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8 protocols using brca1 sc 6954

1

Protein Extraction and Western Blot Analysis

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Cell lysates were generated by lysis in NETN buffer (50 mM Tris-HCl pH = 7.4, 250 mM NaCl, 5 mM EDTA, 0.1% NP-40, 10 mM NaF, 200 μM Na2VO3, 0.5 mM PMSF, and 1x protease inhibitor cocktail) on ice for 30 min. Non-soluble debris was precipitated by a 5 min 12000 rpm spin at 4 °C and discarded. Lysate was treated with 4x loading buffer (0.5 M Tris-HCl pH 6.8, 277 mM SDS, 40% glycerol, bromophenol blue, 4% 2-mercaptoethanol), ran on a 10% SDS-PAGE gel, and transferred onto a PVDF membrane for 1–2 hr at 500 mA. The following Santa Cruz (Dallas, TX, USA) antibodies were used: BRCA1 (sc-6954) and RAD51 (sc-8349 and in-house aliquot B32). The following Cell Signaling (Danvers, MA, USA) antibodies were used: ATM (2873), GAPDH (5174), Chk2 (2662), pChk2 T68 (2661), Chk1 (2345), and pChk1 S345 (2341). Other antibodies included DEK (610948 BD Bioscience, San Jose, CA, USA), DEK (16448-1-AP, Protein Tech, Rosemont, IL, USA), DEK (in-house K-877)72 (link), DNA-PKcs (ab1832, Abcam, Cambridge, MA, USA), pDNA-PKcs S2056 (ab18192), pATM S1981 (AF1655, R&D Systems, Minneapolis, MN), γH2AX (05-636, Millipore, Darmstadt, Germany), MRE11 (GTX70212, genetex, San Antonio, TX, USA), and NBS1 (NB100-143SS, Novus Biologicals, Littleton, CO, USA).
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2

Olaparib Cytotoxicity and Apoptosis Assessment

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Olaparib (AZD2281, Ku-0059436) was obtained from Targetmol (Shanghai, China). Proguanil was obtained from Selleck Chemicals (Shanghai, China). Acridine orange/ethidium bromide (AO/EB) staining was obtained from Kehang Biotechnology (Changsha, China), and the FITC Annexin V Apoptosis Detection kit was from BD Pharmingen (NJ, USA). Rabbit anti-human antibodies specific for the following proteins were obtained from Cell Signaling (MA, USA): Phospho-Histone H2A.X (Ser139) and β-actin. Phospho-ATM (Ser1987) was obtained from Abcam (MA, USA). BRCA1 (sc-6954) was obtained from Santa Cruz Biotechnology (Texas, USA). Bcl-2 polyclonal antibody and Bax polyclonal antibody were obtained from Bioworld Technology (MN, USA) and Biyotime (Shanghai, China) respectively.
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3

Analyzing Protein Expression via Immunoblotting

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To analyze protein expression in cells, immunoblotting analysis was performed as previously described [2 (link)]. Antibodies against the following proteins were obtained from Santa Cruz Technology (California, US): Aur A (sc-25425), Aur B (sc-25426), BRCA1 (sc-6954), CDK2 (sc-163), CDK4 (sc-260), CDK6 (sc-177), cyclin D1 (sc-718), cyclin E (sc-247), cyclin A (SC-751). Antibodies against BRCA2 (19791-1-AP) and cyclin B1 (cs-4135) were obtained from Proteintech (Chicago, USA) and Cell Signaling Technology (Massachusetts, US), respectively. The detection of β-actin (A2228, Sigma Aldrich, St. Louis, MO) was used as a loading control. The secondary antibodies were F(ab)2 fragments of donkey anti-mouse immunoglobulin or of donkey anti-rabbit immunoglobulin linked to horseradish peroxidase from Cell Signaling Technology (Massachusetts, US). Immunoblotting reagents were from an electrochemiluminescence kit (Amersham Biosciences). To test whether the expression levels of proteins were regulated through proteasome-mediated degradation, cells were exposed with 20 μM MG132 (#S2619, Selleck Company, Texas, America) for 3 h and then harvested for Western blotting analysis.
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4

