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68 protocols using anti gfp

1

Protein Analysis by Western Blotting

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A small proportion of cells were reserved for cell counting. Cells were lysed in Laemmli sample buffer supplemented with 10% 2-mercaptoethanol (133-1457, Wako) and incubated at 95°C for 5 min to denature proteins. We then performed 10% tris-glycine sodium dodecyl sulfate (SDS)–polyacrylamide gel electrophoresis to separate the proteins. Proteins in the gel were transferred to an Immobilon-P membrane (IPVH00010, Merck) and blocked with phosphate-buffered saline (PBS) with Tween 20 containing 5% nonfat milk (190-12865, Wako) for 30 min at room temperature. Proteins were detected using anti-RPA194 (1:1000 dilution; sc48385, Santa Cruz Biotechnology), anti–β-actin (1:50,000 dilution; A5441, Sigma-Aldrich), anti-HaloTag (1:1000 dilution; G9211, Promega), and anti-GFP (1:2000 dilution; 632381, TaKaRa) antibodies.
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2

Western Blot Analysis of Cellular Proteins

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Cells were grown as described above and harvested by centrifugation 60 min after the second resuspension in LB + glucose (0.2% w/v). After centrifugation, cells were resuspended in 12.5 mM Tris pH 6.8, 4% SDS and heated to 90°C for 10 min. 5x loading dye (250 mM Tris pH 6.8, 20% glycerol, 30% β-mercaptoethanol, 10% SDS, saturated bromophenol blue) was added and lysate was heated to 90°C for 10 min. Protein was separated by 4–12% Criterion XT Bis-Tris protein gel (Bio-Rad) and XT MES buffer and transferred to PVDF membrane by Trans-Blot Turbo Transfer system (Bio-Rad). Membranes were blocked in 5% milk for 1 hr at room temperature. The membranes were probed by antibodies diluted in TBS-tween. FLAG-tagged proteins were detected by anti-FLAG-HRP in 1:10,000 dilution (Sigma). GFP was detected by anti-GFP in 1:2000 (Takara) and anti-mouse-HRP in 1:10,000 (Thermo Fisher). Cysteinyl-tRNA synthetase (CysRS) was detected by anti-CysRS in 1:2000 (from Dr. Ya-Ming Hou) and anti-rabbit-HRP in 1:4000 (from Dr. Ya-Ming Hou). Chemiluminescent signals of HRP were developed by SuperSignal West Pico PLUS Chemiluminescent Substrate (Thermo Fisher) or SuperSignal West Femto Maximum Sensitivity Substrate (Thermo Fisher), and exposed on Amersham Hyperfilm ECL (GE).
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3

Protein Expression and Co-IP Analysis

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For protein expression analysis, total proteins were extracted from N. benthamiana tissues with buffer containing 150 mM Tris–HCl, 50 mM NaCl, 1 mM EDTA, 2 mM CaCl2, 5 mM MgCl2, 0.15% NP-40, 0.1% Triton X-100 (pH 7.5), 10 mM dithiothreitol, 1 mM phenylmethanesulfonyl fluoride (PMSF), plant protease inhibitor cocktail (VWR), and 20 μM MG132. Protein samples were separated on 10% Bis-Tris PAGE gels, transferred electrophoretically to 0.45-μm Amersham Protran Premium nitrocellulose membranes (GE Healthcare), and detected with anti-GFP (Takara), anti-HA, anti-FLAG, or anti-Myc (BioLegend) antibodies.
For co-IP assays, protein extracts were incubated with an anti-Myc antibody (1:2000, Sigma-Aldrich) at 4°C for 16 h followed by incubation at 4°C for 4 h with protein A/G magnetic beads (VWR) equilibrated with the extraction buffer. The beads were washed six times with 1 ml of extraction buffer, and immunoprecipitated samples were analyzed by western blotting with anti-HA, anti-FLAG, or anti-Myc (BioLegend) antibodies.
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4

