anti-MDA5, Anti-RIG-I, Anti-pTBK1/TBK1, Anti-pIRF3/IRF3, Anti-MxA, Anti-OAS1, and Anti-RNaseL antibodies were from Cell Signaling Technology. Anti-SARS-CoV/SARS-CoV-2 Nucleocapsid Antibody (Sino Biological), while Anti-IFV NP antibody and Anti-ZIKV E antibody were purchased from GeneTex. The blots were washed with TBST for three times and incubated with HRP-conjugated secondary antibodies (Cell Signaling Technology, Danvers, MA, USA). Proteins were visualized with ECL Western Blotting Substrate (Thermo Fisher Scientific, Waltham, MA, USA). Densitometry to quantify immunoblot bands was performed using ImageJ software.
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8

Quantifying Protein Expression via Western Blot

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Western blot was applied to analyze protein expression. In brief, denatured protein samples (30 µg) were separated by 12% SDS-PAGE, transferred to PVDF membranes (EMD Millipore), blocked in 5% skimmed milk (Beijing Solarbio Science & Technology, Co., Ltd.) for 2 h at room temperature, washed with PBS containing Tween-20 (PBST) and incubated with primary antibodies [total OXPHOS human WB antibody cocktail (cat no. ab110411); anti-myc tag (cat no. ab206486); anti-Flag (cat no. ab205606); and anti-6×His tag (cat no. ab18184); all 1:1,000 dilution; Abcam] at 4°C overnight on an orbital shaker. PVDF membranes were then washed with PBST and incubated with horseradish peroxidase-conjugated anti-mouse IgG (cat no. sc-2005; 1:1,000 dilution; Santa Cruz Biotechnology, Inc.) at room temperature for 1 h prior to washing with PBST and adding a working solution of Enhanced Chemiluminescence Reagent Kit (Beyotime Institute of Biotechnology). Membranes were imaged using the iBright FL1000 Imaging System (Invitrogen; Thermo Fisher Scientific, Inc.). Image J software 1.53a (National Institutes of Health) was used to quantify the gray value of western blot bands and the protein expression level was normalized as the gray value of the target protein/the loading control protein.
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9

Antibody Purchase and Validation Protocol

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Anti‐Arf1 antibody (#10790‐1‐AP and #20226‐1‐AP), anti‐Rab35 antibody (#11329‐2‐AP), anti‐HDAC6 antibody (#16167‐1‐AP), anti‐NAT10 antibody (#13365‐1‐AP), anti‐Ran antibody (#10469‐1‐AP), anti‐TPX2 antibody (#11741‐1‐AP), anti‐Myt1 antibody (#67806‐1‐lg), anti‐GAPDH antibody (#60004‐1‐lg), and anti‐α‐tubulin antibody (#11224‐1‐AP) were purchased from Proteintech (Rosemont, IL, USA). Anti‐GM130 antibody (#DF7556) was purchased from Affinity Biosciences (Cincinnati, OH, USA). Anti‐Aurora A antibody (#AF1708) was purchased from Beyotime (Shanghai, China). Anti‐Plk1 antibody (#37‐7000) was purchased from Invitrogen (Carlsbad, CA, USA). Anti‐Ac‐tubulin antibody (#T7451), anti‐α‐tubulin‐FITC antibody (#F2168), and Hoechst 33 342 were purchased from Sigma–Aldrich (St. Louis, MO, USA). Anti‐Myc tag (#ab18185), Alexa Fluor 594 Goat Anti‐Rabbit IgG (H + L) (#ab150080), Alexa Fluor 594 Goat Anti‐Mouse IgG (H + L) (#ab150116), anti‐CDK1 antibody (#ab18), anti‐cyclin B1 antibody (#ab181593), and Anti‐GM130 antibody (#ab52649) were purchased from Abcam (Cambridge, UK). Anti‐phospho‐Aurora A (Thr288)/Aurora B (Thr232)/Aurora C (Thr198) antibody (#2914T) and antiactin antibody (#3700) were purchased from Cell Signaling Technology (Danvers, MA, USA). Horseradish peroxidase–conjugated goat antirabbit/mouse antibodies (CW0103/CW0102) were purchased from CWBIO (Beijing, China).
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10

Western Blot Analysis of Protein Expression

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HEK293 cells were transfected in 6-well plates and cultured for 48 h. Cells were lysed in 300 μL of Laemmli sample buffer containing 10% Tris(2-carboxyethyl)phosphine hydrochloride (TCEP) and incubated for 10 min at 95 °C. Proteins were resolved on 10% SDS-polyacrylamide gels and transferred to PVDF membranes using a TransBlot Turbo Blotting apparatus (Bio-Rad). Membranes were blocked in PBS containing 5% milk and 0.1% Tween-20 and incubated overnight at 4 °C with primary antibody. The following antibodies were used: anti-GFP (Clontech cat. no. 632380, 1:8000, for YFP constructs); anti-mCherry (Novus cat. no. NBP1-96751, 1:1000); anti-V5 tag (Genetex cat. no. GTX42525, 1:3000); anti-Myc tag (Abcam cat. no. ab9106, 1:1000); anti-β-actin (Sigma cat. no. A5441, 1:10,000). After washing, membranes were incubated with horseradish peroxidase-conjugated goat anti-mouse or anti-rabbit IgG for 45 min at room temperature. Proteins were visualized using Novex ECL Chemiluminescent Substrate Reagent Kit (Life Technologies) and a ChemiDoc XRS + imaging system (Bio-Rad). Densitometry was performed using the Chemidoc XRS + System image analysis software (Bio-Rad).
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