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46 protocols using pvdf fl membrane

1

Western Blot Analysis of DPD Protein

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Protein lysates were separated by SDS-PAGE and transferred to polyvinylidene difluoride (PVDF)-FL membrane (EMD Millipore, Saint Charles, MO). Membranes were blocked using Odyssey blocking buffer (LI-COR Biosciences, Lincoln, NE). Blots were probed with primary antibodies against DPD and α-tubulin (ab6556 and ab186407, respectively; Abcam, Cambridge, MA). IRDye800-conjugated goat anti-mouse and IRDye680-conjugated goat anti-rabbit secondary antibodies (LI-COR) were used for detection. Blots were scanned on a LI-COR Odyssey imager.
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2

Mitochondrial Protein Complex Analysis

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The mitochondrial fraction was solubilized with 5% (w/v) digitonin (Invitrogen)31 (link),32 (link) for 15 min on ice. After centrifugation at 20,000 × g for 30 min at 4 °C, the clear supernatant was loaded onto 3–12% BN gels (Invitrogen). For the immunoblot analysis, proteins in the gels were transferred onto a PVDF-FL membrane (Merck). The in-gel CcO activity of CIV was visualized by the precipitation of 3, 3′-diaminobenzidine oxides and indamine polymers in test buffer containing 50 mM sodium phosphate, 0.5 mg/ml 3, 3′-diaminobenzidine-tetrahydrochloride (D5905; Sigma), 0.25 mg/l cyt c (C2037; Sigma), and 75 mg/ml sucrose, pH 7.432 (link).
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3

Western Blot Protein Detection

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Protein lysates were separated on a 10% SDS-PAGE gel and transferred to PVDF-FL membrane (EMD Millipore). Membranes were blocked using Odyssey blocking buffer (LI-COR, Lincoln, NE). Blots were probed with primary antibodies against DPD and alpha-tubulin (both AbCam, Cambridge, MA) and subsequent secondary IRDye800 conjugated goat anti-mouse and IRDye 680 conjugated goat anti-rabbit (both LI-COR). Blots were scanned and band intensities quantified using the Image Studio 3.1 and LI-COR Odyssey Infrared Imaging system according to manufacturer’s instructions.
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4

Western Blot Protein Expression Analysis

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Cells were seeded in 6-well plates 24 hours prior to transfection or drug treatment. Samples were harvested 48 hours after drug treatment and 72 hours after transfection. Cells were lysed in RIPA buffer containing protease and phosphatase inhibitor cocktails. Running samples were prepared with 4X Novex NuPAGE LDS sample buffer (Life Technologies) and supplemented with 10% beta-mercaptoethanol. Twenty micrograms of protein were loaded per lane of 4–12% Bis-Tris NuPAGE gels (Life Technologies) and ran in MOPS buffer. Proteins were then transferred to PVDF-FL membrane (Millipore) in Tris-Glycine transfer buffer. Primary antibody incubation was carried out overnight at 4°C on a rocking platform. Secondary antibody incubation was carried out at room temperature the next day. Proteins were detected using the LI-COR Odyssey imaging system (LI-COR Biosciences). Image analysis and protein quantitation were performed with ImageJ (NCI).
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5

Immunoblotting of Cell Signaling Proteins

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Cells were trypsinized and washed in cold PBS before being lysed in 2X Laemmli sample buffer containing 0.5% beta-mercaptoethanol, 1% each of Protease Inhibitor Cocktail, Phosphatase Inhibitor Cocktail 2, and Phosphatase Inhibitor Cocktail 3 (Sigma-Aldrich, P8340, P5726, P0044, respectively). Samples were run on 4-20% Tris-Glycine gels (Life Technologies) and transferred to 0.45 μm PVDF-FL membrane (Millipore). Membranes were blocked in 2% milk solution and probed with the following antibodies: NMIIB (Biolegend, rabbit pAb; 1:1000 cat #909901), GAPDH (Santa Cruz Biotechnology rabbit pAb; 1:5000). EGFR (Cell Signaling Technology, rabbit pAb; 1:1000). Blots were analyzed with LiCor Odyssey CL imaging system.
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6

SDS-PAGE and Western Blotting Quantification

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Protein samples were resolved on 4–20% SDS-gradient gels (BioRad, Hercules, CA), then transferred to PVDF-FL membrane (Millipore Burlington, MA). Detection and quantification was carried out using a LI-COR Odyssey infrared scanning system using fluorescently labelled secondary antibodies. All western blots were scanned using the Odyssey Clx infrared imaging system from LICOR.
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7