Western Blot Protein Detection Protocol

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Equal volumes of lysate were loaded for each sample onto 4–12% Criterion XT Bis-Tris protein gels in 1x XT MES buffer. Protein was transferred to PVDF membrane via turbo blot. Membranes were then placed in 2.5% milk, 1x TBST blocking solution for 1 hr. Primary antibody was used in 1x TBST at either 1:50,000 for anti-eEF2 (Kerafast, rabbit), or 1:5000 for anti-PGK1 (Invitrogen, mouse), anti-HA (Roche, rat), anti-FLAG (Sigma, mouse), and anti-GFP (Takara, mouse) and incubated on a rotator overnight at 4°C. Membranes were washed in 1x TBST three times, 10 min each. The corresponding HRP-conjugated secondary antibody was added to the membrane at 1:5000 in 1x TBST and incubated for 1–2 hr. Membranes were washed three times for 10 min each. Pico solution (details) was added to membranes for approximately 3 min and then membranes were scanned using a G:BOX Chemi XX6 (Syngene) with varying exposure times.
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5

Western Blot Analysis of Viral Proteins

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Whole cell lysates were prepared from monolayers of infected CESCs, non-infected CESCs or VP22 expressing LMH by resuspending the cells in laemmli 2× sample buffer. Solubilized proteins were separated on a 10% SDS-PAGE. Resolved proteins were transferred to nitrocellulose membrane, blocked in Tris 10 mM pH 8.25, NaCl 150 mM, Tween 0.2% containing milk 3% and subsequently incubated with the mouse monoclonal anti-MDV VP5 (F19), the rabbit polyclonal serum anti-PRV VP22, the mouse monoclonal anti-MDV VP22 (L13a), the rabbit polyclonal anti-ILTV VP22, a rabbit polyclonal anti-GFP (# 632593, Takara, Shiga, Japan) or a mouse monoclonal anti-GAPDH (MAB374, Millipore, Bedford, MA, USA) primary antibody. Subsequently, goat anti-mouse IgG (#A3562, Sigma) and anti-rabbit IgG alkaline phosphatase-conjugated antibodies (#A3687, Sigma) or goat anti-mouse IgG (#A4416, Sigma) and anti-rabbit IgG (#A0545, Sigma) peroxidase-conjugated antibodies were used. Alkaline phosphatase and peroxidase signals were revealed using NBT-BCIP (Zymed, South San Franscisco, Calif, USA) or Immobilon Western Chemiluminescent HRP substrate (P90720, Millipore), respectively.
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6

Monoclonal and Polyclonal Antibody Detection

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The following monoclonal and polyclonal antibodies or nanobodies were used in this study: anti-E-cadherin (C-terminus: BD Transduction Laboratories, 61018; N-terminus: Genetex/Biozol GTX134997), anti-Tsg101 (Abcam, 4A10), anti-GFP (Takara, 632592), anti-GFP-nanobodies (Chromotek), anti-actin (BD Transduction Laboratories, 612656), anti-Hrs (Enzo, A-5; GeneTex, GTX89364), anti-GAPDH (Abcam, 6C5), anti-giantin (Covance, PRB-114C), anti-PDI (BD Transduction Laboratories, 610946), anti-TOM20 (Santa Cruz, Sc11415).
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7

