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9 protocols using complete protease inhibitor cocktail mix

1

Western Blot Analysis of Oct3/4 Expression

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The cell lysate was prepared by NP40 lysis buffer containing 20 mM Tris–HCl (pH 8.0), 137 mM NaCl, 1% NP40, 10% glycerol, and 4% complete protease inhibitor cocktail mix (Roche, Mannheim, Germany). 60 μg protein was used for sodium dodecyl sulphate–polyacrylamide gel electrophoresis and transferred blotting to polyvinylidene fluoride (PVDF) (Immobilon; Millipore Corp, Billerica, MA, USA). Membranes were blocked using TBST solution containing 4% skim milk for 1 h with gentle shaking and were then washed three times for 15 min with TBST solution. Membranes were incubated overnight at 4°C with rabbit anti-Oct3/4 (dilution 1 : 500), followed by shaking in TBST. After washing, membranes were incubated with secondary antibodies for 2 h at room temperature. While washing repeatedly as described earlier, membranes were incubated with ECL for 1 min at room temperature. We detected the protein using the BioImaging Systems (UVP Inc., Upland, CA, USA), when bands reached the desired darkness. Relative amount of protein was quantified with the reference of β-actin (dilution 1 : 1000, Santa Cruz Biotechnology, Santa Cruz, CA,USA).
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2

Western Blot Protein Analysis Protocol

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Total cell homogenates were prepared by lysing cells in NP40 lysis buffer containing 1% NP40, 10% glycerol, 20 mM Tris-HCl pH 8.0, 137 mM NaCl and 4% complete protease inhibitor cocktail mix (Roche, Mannheim, Germany). Eighty micrograms of total protein was resolved by SDS-PAGE and subsequently transferred onto a PVDF membrane (Immobilon, Millipore, Billerica, MA, USA). Membranes were blocked with 5% non-fat dry milk in PBS for 1 h with gentle shaking. The membranes were then washed three times for 10 min each with PBS containing 0.1% Tween-20 (PBST). The membranes were incubated with the primary antibodies (Santa Cruz; Table 1) diluted in 1% BSA in PBS overnight at 4°C with shaking. The following day, the membranes were washed three times with PBST as described and incubated with the secondary antibodies (Table 1) for 2 h at room temperature. After an additional three washes with PBST, the membranes were incubated with DAB for 2–3 min at room temperature. The blots were subsequently developed in the dark, dried, and photographed. After scanning, densitometric analysis was performed using the IMAGEJ 1.33 software (National Institutes of Health, Bethesda, MD, USA).
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3

ATF4 Induction and Co-Immunoprecipitation

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MEFs were cultured in DMEM without glutamine or in the presence of 2 μg/ml tunicamycin for 24 hours to induce ATF4 expression. Cells were collected by trypsinization and lysed in RIPA buffer (150 mM NaCl, 1% NP40, 5 mM EDTA, 50 mM Tris, 0,5% deoxycholate, 0,1% SDS) supplemented with complete protease inhibitor cocktail mix (Roche). For Co-IP, lysates were incubated with antibody at 4°C overnight in a turning wheel. Subsequently, 25 μl of protein G Sepharose beads (GE healthcare) was added to the lysates and incubated at 4°C for 1 hour in a turning wheel. Protein-protein interactions were determined by immunoblot analysis.
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4

