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33 protocols using p bad

1

Molecular Pathways of Embelin-Induced Apoptosis

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Embelin was purchased from Tocris Bioscience (Ellisville, MO). MTT was purchased from Sigma (St. Louis MO, MA). LY294002 and zVAD-fmk was purchased from Calbiochem (San Diego, CA, USA). XIAP antibody was purchased from BD Transduction lab (San Jose, CA, USA). Antibodies against caspase-9, caspase-3, PARP, p-AKT, p-Bad, Bcl-2, Bcl-Xl, Beta-actin, Survivin and Bid were purchased from Cell Signaling Technologies (Beverly, MA, USA). Cytochrome c and GAPDH antibodies were purchased from Santa Cruz Biotechnology, Inc. (Santa Cruz, CA, USA). cIAP-1 antibody was purchased from R&D (USA). Annexin V/PI staining kit was purchased from Molecular Probes (Eugene OR, USA).
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2

Protein Expression and Pathway Analysis

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Protein samples were prepared with RIPA buffer (Thermo Scientific Inc., Waltham, MA, USA) containing 1% protease inhibitor. Equal weight of total protein was separated by electrophoresis on SDS/PAGE. After the proteins had been transferred onto a polyvinylidene difluoride membrane (Millipore, Bedford, MA, USA), the blots were incubated with blocking buffer (1 X PBST and 5% skim milk) for 1 hour at room temperature and then hybridized with primary antibodies overnight at 4°C, followed by incubation with horseradish peroxidase-conjugated secondary antibody for 1 hour at room temperature. The blots were obtained by X-ray film exposure, and the intensities were quantified by densitometry analysis (Digital Protein DNA Imagineware, Huntington Station, NY).
The primary antibodies used in this study were anti-Flag (Sigma-Aldrich Co. LLC., St. Louis, MI, USA, F1804), AKT (cell signaling, #9272), p-Akt-308 (cell signaling, #13038), p-AKT-473 (cell signaling, #4060), Bad (cell signaling, #9239), p-Bad (cell signaling, #5284), Bax (cell signaling, #2772), cleaved-caspase-3 (cell signaling, #9661), cleaved-PARP (cell signaling, #5625), IL-6 (R&D system, #6708) and beta-actin (sigma, A5316).
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3

Western Blot Analysis of Cellular Proteins

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Cells were lysed in RIPA buffer containing 150 mM NaCl, 50 mM Tris pH 8.0, 1% NP-40, 0.5% sodium deoxycholate and 0.1% SDS supplemented with protease inhibitors (Complete, Roche) and phosphatase inhibitor cocktails II and III (Sigma) and boiled for 10 min after addition of sample buffer (60 mM Tris pH 6.8, 5% glycerol, 1% SDS, 2% β-mercaptoethanol, 0.02% bromophenol blue) before SDS gel electrophoresis followed by western blotting. Primary antibody against HSP90 (SC-7947) was purchased from Santa Cruz. Antibodies against acetyl CoA carboxylase 1 (#4190), beta-actin (#4967), cl-PARP (#9542), p-AKT (#4060), p-PRAS40 (#2997), p-S6 (#2211), p-4EBP1 (#9456) and p-BAD (#5284) were from Cell Signaling. Secondary antibodies were obtained from Bio-Rad Laboratories and Thermo Scientific. Uncropped blots are shown in Supplementary Fig. 7.
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4

Comprehensive Protein Expression Analysis

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Western blot analysis was performed as preciously described. Lysates of treated cells or tumor samples were collected and lysed in radioimmunoprecipitation assay buffer. Equal amounts of proteins were resolved on SDS-PAGE and then transferred onto a polyvinylidene difluoride membrane. Specific primary antibodies were used for the following molecules : IĸBα(Cabiochem, San Diego, CA, USA), p65, Iĸĸα, Iĸĸβ, AKT, p-AKT, MEK, p-MEK, ERK, p-ERK, p38, caspase-10, caspase-1, cyclinA, cyclinB, PUMA, BID, CIAP, Bad, p-Bad, PKC (Cell signaling Technology), JNK2/1, p-JNK, TSP1, Bcl-2, Bcl-xL, Bax, APAF1, Fas, caspase-8, Mrg1, cyclinD, p53, MMP1 (Santa Cruze Biotechnology, CA), caspase-9, caspase-3 (BioLegend). β-Actin (Santa Cruze Biotechnology, CA) was used to assess the equal loading. The phosphorylated protein controls obtained from blots that had been stripped and re-probed for the same sample lane. Sixty microgram of cell protein extract was loaded per lane. CS-710 Calibrated Imaging Densitometer (Bio-Rad) was utilized for densitometric quantification.
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5

Immunoblotting Analysis of Signaling Pathways

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MM cells were harvested and lysed as mentioned previously.9 (link) Lysates were then measured for protein quantification, boiled (100 °C for 5 min), run on sodium dodecyl sulfate-polyacrylamide gel electrophoresis 4–15% gradient gels at 110 V (Bio-Rad, Hercules, CA, USA), transferred to nitrocellulose membranes and immunoblotted with antibodies to the following: pCHK2 (Thr68), pCHK1 (Ser345), pH2AX (Ser139), PIM1, PIM2, PIM3, Caspase-3, PARP, BAD, pBAD (Ser112), p21 Waf1/Cip1, MDR-1, pYAP1 (Ser127), YAP1, ABL1 and GAPDH (Cell Signaling, Beverly, MA, USA), which was used as a loading control. All antibodies were diluted 1:1000 in 5% bovine serum albumin/TBST (TBS plus Tween-20).
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6

