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93 protocols using p s6k

1

Neferine and Temozolomide Experimental Protocol

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Neferine was isolated according to the previous method [6 (link)]. Temozolomide was obtained from Orion Corporation (New Jersey, USA). The primary antibodies of FAK, p-FAK, S6K, p-S6K, Beclin-1, LC3, Cleaved Caspase-3, and PARP were purchased from Cell Signaling (Danvers, MA, USA). The antibody for β-actin was obtained from Sigma (Kawasaki, Japan), the anti-mouse and anti-rabbit IgG horseradish peroxidase-conjugated secondary antibodies were purchased from GE Healthcare (Chicago, IL, USA).
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2

Protein Expression Analysis via Western Blot

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Tissues or cells were lysed in lysis buffer containing protease inhibitor cocktail. Following quantification, the protein lysates were resolved in an SDS-PAGE gel, transferred to a PVDF membrane (Millipore, Billerica, MA, USA), and immunoblotted with an antibody directed against GOLPH3, cyclin D1, p27, MMP9, AKT, p-AKT, mTOR, ERK, S6K (Proteintech Inc., Chicago, IL,USA), p-mTOR, p-ERK, p-S6K(Cell Signaling Technology Inc., Danvers, MA, USA), or β-actin (Vazyme, Piscataway, NJ, USA) and then a horseradish peroxidase-conjugated secondary antibody (Vazyme, Piscataway, NJ, USA). Bound antibody was visualized using standard chemical luminescence methodology. β-actin was used as a loading control.
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3

Eribulin and PI3K/mTOR Inhibitor Interactions

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Eribulin was kindly provided by Eisai Co. Ltd. (Tokyo, Japan). Everolimus (RAD001), BKM120, and BEZ235 were kindly provided by Novartis (Basel, Switzerland). Antibodies against p-AKT (S473), AKT, p-S6K, S6K, p-S6, S6, and GAPDH were obtained from Cell Signaling Technology (Danvers, MA, USA). Anti-β-actin was obtained from EMD Millipore (Billerica, MA, USA).
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4

Immunoblotting Analysis of TSCC Cells

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Western blot analysis was performed as described previously43 (link) to detect the expression levels of CyclinD1, p53, Bcl-2, caspase-3, cleaved-caspase-3, ERK1/2, p-ERK1/2, LC3, p62, PTEN, Akt, p-Akt, mTOR, p-mTOR, p-S6K, p-4E-BP1 and GAPDH (Cell Signaling Technology, MA, USA) in TSCC cells. GAPDH was used as the internal control. The intensity of each band was quantified using the image analyzing computer software Quantity One (Bio-Rad software).
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5

Antibody Immunoblotting Panel

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Antibodies against CaMKII, pCaMKII, AMPK, pAMPK, mTOR, pmTOR, S6K, pS6K, 4E-BP, ACC, pACC, and Cleaved caspase-3 were obtained from Cell Signaling Technology (Beverly, MA, USA). Antibodies against NQO were purchased from Invitrogen (Carlsbad, CA, USA). Anti-β-actin, anti-rabbit IgG, and anti-mouse IgG antibodies were purchased from Sigma-Aldrich Co. (St. Louis, MO, USA).
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6

Antibody Immunostaining and Invasion Assay

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The antibodies were purchased from indicated vendors: NEDD8, DEPTOR, pIκBα, pERK, ERK, pAKT, BIM, pS6K, p4EBP1, and 4EBP1 (Cell Signaling); ERBIN (Novus Biologics); CUL1, IκBα, AKT, and S6K (Santa Cruz); p21, and p27 (BD Biosciences); NOXA (Millipore), and NAE1 and β-actin (Sigma). The siRNAs targeting NOXA, ERBIN and control siRNA were described previously [22] (link), [23] (link). Immunostaining kit was obtained from DakoCytomation California, Inc. (Carpinteria, CA). ATP-lite kit was obtained from pERKin Elmer (Boston, MA). Boyden chamber for invasion assay was obtained from BD Bioscience (San Jose, CA).
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7

Hippocampal Protein Extraction and Analysis

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Individual hippocampi were sonicated in lysis buffer (10mM Tris, pH7.4, 100 mM NaCl, 1 mM EDTA, 1mM EGTA, 1mM NaF, 20 mM Na 4 P 2 O 7, 2mM Na 3 VO 4, 1% Triton X-100, 10 % glycerol, 0.1% SDS, and 0.5% deoxycholate) with Complete protease inhibitor cocktail (Roche, Indianapolis, IN) as we have previously published (14 (link)). Reducing agent (Thermo Scientific, Waltham, MA) and LDS (Thermo) were added to each sample. 20–30 μg of total protein was separated using NuPAGE 4–12% Bis-Tris gels (Thermo) and transferred onto nitrocellulose membrane (Bio-Rad, Hercules, CA) as previously described (13 (link)). Using Rockland (Pottstown, PA) Blocking Buffer for Fluorescent Western Blotting and the following antibodies, the blots were imaged and analyzed with Odyssey infrared scanning (LiCor Bioscience, Lincoln, NE) as previously described. Mouse monoclonal anti-β-actin antibody was purchased from Sigma-Aldrich (St. Louis, MO) and used at 1:10,000. Primary antibodies purchased from Cell Signaling Technology (Danvers, MA) and used at 1:500 included: pS6K (Thr389, #9205), S6K (#9202), pAkt (Ser473, #9271), pAkt (Thr308, #9275), Akt (#9272), p-mTOR (Ser2448, #2971), mTOR (#2972), pAMPKα (Thr172, #2531), AMPKα (#2532). Secondary antibodies were Alexa Fluor 680 conjugated anti-mouse IgG (1:12,500, Thermo) and Infrared Dye 800 conjugated anti-rabbit IgG (1:12,500, Rockland).
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8

