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7 protocols using complete protease and phosphatase inhibitors

1

Ubiquitination of IRF Transcription Factors

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HEK293T cells were cotransfected with plasmids expressing FS-IRF5, FS-IRF1, or FS-IRF8 along with LYN using Lipofectamine 2000. Forty-eight hours after transfection, cells were treated with 10 μM MG132 for 4 hours. IRF-expressing RAW264.7 cells were treated with 10 μM MG132 for 1 hour followed by CpG-DNA stimulation (1 μM) for 1 hour. HEK293T and RAW264.7 cells were lysed in urea buffer [8 M urea, 20 mM Hepes/NaOH (pH 7.5), 1.5 mM MgCl2, 150 mM NaCl, 1 mM EDTA, 0.5% NP-40, and 10% glycerol] supplemented with complete protease and phosphatase inhibitors (Sigma-Aldrich) and 20 mM N-ethylmaleimide. After clearance by centrifugation (10 min, 20,817g, 4°C), lysates were subjected to IP using strep-XT beads for 4 hours at 4°C. Denatured IP samples were analyzed by IB using antibodies against K48-linked polyubiquitin.
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2

Hippocampal Slice Protein Extraction and Western Blot Analysis

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Hippocampal slices used for electrophysiological experiments were rapidly dissected to isolate CA1 regions and then homogenized in ice-cold RIPA buffer containing 1x complete protease and phosphatase inhibitors (Sigma). Protein concentration was assessed by the Micro BCA Protein Assay Kit (Pierce). Proteins (30 μg) were subjected to SDS-polyacrylamide gel electrophoresis (SDS-PAGE) on polyacrylamide gels and electrophoretically transferred to nitrocellulose membranes as previously described [14 (link)]. Loading of protein samples was verified by Coomassie and Ponceau staining. Primary antibodies directed against phospho-p44/p42 MAPK (Thr202/Tyr204), total p44/p42 MAPK were obtained from Cell Signaling Technology. Membranes were first processed to visualize the phosphorylated forms of proteins, dehybridized (Restore Western Blot Stripping Buffer, Pierce, Rockford, IL, USA), and then reprobed with antibodies directed against total proteins for normalization. Quantitation was carried out by densitometric film analysis.
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3

Immunoprecipitation of WIP1 Protein

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HEK293 or U2OS-WIP1-KO cells were transfected with GFP-WIP1 plasmid using polyethylenimine. Cells treated as indicated were extracted in lysis buffer [50 mM Tris pH 8.0, 120 mM NaCl, 1% Tween-20, 0.1% NP-40, 1.0% glycerol, 2 mM EDTA, 3 mM EGTA, 10 mM MgCl2, complete protease and phosphatase inhibitors (Sigma-Aldrich, St. Louis, MO, USA)] supplemented with benzonase (100 U/mL), briefly sonicated and EtBr (50 μg/mL) was added before centrifugation 30 min 4 °C at 20,000 g. GFP-Trap beads (Chromotek, Planegg, Germany) were added to lysate for 1 h before washing 4× with lysis buffer. Alternatively, endogenous WIP1 was immunoprecipitated from U2OS cells by a rabbit affinity-purified antibody generated against human WIP1 and immobilized on protein A/G UltraLink resin (Thermo Fisher Scientific, Waltham, MA, USA). Bound proteins were eluted with 2× loading buffer and analyzed by Western Blotting.
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4

Lentiviral Transduction of Bmal1 in Cells

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Flag-tagged mouse Bmal1 was cloned into pENTR/D-TOPO vector (Life Technologies) then recombined with pLV7 destination vector as previously described (Ramanathan et al., 2012 ). Mutations were introduced by PCR-based mutagenesis and all constructs were verified by sequencing. Production of recombinant lentiviral particles, infection and selection of Bmal1-complemented Bmal1−/−; Per2Luc lines was performed as described previously (Liu et al., 2008 (link)). Clonal cell lines were validated by genomic sequencing of the complemented Bmal1 gene.
Expression of Flag-tagged Bmal1 genes in the complemented cell lines was analyzed as before (Xu et al., 2015 (link)). Briefly, cells were lysed in RIPA buffer containing complete protease and phosphatase inhibitors (Sigma). Immunoblotting was done using the following primary antibodies: mouse anti-Flag (M2) (Sigma Cat. # F3165) and goat anti-beta actin (C-11) (Santa Cruz Biotechnology Cat. # sc-1615), and the following secondary antibodies: anti-mouse IgG-HRP (Santa Cruz Biotechnology Cat. # sc-2005) and anti-goat IgG-HRP (Santa Cruz Biotechnology Cat. # sc-2020). SuperSignal West Pico substrate (Pierce) was used for chemiluminescent detection on autoradiograph film.
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5

Proteomics and Phosphoproteomics Materials

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Materials used in proteomics and phosphoproteomics assessments: Isobaric TMT reagents (Thermo Fisher Scientific), BCA protein concentration assay kit (Thermo Fisher Scientific), Empore-C18 material for in-house made StageTips (3 M), Sep-Pak cartridges (Waters), Mass spectrometry (MS)-grade trypsin (Thermo Fisher Scientific), Lys-C protease (Wako), High-Select Fe-NTA phospohpeptide enrichment kit (Thermo Fisher Scientific), and cOmplete protease and phosphatase inhibitors (Millipore Sigma). Unless otherwise noted, all solvents used for liquid chromatography (LC) were purchased from J.T. Baker all other chemicals were purchased from Thermo Fisher Scientific.
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6

Immunoblotting Protein Analysis Protocol

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Cells were harvested in lysis buffer containing 1% NP40, 150mM NaCl and 150mM Tris-HCl (pH 8.3) supplemented with cOmplete protease and phosphatase inhibitors (catalog numbers 11836170001 and 4906837001; MilliporeSigma) and subjected to immunoblotting. Briefly, total protein amounts were adjusted across samples using a bicinchoninic assay (BCA) kit (23225, Thermo Fisher Scientific). Equal amounts of total proteins in extract samples were run on SDS-PAGE gels and transferred to 0.45 μm polyvinylidene fluoride (PVDF) membranes (IPVH00010, MilliporeSigma). Unspecific binding sites in PVDF membranes were blocked with 10% skim milk, followed by overnight incubation with primary antibodies. After extensive washing with TBS-Tween, the membranes were incubated with secondary antibodies and immunoreactive bands were visualized on X-ray films or a LI-COR Odyssey Fc digital imaging system (LI-COR Biosciences, NE).
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7

Proteomics and Phosphoproteomics Materials

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Materials used in proteomics and phosphoproteomics assessments: Isobaric TMT reagents (Thermo Fisher Scientific), BCA protein concentration assay kit (Thermo Fisher Scientific), Empore-C18 material for in-house made StageTips (3 M), Sep-Pak cartridges (Waters), Mass spectrometry (MS)-grade trypsin (Thermo Fisher Scientific), Lys-C protease (Wako), High-Select Fe-NTA phospohpeptide enrichment kit (Thermo Fisher Scientific), and cOmplete protease and phosphatase inhibitors (Millipore Sigma). Unless otherwise noted, all solvents used for liquid chromatography (LC) were purchased from J.T. Baker all other chemicals were purchased from Thermo Fisher Scientific.
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