Molecular Mechanisms of Anti-VEGF Therapies

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Vascular endothelial growth factor was purchased from R&D systems (Minneapolis, MN, USA). Antibodies against phosphor-VEGFR2 (p-VEGFR2, Y1175), VEGFR2, Akt, p-Akt (S473), Caspase (cysteine-aspartic proteases) 9, and p-BAD (Cell Signaling Technology; Danvers, MA, USA). Aflibercept (40 μg/μL) and ranibizumab (10 μg/μL) were from the pharmacy of Massachusetts Eye and Ear (Boston, MA, USA). The primary antibody against β-actin and secondary antibodies of the horseradish peroxidase (HRP)-conjugated goat anti-rabbit IgG and anti-mouse IgG were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, USA). Enhanced chemiluminescent substrate for detection of HRP was obtained from Thermo Fisher Scientific (Waltham, MA, USA).
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7

Western Blot Analysis of Apoptosis Markers

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Ganetespib was purchased from Medkoo Biosciences, Inc. (Chapel Hill, NC). Lapatinib was purchased from LC Laboratories (Woburn, MA). Cycloheximide was purchased from Sigma-Aldrich (St. Louis, MO). Primary antibodies specific to cleaved PARP, cleaved caspase 3, cleaved caspase 8, cleaved caspase 9, Bcl-2, ErbB2, phospho-ErbB2 (pErbB2), Akt, pAkt, Erk2, pErk1/2, mTOR, pmTOR, Cyclin B1, Src, pSrc, Bad, pBad, GSK3, and pGSK3 were purchased from Cell Signaling Technology (Danvers, MA). Primary antibodies against CDK1, Cyclin D1, p27, caspase 8, caspase 9, HSP90, HSP70, and β-actin were purchased from Santa Cruz Biotechnology (Santa Cruz, CA). Secondary mouse and rabbit antibodies were purchased from Thermo Scientific (Rockford, IL).
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8

Protein Signaling Pathway Analysis

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All chemicals and reagents used in this study were purchased from Merck (Merck KGaA, Darmstadt, Germany). The antibodies used in this study were purchased from different manufactures including CD90 and CD45 (BD Biosciences, East Rutherford, NJ, USA); p-Akt, p-IGF1R, PI3K, p-PI3K, Akt, p-Bad, Bcl-xL, Fas-L, and FADD (Cell Signaling Technology, Danvers, MA, USA); b-actin, AMPKa, p-AMPKa, and Sirt1 (Santa Cruz Biotechnology, Dallas, TX, USA); and Caspase-8 and TGF-b (Promega-US).
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9

Investigating Lapatinib-Induced Apoptosis

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Lapatinib was purchased from LC Laboratories (Woburn, MA). MG132, CHX, RNase A, and propidium iodide (PI) were purchased from Sigma-Aldrich (St. Louis, MO). LY294002 and PD98059 were purchased from Alexis Biochemicals (San Diego, CA). EGF was purchased from Peprotech (Rocky Hill, NJ). Rapamycin and antibodies against pErbB2 (Tyr1221/1222), ErbB2, pEGFR (Tyr1068), EGFR, pmTOR (Ser2448), mTOR, pAkt (Ser473), Akt, pBad, Bad, and PARP were purchased from Cell Signaling Technology (Danvers, MA). Antibodies against CIP2A, c-Myc, pErk1/2 (Thr202/Tyr204), Erk2, Caspase-3, cleaved Caspase-3, cyclin D1, and β-actin were purchased from Santa Cruz Biotechnology (Santa Cruz, CA).
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10

Western Blot Analysis of AKT Signaling

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Western analyses were performed as described25 (link). For each experiment, lysates from a cell line grown with or without serum were run on the same gel and all gels were run at the same time. Two gels were transferred to a single membrane. If more than one membrane was used for an experiment, a single solution for each primary and secondary antibody pair was made and divided between the two membranes that were subsequently hybridized in separate trays. Antibodies used included pAKT(S473) (product #4060), pAKT(T308) (product #2965); pan-AKT (product #2920 and 4691), pPRAS40 (product #2997), PRAS40 (product # 2610), pS6(S235) (product #2211), pS6(S240) (product #5364) S6 (product #2317 and 2217), pFOXO1/FOXO3a (product #9464), FOXO3a (product #2497), pGSK3α/β (product #9331), GSK3α/β (product #5676), pBAD (product #4366) and BAD (product #9239) from Cell Signaling Technologies (Danvers, MA, USA) or β-actin (product #A5441) from Sigma-Aldrich (St. Louis, MO, USA). Membranes were scanned and intensities calculated using a semi-automated infrared imaging system (Odyssey scanner and Image Studio Lite software, LiCor BioSciences Inc., Lincoln, NE, USA). Histograms show ratios of infrared signal intensities of indicated antibodies. For experiments using two membranes, histograms of infrared signal ratios graphed by membrane are shown in Supplementary Fig. 8.
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