Immunoprecipitation and Western Blotting

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Anti-FLAG monoclonal antibody M2 (Sigma-Aldrich), anti-MSI2 monoclonal antibody EP1305Y (Abcam) and normal Rabbit IgG PP64B (Millipore) were used for immunoprecipitation. For Western blotting the following antibodies were used: mouse monoclonal BCAT1 (clone ECA39, BD Transduction Laboratories) and Bcat1 OTI3F5 (OriGene), rabbit monoclonal S6K (#9202 and #2708), pS6K (#9234), AKT (#4691), pAKT, T308 (#13038) and pAKT, S473 (#4060) from Cell Signaling, rabbit monoclonal MSI2 EP1305Y, mouse monoclonal HSP90 F-8 (Santa Cruz Biotech) and mouse monoclonal β-tubulin BT7R (Thermo Fisher Scientific).
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9

Cell Lysis and Protein Analysis

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Cells were lysed in ice-cold buffer containing 50 mmol/L Tris-HCl, pH 7.4, 0.1 mmol/L EDTA, 0.1 mmol/L EGTA, 1% NP-40, 0.1% sodium deoxycholate, 0.1% SDS, 100 mmol/L NaCl, 10 mmol/L NaF, 1 mmol/L sodium pyrophosphate, 1 mmol/L sodium orthovanadate, 1 mmol/L Pefabloc SC, and 2 mg/mL protease inhibitor cocktail (Roche Diagnostics Corp). Protein concentrations were determined using the DC Protein Assay Kit (Bio-Rad Laboratories). Cell lysates containing 12.5 to 25 μg of protein were analyzed by SDS-PAGE and immunoblotting. Primary antibodies used include the following: Cav-1 (No. 610058; BD Biosciences), LC3B (No. 2775; Cell Signaling), SQSTM1/p62 (No. ab56416; Abcam), and β-actin (No. sc-69879; Santa Cruz Biotechnology), PKB/AKT (protein kinase B, also known as Akt; No. 9272; Cell Signaling), p-AKT (No. 9277; Cell Signaling), pS6K (No. 9205; Cell Signaling), S6K (No. 9202; Cell Signaling), ATG5 (No. 2630; Cell Signaling), connexin-43 (Cx-43; No. ab11370; Abcam), vinculin (No. v9131; Sigma), and HSP90 (No. 610419; BD Biosciences). Secondary antibodies were fluorescence-labeled antibodies (LI-COR Biotechnology). Bands were visualized using the Odyssey Infrared Imaging System (LI-COR Biotechnology). Densitometry analysis was performed with ImageJ software (National Institutes of Health) or Image Studio Lite (LI-COR Biosciences).
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10

Immunoblotting Analysis of Histone Modifications

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Immunoblotting analysis was performed as previously described65 (link). Cells were washed twice with ice cold PBS, and harvested in protein lysis buffer (50 mM HEPES [pH7.4], 150 mM NaCl, 1% Triton X-100, 1 mM EDTA, 1 mM EGTA, 1 mM glycerophosphate, 2.5 mM sodium pyrophosphate, 1 mM Na3VO4, 20 mM NaF, 1 mM phenylmethylsulfonyl fluoride, 1 mM DTT, 1× complete protease inhibitor tablet [Roche]). Total cell lysates were separated on 4-12% Bis-Tris gels (Life Technologies), transferred onto PVDF membrane (Merck Millipore). The blots were probed with antibodies for H3, H3K4me2, H3K9me2, H3K27me2 (#9847 from Cell Signaling Technologies for above antibodies; 1:1000), H3K27me3 (Cell Signaling Technologies; #9733, 1:1000), SUZ12 (Cell Signaling Technologies; #3737, 1:1000), Ezh2 (Cell Signaling Technologies; #5246, 1:1000), RpAb46/48 (Santa Cruz Biotechnology; #33170, 1:1000), EED (Santa Cruz Biotechnology; #28701, 1:1000), p-S6K (Thr389, Cell Signaling Technologies; #9234, 1:1000) and S6K (Cell Signaling Technologies, MA, USA; #9202, 1:1000) as indicated in figures. Protein signals were detected using HRP conjugated secondary antibodies and enhanced chemiluminescence (ECL) western blotting detection regents (Thermo Fisher Scientific, MA, USA).
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