Western Blotting of Transgenic Hairy Roots

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The fresh hairy root samples were homogenized in 500 μL of plant protein extraction reagent containing 1X protease inhibitor cocktail, according to the manufacturer’s recommendation (CoWin Biosciences, China). The whole protein extracts from the H. niger transgenic lines and control lines were mixed with 5X sample loading buffer (50% glycerol, 10% SDS, 5% β-mercaptoethanol, 0.5% bromophenol blue, and 0.25 M Tris, pH 6.8), heated to 100 °C for 5 min, loaded onto a 10% SDS-polyacrylamide gel, and electrophoresed at 80 V for 120 min in a Bio-Rad Mini Trans-Blot cell. The total protein was subsequently transferred to PVDF membrane. The membranes were blocked using 5% non-fat dry milk in PBS-0.05% Tween-20 and incubated overnight with the primary antibody (anti-β-actin, Sigma, USA or anti-GFP, Takara, Japan) at a 1:5000 dilution in 3% Bovine serum albumin. The blots were washed three times with TBST (137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 2 mM KH2PO4, 0.3% Tween-20 (V/V)) and incubated for 4 h with goat anti-mouse IgG antibody (1:5000) (Abmart, China). The bands were developed using a chemiluminescent substrate (Thermo, USA).
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8

Protein Interaction Profiling in Plants

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The cDNAs of PARP1, PARP2, PARG1, PARG2, UBC13A, UBC13B, PDI1, PDI2, PDI3, and PDI4 were cloned into the Gateway destination vector pGWB405 with a C-terminal GFP tag and/or pGWB417 with a C-terminal 4×myc tag, and the resulting constructs were transformed into Agrobacterium tumefaciens GV3101(pMP90). Leaves of 3- to 4-week-old N. benthamiana plants were agroinfiltrated with Agrobacterium cultures at an OD600 of 0.4. For flg22 treatment, 1 μM flg22 was infiltrated into leaves 1 h prior to harvest. Samples were harvested 2 days after agroinfiltration, and total proteins were prepared in extraction buffer (50 mM Tris-HCl, pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.2% Triton X-100, 10% glycerol, and plant protease inhibitor cocktail at 1:100). Immunoprecipitation was carried out with GFP-Trap magnetic beads (ChromoTek) at 4°C for 1 h with gentle rotation, followed by three washes with extraction buffer without protease inhibitors. The precipitated proteins were eluted with the SDS loading buffer, subjected to SDS-PAGE, immunoblotted with anti-myc (BioLegend) or anti-GFP (TaKaRa) antibody, and detected using SuperSignal West Dura or Femto Chemiluminescent Substrates (Thermo Scientific).
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9

Immunofluorescence Assay for DNA Damage

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Cells were plated in 6- or 24-well tissue culture plates (Greiner) and allowed to adhere overnight, then infected with VLP (equal protein expression), rAAV-2.5 (1.4 × 108 copies/well), or etoposide (Sigma). U2OS cells were permeabilized with 0.5% Triton X-100 in PBS at 4°C for 5 min and fixed in 4% PFA for 20 min, MDM cells were permeabilized with 0.1% Saponin (Fisher) in PBS at 4°C for 15 min and fixed in 4% PFA for 15 min. Cells were washed, incubated with blocking buffer (3% BSA, 0.05% Tween 20, and 0.04 NaN3 in PBS for U2OS cells or 3% FBS in 0.1% Saponin for MDM cells) for 30 min. Cells were probed with appropriate primary antibodies (anti-γH2A.x Ser139, anti-53BP1, or anti-RelA(p65) [Cell Signaling], anti-GFP [Takara], and anti-MRE11 [Novous]) and then washed and probed with Alexa Fluor-conjugated secondary antibodies (Life Technologies). Nuclei were stained with diamidino-2-phenylindole (DAPI; Life Technologies). Images were acquired on the LSM 980.
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10

Western Blot Analysis of Proteins

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We separated total or membrane proteins by gel electrophoresis (3-8% tris-acetate or 12% bis-tris NuPage gel [Thermo-Fisher Scientific®, Waltham, MA]), transferred to nitrocellulose membrane, probed with full-length polyclonal anti-GFP (Takara Bio®, Mountain View, CA) or monoclonal anti-β-actin (MilliporeSigma®, Burlington, MA) followed by horseradish peroxidase-conjugated secondary antibody (GE Healthcare®, Pittsburgh, PA). After chemiluminescent labelling (Amersham ECL Detection Reagent, GE Healthcare®), we captured images by film exposure.
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