ATM Signaling Pathway Analysis

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Cells were lysed in cell lysis buffer (9803, Cell Signaling) and lysate (10 µg) was separated by SDS-PAGE and analyzed by western blotting. Proteins were transferred to PVDF-FL membrane (Millipore) and probed with antibodies directed against ATM (GRX70103, Genetex), phospho-ATM Ser-1981 (AF-1655, R&D Systems), p53 (GTX70214, Genetex), phospho-p53 Ser-15 (9286, Cell Signaling), Smc1 (4802, Cell Signaling), phospho-Smc1 Ser-957(4805S, Cell Signaling), Kap1 (ab22553, Abcam), phospho-Kap1 Ser-824 (A300-767A, Bethyl Laboratories), Nbs1 (GTX70224, Genetex), phospho-Nbs1 Ser-343 (ab47272, Abcam), Chk2 (GTX70295, Genetex), and phospho-Chk2 Thr-68 (2661S, Cell Signaling) followed by detection with IRdye 800 anti-mouse (Rockland, RL-610-132-121) or Alexa Fluor 680 anti-rabbit (Invitrogen, A21076) secondary antibodies. Western blots were analyzed and quantitated using a Licor Odyssey system.
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8

Western Blot Protein Detection Protocol

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Cells were lysed in RIPA buffer containing protease and phosphatase inhibitor cocktails, and protein was quantified using BCA assay. Samples were prepared with 4X Novex NuPAGE LDS sample buffer (Life Technologies) and supplemented with 10% beta-mercaptoethanol. Twenty micrograms of protein was loaded per lane of 4%–12% Bis-Tris NuPAGE gels (Life Technologies) and run in MOPS buffer. Following gel electrophoresis, proteins were transferred to a PVDF-FL membrane (Millipore) in tris-glycine transfer buffer. Primary antibody incubation was carried out overnight at 4 °C on a rocking platform. Incubation with IRDye-conjugated secondary antibodies was carried out at room temperature the next day. Proteins were detected using the LI-COR Odyssey imaging system (LI-COR Biosciences). Image analysis and protein quantitation (i.e., band densitometry) was performed with ImageJ (NIH, Washington, DC, USA).
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9

DDR Signaling Activation Assay

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For the experiment with IR, cells were irradiated with 10 Gy and incubated for 1hr before harvesting. For the experiments with CPT, H2O2, and arsenite, cells were incubated with media containing 10 μM CPT, 100 μM H2O2, or arsenite for 1hr before harvesting. Cells were lysed in 10× cell lysis buffer (9803, Cell Signaling) and lysate (20 μg) was separated by 8% SDS-PAGE gel and analyzed by western blotting. Proteins were transferred to PVDF-FL membrane (Millipore) and probed with antibodies directed against ATM (sc-135663, Santa Cruz), phospho-ATM Ser-1981 (AF-1655, R&D Systems), KAP1 (ab22553, Abcam), phospho-KAP1 Ser-824 (A300-767A, Bethyl Laboratories), Chk2 (GTX70295, Genetex), and phospho-Chk2 Thr-68 (2661S, Cell Signaling) followed by detection with IRdye 800 anti-mouse (RL-610-132-121, Rockland) or Alexa Fluor 680 anti-rabbit (A21076, Invitrogen) secondary antibodies. Western blots were analyzed and quantitated using a Licor Odyssey system.
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10

Western Blotting of Phospho-Proteins

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Cellular lysates were separated by polyacrylamide gel electrophoresis (SDS-PAGE) using 4-15% Criterion gels (Biorad) and transferred to PVDF-FL membrane (Millipore). To analyze site-specific phosphorylation the membranes were blocked for 1 hr at room temperature in a blocking buffer that was 1:1 1x PBS:SEA Block (Thermo Scientific). The PVDF membranes were incubated with primary antibodies against LAT pY132 (Biosource), LAT pY226 (BD Pharmingen), ZAP-70 pY319 (Cell Signaling Technologies), SLP-76 pY128 (BD Pharmingen), PLC-γ1 pY783 (Cell Signaling Technologies), ERK1/ERK2 pT185/pY187 (Thermo Scientific) and GAPDH (Meridian Life Sciences). IRDye 800CW or IRDye 680-conjugated secondary antibodies were diluted in SEA Block as above and incubated with the PVDF membrane for 30 min at room temperature. The membranes were then imaged using the Licor Odyssey. The intensity of the immunoblotting bands was determined using Odyssey’s v3.0 software. Phosphorylated proteins were normalized to GAPDH and the relative amount of phosphorylation to the 2 minute (for LAT pY132, LAT pY226, ZAP-70, SLP-76 and PLC-γ1) or 5 minute (ERK1/ERK2) LAT WT bands were determined as described previously (35 (link)-37 (link)). The data from 4-5 independent replicates were compiled and then plotted using Prism (GraphPad Software).
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