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8 protocols using anti cyclophilin b

1

Reagents and Antibodies for Cell Assays

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TSA was purchased from Enzo Life Sciences. Carbobenzoxy-Asp-Glu-Val-Asp-7-amino-4-trifluoromethyl coumarin (DEVD-AFC) and 7-amino-4-trifluoromethyl coumarin (AFC) were from Enzyme Systems Products (Livermore, CA). Unless indicated, all other reagents including cisplatin and chloroquine were purchased from Sigma (St. Louis, MO). The following primary antibodies were used: anti-LC3B from Novus Biologicals (Littleton, CO); anti-ATG7, anti-β-actin and anti-cyclophilin B from Abcam; and anti-cleaved caspase3, anti-AMPK, anti-phospho-AMPK (Thr172), anti-P70S6K, anti-phospho-P70S6K (T389) from Cell Signaling Technology (Danvers, MA). All secondary antibodies for immunoblot analysis were from Thermo Scientific (Rockford, IL).
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2

Fetal Membrane NF-κB and MAPK Analysis

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Western blot analysis of NF-κB and MAPK was performed in the fetal membrane samples. Tissues were lysed in RIPA buffer (J63306: Thermo Fisher Scientific, Waltham, MA, USA) containing protease inhibitor (165-26021: Fuji film, Osaka, Japan), and 1000 μg of protein extracts were subjected to electrophoresis using 4–12% SDS-PAGE gels (NW04127: Thermo Fisher Scientific, Waltham, MA, USA). Proteins were transferred to membranes using an iBlot2 Dry Blotting System (IB21001: Thermo Fisher Scientific, Waltham, MA, USA). The membranes were incubated overnight with the following primary antibodies: anti-phosphorylated-NF-κB p65 (1:1000; #3033: Cell Signaling Technology (CST), Danvers, MA, USA), anti-NF-κB p65 (1:3000; #8242: CST), anti-phosphorylated-JNK (1:1000; #4668: CST), anti-JNK (1:1000; #9252: CST) anti-phosphorylated-p38 MAPK (1:3000; #4511: CST), anti-p38 MAPK (1:3000; #8690: CST), and anti-cyclophilin B (1:20,000; ab178397: Abcam, Cambridge, UK). Cyclophilin B was used as a loading control. Protein bands were densitometrically analyzed using Image Saver 5 for the Ez-Capture series (ATTO Corporation, Tokyo, Japan). Image J version 1.51 was used to calculate the relative densities of the bands (National Institutes of Health, Bethesda, MD, USA).
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3

Immunoblotting of Cell Signaling Proteins

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Protein from cell cultures or homogenized tumors was extracted by TRI Reagent (Sigma). Primary antibodies: anti-BPTF (Millipore), anti-OVALBUMIN, anti-PMEL17 (Santa Cruz Biotechnology), anti-CYCLOPHILIN B (Abcam), anti-PSMB9, anti-TAP2 (Thermo Scientific), anti-PSMB8 and anti-TAP1 (Cell Signaling). Secondary antibody: horseradish peroxidase (HRP)-conjugated anti-rabbit or anti-mouse secondary antibody (Cell Signaling).
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4

Molecular mechanisms of cisplatin-induced nephrotoxicity

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Antibodies used in this study were from the following sources: rabbit monoclonal anti-DNMT1 (5032), rabbit monoclonal anti-Caspase-3 (9665), rabbit polyclonal anti-Cleaved caspase 3 (9661), rabbit monoclonal anti-PARP (9532), and rabbit monoclonal anti-GAPDH (5174s) from Cell Signaling Technology (Danvers, MA); rabbit polyclonal anti-Cyclophilin B from Abcam Inc. (Cambridge, MA); and rabbit polyclonal anti-DNMT3a (sc-20703), mouse monoclonal anti-DNMT3b (sc-81252), goat polyclonal anti-ICSBP (Irf8, sc-6058) from Santa Cruz Biotechnology Inc. (Dallas, TX). Secondary antibodies for immunoblotting were from Thermo Scientific (Rockford, IL) and for immunohistochemical staining from Dako (Carpinteria, CA), respectively. Fluorescein-labeled lotus tetragonolobus lectin (LTL) was bought from Vector Labs (FL-1321). cis-Diammineplatinum(II) dichloride crystalline (Cisplatin, P4394-1G) and 5-aza-2′-deoxycytidine (A3656-50MG) were purchased from Sigma-Aldrich (St. Louis, MO). Enhanced chemiluminescence kit was purchased from Thermo Scientific (Rockford, IL). All the primers were purchased from Integrated DNA Technologies (Coralville, IA). Unless specifically indicated, all other reagents were from Sigma.
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5