Rat Liver Protein Extraction and Western Blot

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Homogenized rat liver was lysed in 200 μl RIPA lysis buffer (Beyotime, P0013B) with 1% phenylmethyl sulfonylfluoride and 4% complete protease inhibitor cocktail mix (Roche, Mannheim, Germany). Extracts were centrifuged at 14,000 g for 15 min at 4°C. Eighty micrograms of total protein were used for sodium dodecyl sulfate‐polyacrylamide gel electrophoresis, followed by transferring blotting to nitrocellulose membrane (Millipore Corp., Billerica, MA, USA). Membranes were then blocked with 5% nonfat dried milk in PBS for 1 hr with gentle shaking. Membranes were incubated first with anti‐Janus kinase 2(JAK2), anti‐signal transducer and activator of transcription 3 (STAT3) and their phosphorylated species, anti‐cytochrome P450 2E1(CYP2E1), anti‐Nuclear factor erythroid 2 related factor 2 (Nrf2), anti‐heme oxygenase‐1(HO‐1), anti‐NAD(P)H: quinone oxidoreductase 1 (NQO‐1), and anti‐β‐actin antibody [Cell Signaling Technology] were incubated overnight at 4°C, in 1% BSA in PBS overnight at 4°C with shaking, washed and incubated with secondary antibodies for 2 hr at room temperature. Finally, the samples were visualized by enhanced chemi‐luminescence. After scanning, band density was analyzed using Image J 1.33 software (National Institutes of Health, Bethesda, MD, USA).
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5

Protein Extraction and Western Blot

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Directly after image acquisition at the microscope, cells were washed twice with sterile PBS and then lysed on ice for 10 min in lysis buffer as previously described17 (link) or RIPA buffer (50 mM Tris, 150 mM NaCl, 1% Triton X-100, 2 mM EDTA, 0.5% DOC, 0.1% SDS, complete protease inhibitor cocktail mix, Roche). Lysates were centrifuged at 13 000 r.p.m. for 10 min at 4 °C. Supernatants were collected and protein concentration was determined by the Bradford method. Samples were stored at −80 °C until used. 10 to 30 μg of protein per slot were separated on a 12% SDS polyacrylamide gel and transferred to a polvinylidene difluoride membrane. Membranes were incubated for 1 h in TBST (50 mM Tris, 150 mM NaCl, 0.05% Tween, pH 7.5) containing 5% milk to saturate all non-specific binding sites. Incubation with primary antibodies was overnight at 4 °C in 1% milk+TBST (1 : 1500 goat anti-DJ-1, Santa Cruz Biotechnology, Dallas, TX, USA; #Sc-27006; 1 : 3000 mouse anti-α-Synuclein, BD #610787; 1 : 5000 mouse anti-β-actin, Sigma-Aldrich, St. Louis, MO, USA; #A5441). Blots were developed using horseradish peroxidase (HRP)-conjugated secondary antibodies (anti-goat 1 : 10 000 Jackson Immunoresearch, West Grove, PA, USA; #705-035-003, anti-mouse 1 : 10 000 Sigma #50185-ILM-F) and the Immobilon chemiluminescent HRP substrate (Millipore, Billerica, MA, USA).
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6

Western Blot Analysis of Myocardial Proteins

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Homogenized mice myocardium was lysed in 200 µL RIPA lysis buffer (Beyotime, P0013B) with 1% phenylmethyl sulfonylfluoride and 4% complete protease inhibitor cocktail mix (Roche, Mannheim, Germany). Extracts were centrifuged at 14,000 g for 15 min at 4°C. Eighty micrograms of total protein were used for sodium dodecyl sulphate-polyacrylamide gel electrophoresis, followed by transfer to nitrocellulose membrane (Millipore Corp., Billerica, MA, USA). Membranes were then blocked with 5% non-fat dried milk in PBS for 1 h with gentle shaking. Membranes were incubated first with CCR7, CCL21, MMP-2 and MMP-9 (Santa Cruz Biotechnology) overnight at 4°C, then placed in 1% BSA in PBS overnight at 4°C with shaking, and washed and incubated with secondary antibodies for 2 h at room temperature. Finally, the samples were visualized by enhanced chemiluminescence [22] .After scanning, band density was analyzed using Image J 1.33 software (National Institutes of Health, Bethesda, MD, USA).
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7

