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27 protocols using anti p53

1

Antibodies and Reagents for Cell Signaling

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Anti-LEFTY, anti-Smad2, and anti-phospho-Smad2 at serine 255 (pSmad2) antibodies were purchased from Abcam (Cambridge, MA, USA). Anti- XIAP, anti-bax, anti-β-catenin, anti-HNF-1β, and anti-p27Kip1 antibodies were bought from BD Biosciences (San Jose, CA, USA). Anti-p21waf1, anti-cyclin D1, anti-p53, anti-bcl2, and anti-Ki-67 antibodies were purchased from Dako (Copenhagen, Denmark). Anti-cyclin A, and anti-cleaved caspase 3 antibodies were from Novocastra (Newcastle, UK), and Cell Signaling Technology (Danvers, MA, USA), respectively. CDDP and the anti-β-actin antibody were purchased from Sigma-Aldrich Chemicals (St. Louis, MO, USA). Recombinant transforming growth factor (TGF)-β1 was purchased from R&D Systems (Minneapolis, MN, USA).
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2

Western Blot Protein Analysis Procedure

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Western blot analysis was carried out as described (Corno et al., 2017 (link)). Briefly, samples were fractionated by SDS-PAGE and blotted on nitrocellulose membranes. Blots were pre-blocked in PBS containing 5% (w/v) dried no fat milk, and then incubated overnight at 4°C with the following antibodies: anti-phospho-Akt (Ser473), anti-Akt (BD Science, Franklin Lakes, NJ, United States), anti-phospho-ERK1/2 (Thr202/Tyr204, Thr185/Tyr187), anti-ERK1/2, anti-AR (Millipore, Burlington, MA, United States); anti-Hsp90 (ac-Lys294) (Novus, Centennial, Colorado, United States), anti-Hsp90 (Santa Cruz Biotechnology, Dallas, TX, United States), anti-acetylated alfa-tubulin (Sigma-Aldrich, Milan, Italy), anti-Bax and anti-FLIPL (Sigma-Aldrich, Milan, Italy), anti-p53 (Dako, Santa Clara, CA, United States), anti-cleaved caspase-3 (Asp175) and anti-cleaved caspase-7 (Asp198) (Cell Signaling, Danvers, MA, United States). Anti-vinculin (Sigma-Aldrich, Milan, Italy), anti-β-tubulin (Abcam, Cambridge, United Kingdom) or anti-actin (Sigma) antibodies were used as control for loading. Antibody binding to blots was detected by chemo-luminescence (Amersham Biosciences, Cologno Monzese, Italy). Three independent experiments were performed.
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3

Immunohistochemistry for Cancer Biomarkers

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Immunohistochemistry (IHC) for P53, PAX8, FOXJ1, estrogen receptor and β-catenin was performed on 4-μm TMA sections using a BOND-MAX automated immunostainer and a Bond Polymer Refine Detection kit (Leica Microsystems, Wetzlar, Germany) according to the manufacturer’s guidelines. The primary antibodies were anti-P53 (DAKO, 1:1000), anti-PAX8 (Proteintech, 1:300), anti-FOXJ1 (Invitrogen, 1:100), anti-estrogen receptor (DAKO, 1:100), and anti-β-catenin (BD Transduction, 1:800). Estrogen receptor and β-catenin were considered positive when more than 10% of tumor cell nuclei were strongly stained.
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4

Prostate Cancer Protein Regulation

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anti-AR (Santa Cruz Biotechnology; N20 and C19 clones), anti-AR-v7 (Precision Antibodies), anti-H2A.Z (19 (link)), anti-MDM2 (Santa Cruz N20 and SMP14), anti-HA (Santa Cruz Biotechnology; Y11 clone), anti-FLAG (Sigma), anti-p53 (Dako), anti-α-tubulin (Sigma), and anti-ubiquitin (Santa Cruz Biotechnology) were included in this project. Plasmids used were pPSA-Luc, pARE3-Luc, pCMV-β-gal, pHA-ubiquitin, pMYC-MDM2, pFLAG-His-AR (20 (link)) and pFLAG-His-AR-K311R and pFLAG-V7-AR mutants generated by in vitro mutagenesis (QuikChange; Stratagene). Lentiviral AR careers were prepared as previously described (21 (link)).
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5

Western Blot Analysis of Cell Signaling

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Samples were treated with lysis buffer [Tris–HCl 50mM pH7.4, 10% NP-40, 0.25% NaDesoxycholate, EDTA 1mM, NaCl 150mM, PMSF 1mM, protease inhibitor cocktail (Roche)] and loaded onto pre-cast 4–12% gradient acrylamide gels (NuPAGE, Invitrogen). After electro-blotting, filters were incubated with anti-AKTIP (Sigma), anti-TRF2 (Novus Biologicals), anti-actin-HRP conjugated (Santa Cruz), anti-cyclin A (Santa Cruz), anti-cyclin B (Santa Cruz), anti-cyclin E (Upstate Biotechnology), anti-p53-pSer15 (Cell Signaling Technology), anti-p53 (DakoCytomation), anti-ATM-pS1981 (Rockland Immunochemicals), anti-ATM (Genetex), anti-ChK1-PSer345 (Cell Signaling Technology), anti-AKT (Cell Signaling Technology), anti-PCNA (Santa Cruz), anti-RPA70 (Santa Cruz), or anti-TRF1 (Santa Cruz). Filters were then incubated with appropriate HRP-conjugated secondary antibodies (Santa Cruz), which were detected using the enhanced chemiluminescence system (ECL plus, Amersham). Signals were quantified with Image J software.
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6