Western Blot Analysis of Cdx2, NICD, and Actin

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Cells were disrupted using RIPA lysis buffer and cleared by centrifugation. Proteins were resolved on a 12% SDS-PAGE gel, transferred to a PVDF membrane (Millipore, Etobicoke, ON, Canada), which was blocked with 5% non-fat milk powder in PBS: 0.1% Tween 20 (PBST), then incubated overnight with the appropriate primary antibody at 4°C. Primary antibodies used were rabbit polyclonal anti-Cdx2 (1/1000 dilution, Savory et al., 2009); anti-NICD (1/500 dilution, BD Biosciences); anti-β-actin (1/2000 dilution, Abcam, Branford, CT, USA) or anti-CyclophilinB (1/10,000 dilution, Abcam). Membranes were then washed, incubated with secondary antibodies (HRP-conjugated anti-rabbit or anti-mouse IgG, as appropriate; 1/25,000 dilution, Santa Cruz Biotechnology, Dallas, TX, USA) and immunoreactivity detected by ECL (Millipore) according to the manufacturer’s instructions.
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6

Protein Expression Analysis in Myoblasts

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Western blotting was performed as described (Fu et al., 2015) . Briefly, whole cell lysate of primary myoblasts was prepared by lysing buffer containing protease inhibitor cocktail (Roche).
Protein concentration was determined with the BCA Protein Assay Reagent (Pierce Biotechnology) using Bovine Serum Albumin as standard. Samples were subjected to SDS-PAGE gels and transferred to PVDF membranes (Millipore). Proteins were detected by the following antibodies: anti-Smad2 antibodies (Cell signaling, 5339S), anti-GKLF (KLF4) antibodies (Santa Cruz BioTech, sc-20691) , anti-Myogenin antibodies (DSHB, F5D), anticyclophilin B (Abcam, ab16045) and anti-αTubulin antibodies (Santa Cruz BioTech, sc-5286).
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7

Protein Expression Analysis in Myoblasts

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Western blotting was performed as described (Fu et al., 2015) . Briefly, whole cell lysate of primary myoblasts was prepared by lysing buffer containing protease inhibitor cocktail (Roche).
Protein concentration was determined with the BCA Protein Assay Reagent (Pierce Biotechnology) using Bovine Serum Albumin as standard. Samples were subjected to SDS-PAGE gels and transferred to PVDF membranes (Millipore). Proteins were detected by the following antibodies: anti-Smad2 antibodies (Cell signaling, 5339S), anti-GKLF (KLF4) antibodies (Santa Cruz BioTech, sc-20691) , anti-Myogenin antibodies (DSHB, F5D), anticyclophilin B (Abcam, ab16045) and anti-αTubulin antibodies (Santa Cruz BioTech, sc-5286).
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8

Fetal Membrane Protein Expression Analysis

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Western blot analysis of fetal membrane samples was performed to determine protein levels of NF-kB and MAPK. Protein extracts (1000 mg) were subjected to electrophoresis using 4% to 12% sodium dodecyl sulfate polyacrylamide electrophoresis gels, and the proteins were transferred to membranes using an iBlot 2 Dry Blotting System (Life Technologies, Carlsbad, California). Membranes were incubated overnight with primary antibodies as follows: anti-phosphorylated-NF-kB p65 (1:1000; Cell Signaling Technology [CST], Danvers, Massachusetts), anti-NF-kB p65 (1:3000; CST), antiphosphorylated-p38 MAPK (1:3000; CST), anti-p38 MAPK (1:3000; CST), and anti-cyclophilin B (1:20,000; Abcam, Cambridge, United Kingdom). Cyclophilin B was used as a loading control.
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