Co-immunoprecipitation of Protein Complexes

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The coimmunoprecipitation experiments were carried out essentially as previously described.35 (link) Briefly, cells were lysed 24 h after transfection with 600 μl CHAPS lysis buffer consisting of 10 mM CHAPS, 50 mM Tris-HCl (pH 7.8), 150 mM NaCl, 5 mM NaF, 1 mM DTT, 0.5 mM PMSF and 40 μl/ml 'Complete Mix' protease inhibitor cocktail (Roche, Basel, Switzerland). Extracts were incubated overnight with 40 μl agarose-conjugated anti-Flag antibody (M2, Sigma-Aldrich, St Louis, MO, USA) at 4 °C. Precipitates were washed 6 to 8 times with CHAPS lysis buffer and finally resuspended in SDS-polyacrylamide gel loading buffer. Proteins were resolved via SDS-PAGE and analyzed via western blotting.
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8

Immunoprecipitation and Western Blot Analysis

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HEK293 cells were transfected with the indicated constructs for expression of GFP- and Flag-tagged WT and mutant proteins. 24 hours after transfection cells were lysed with 600 μl CHAPS lysis buffer [10 mM 3-[(3-Cholamidopropyl)dimethylammonio]-1-propanesulfonate hydrate (CHAPS, Roth), 50 mM Tris-HCl (pH 7.8), 150 mM NaCl, 5 mM NaF, 1 mM Dithiothreitol (DTT, Merck), 0.5 mM Phenylmethanesulfonyl fluoride (PMSF, Merck) and 40 μl/ml “Complete Mix” protease inhibitor cocktail (Roche)]. The extracts were incubated with 40 μl agarose-conjugated anti-Flag antibody (M2, Sigma) at 4°C overnight. Precipitates were washed 6 to 8 times with CHAPS lysis buffer and finally resuspended in SDS-polyacrylamide gel loading buffer. For western blotting the proteins were resolved in SDS-polyacrylamide gels and transferred electrophoretically at room temperature to PVDF membranes (Merck) for 1 h at 50 mA using a Tris-glycine buffer system. The membranes were pre-blocked for 1 h in a solution of 3% milk powder in PBS-T (0.1% Tween 20 in PBS) before adding antibodies. The following antibodies were used: anti-GFP (7.1/13.1, mouse monoclonal IgG, secondary antibody peroxidase conjugated sheep anti-mouse IgG, NA931V, GE healthcare) or anti-Flag (M5, Sigma; secondary antibody, NA931V, GE healthcare).
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9

Immunoprecipitation and Western Blot Analysis

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HEK293 cells were transfected with the indicated constructs for expression of GFP- and Flag-tagged WT and mutant proteins. 24 hours after transfection cells were lysed with 600 μl CHAPS lysis buffer [10 mM 3-[(3-Cholamidopropyl)dimethylammonio]-1-propanesulfonate hydrate (CHAPS, Roth), 50 mM Tris-HCl (pH 7.8), 150 mM NaCl, 5 mM NaF, 1 mM Dithiothreitol (DTT, Merck), 0.5 mM Phenylmethanesulfonyl fluoride (PMSF, Merck) and 40 μl/ml “Complete Mix” protease inhibitor cocktail (Roche)]. The extracts were incubated with 40 μl agarose-conjugated anti-Flag antibody (M2, Sigma) at 4°C overnight. Precipitates were washed 6 to 8 times with CHAPS lysis buffer and finally resuspended in SDS-polyacrylamide gel loading buffer. For western blotting the proteins were resolved in SDS-polyacrylamide gels and transferred electrophoretically at room temperature to PVDF membranes (Merck) for 1 h at 50 mA using a Tris-glycine buffer system. The membranes were pre-blocked for 1 h in a solution of 3% milk powder in PBS-T (0.1% Tween 20 in PBS) before adding antibodies. The following antibodies were used: anti-GFP (7.1/13.1, mouse monoclonal IgG, secondary antibody peroxidase conjugated sheep anti-mouse IgG, NA931V, GE healthcare) or anti-Flag (M5, Sigma; secondary antibody, NA931V, GE healthcare).
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