Antibodies and Mitochondrial Inhibitors

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The following antibodies were used in this study: anti-p53 (Dako); anti-Bcl-w, anti-Bcl-XL, anti-Bax, anti-Bak, and anti-phospho-Akt (Cell Signaling Technology); anti-Akt, anti-ND2, anti-NDUFS1, and anti-NDUFV2 (Santa Cruz Biotechnology); anti-complex І, anti-complex II, anti-complex III, and anti-complex IV (Abcam); anti-MMP-2 (Calbiochem); anti-PI3K (Upstate Biotechnology); anti-β-actin (Sigma); anti-ND-1, and anti-ND5 (Novus Biologicals). Inhibitors of the mitochondrial respiratory chain were obtained from Sigma.
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7

Immunohistochemical Analysis of DLL3, BID, CDK4, and P53

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Formalin-fixed tissue paraffin block made 3 mm white plate for IHC analysis. We used anti-DLL3 antibody (1:200; Proteintech), anti-BID antibody (1:200; Proteintech), anti-CDK4 antibody (1:200; Proteintech) and anti-P53 (1:100; Dako) for tissue staining. Three pathologists used a semi-quantitative immune response scoring algorithm to evaluate DLL3 staining independently. The semiquantitative immunoreactivity score (IRS) is between 0 and 30, based on the increase in IHC staining intensity (0, negative; 1, weak; 2, middle; 3, strong) and the percentage of positive tumor cells (one point per 10% increase, the percentage of positive tumor cells 1–10) [19 (link)]. The critical value of p53 staining was 10% (≤ 10% of tumor cells were negative and > 10% were positive) [20 (link),21 (link)]. Disagreements were resolved by three pathologists negotiated under a multi- lens.
Wilcoxon test and paired analysis between normal tissue and tumor tissue in the same patient were used to analyze the expression of DLL3. Kaplan-Meier curve was performed to analyze the survival of DLL3.
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8

Immunoblotting Protocol for Cell Signaling

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For immunoblotting, whole cell protein extracts were prepared with lysis buffer (50 mM Tris-HCl pH 7.4, 150 mM NaCl, 50 mM NaF, 1 mM EDTA, 10-% NP-40, 1% Triton-X and protease inhibitors), subjected to SDS-PAGE (10 or 12%) and blotted onto PVDF membranes (Roth, Karlsruhe, Germany). Primary antibodies against PARP, CDK4, CDK1, cyclin B1, cyclin E, p21, HDAC1, HDAC2, HDAC3, HDAC8, and β-actin were purchased from Santa Cruz Biotechnology (Santa Cruz, CA, US). Anti-p27Kip1, -cyclin D1, -CDK2, -phosphoCDK2 (Thr160), -phosphoCDK4 (Thr172), and -phosphoH2AX (Ser139) were purchased from Cell Signaling Technology (Danvers, MA, US), and anti-p53 from Dako (Glostrup, Denmark). Blots were developed using corresponding horseradish peroxidase- conjugated secondary antibodies (Dako, Jena, Germany) at room temperature for 1 h and the Amersham™ ECL™ prime western blotting detection reagent (GE Healthcare) in accordance with the manufacturer‘s protocol. Chemiluminescence signals were detected by the ChemiDocTouch Imaging System (BioRad Laboratories Inc., Herkules, CA) and images were processed using ImageLab 5.2 Software (BioRad Laboratories Inc.), normalized to their loading controls and expressed as fold-change (Δ) compared to controls.
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9

Immunohistochemical Analysis of ATRX, p53, and CCND1

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Immunohistochemistry was performed on 4-μm-thick sections of formalin-fixed paraffin embedded blocks with a ventana Benchmark XT Device. The following antibodies were used after antigen retrieval to assess ATRX (anti-ATRX, Sigma, polyclonal, dilution 1/400), p53 (anti-p53, Dako clone DO.7, dilution 1/200) and CCND1 (anti-CCND1, Ventana, clone SP4). p53 protein was defined as ‘highly expressed’ when we observed a strong nuclear expression in more than 10% of the nuclei.
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10

Cell Lysis and Western Blot Analysis

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U2OS cells were harvested in lysis buffer (150 mM NaCl, 1% Triton X-100, 50 mM Tris-HCl pH 8.0; Sigma-Aldrich) supplemented with 1x PIC-C (Calbiochem), incubated on ice for an hour, then centrifuged (13,000 rpm at 4 °C for 5 minutes). The supernatant lysates were mixed with the same amount of 2x SDS loading buffer containing 5% β-mercaptoethanol (Sigma-Aldrich) and boiled for 5 minutes. The lysates were separated in SDS-PAGE, transferred to Amersham Hybond ECL-membrane (GE Healthcare) and incubated with the following primary antibodies: anti-p53 (Dako, IS616), anti-S15 P p53 (Cell signalling, 9284), 1BP7G5 anti-RPB1 (from L. Tora, IGBMC), anti-S2P RPB1 (Abcam, ab5095) and anti-S5P RPB1 (Abcam, ab5131), anti-GAPDH (Millipore, MAB374); then the following secondary antibodies: RAM-HRP (Dako, P0260) and GAR-HRP (Dako, P0448). Chemiluminescent detection was conducted using Immobilon Western Chemiluminescent HRP substrate (Millipore).
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