DNA Damage Response Protein Analysis

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The antibodies anti-53BP1 (ab175933, 1:200 dilution), anti-RPA (ab2175, 1: 200 dilution), RAD51 (ab63801, 1:1000 dilution) and DNA2 (ab96488, 1:1000 dilution) were purchased from Abcam, USA. Antibodies anti-γH2AX (2577, 1:800 dilution), GAPDH (5174, 1:1000 dilution) were purchased from Cell Signaling, USA. BRCA1 (sc-6954) was purchased from Santa Cruz Biotechnology. Antibodies anti-SMARCAL1 (A301-616A, 1:1000 dilution), RPA2-pS4/S8 (A300-245A, 1:200 dilution), ZRANB3 (A303-033A, 1:1000 dilution) was purchased from Bethyl. BRCA2 (OP95, 1:500 dilution) was from Milipore. Antibodies specific for FEN1 (NB100-150, 1:1000 dilution), WRN (NBP1-31,895, 1:1000 dilution), HLTF (NB100-280, 1:2000 dilution) were purchased from Novus Biologicals (USA). Mouse anti-BrdU (347,580, 1:40) was purchased from BD Biosciences. AF647 (A-21247, 1:1000) and AF488 (A-11001, 1:1000) were purchased from ThermoFisher Scientific. DNA-PKcs inhibitor: NU-7441 (HY-11006) were purchased from MedChem Express (USA). MRE11 inhibitor: mirin (M9948) was purchased from Sigma-Aldrich.
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5

Western Blot Analysis of Cell Extracts

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Whole cell extracts were either separated on a 7% Tris-Acetate polyacrylamide (PA) gel (HUWE1, BRCA1) or on a 10% Tris-Glycine PA gel and transferred to an Immobilon-FL membrane (Millipore) for subsequent immunoblotting. Primary antibodies were detected using infrared (IR) Dye-conjugated secondary antibodies (Rockland). The signal was visualized using direct IR fluorescence via the Odyssey Scanner, LI-COR Biosciences. Primary antibodies: BRCA1 (sc-6954, Santa Cruz), Cdc6 (ab155759, Abcam), c-Myc (sc-789, Santa Cruz), HDAC2 (sc-9959, Santa Cruz), HUWE1 (A300-486A, Bethyl Laboratories), p53 (sc-6243, Santa Cruz), Polλ (A301-640A-1, Bethyl Laboratories), TopBP1 (NB100-217, Novus Biologicals), Tubulin (T9026, Sigma-Aldrich). All original images of immunoblots are depicted in Supplementary Fig. S1.
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6

Immunofluorescence Analysis of DNA Damage Markers

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Cells were seeded on glass coverslips coated with poly-L-lysine (Sigma-Aldrich, St. Louis, MO, USA) and allowed to attach for 48 hr followed by 1.67 Gy IR treatment (IBL 637, CIS Bio International, Gif-sur-Yvette, France). After washed with phosphate buffered saline (PBS), cells were fixed in 4% paraformaldehyde in PBS for 10 min at room temperature. The fixed cells were then permeabilized with 0.1% Triton X-100 in PBS for 10 min. After 30 min of blocking with 1% BSA in PBS, cells were washed in PBS and incubated with primary antibodies for 3 hr. After three times washed in PBS containing 0.05% Triton-X for 5 min, the cells were incubated with secondary antibodies for 1 hr. Finally, cells were washed three times with PBS containing 0.05% Triton-X and embedded in 1 μg/ml DAPI (Sigma-Aldrich) containing mounting solution on glass slides. The cells were visualised with an Olympus fluorescence microscope. Images were captured using a Spot advanced imaging system. The primary antibodies used were γH2A.X (05-636, Millipore-Upstate, Temecula, CA, USA), BRCA1 (sc-6954, Santa Cruz Biotechnology, CA, USA), 53BP1 (sc-22760, Santa Cruz Biotechnology) and MDC1 (A300-053A, Bethyl Laboratories, Montgomery, TX, USA).
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7

Protein Expression Profiling Protocol

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Protein lysates were extracted in EDTA Lysis Buffer (ELB) (0.25 M NaCl, 0.1% IEPGAL, 0.25 M Hepes, 5 mM EDTA, 0.5 mM DTT), separated on a SDS PAGE gel, transferred to a PVDF membrane followed by immunoblotting. Antibodies were purchased from SantaCruz (Pin1- sc15340, GAPDH - sc32233, Mcl-1 - sc12765, CtIP - sc271339, BRCA1 -sc6954 and Cleaved Caspase 3 - sc56055) and Cell Signalling [Chk2–2662 and 2197 (T68)] (Santa Cruz Biotechnology, Santa Cruz, CA, USA).
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8

Molecular Markers for DNA Damage Response

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Antibody to Phospho‐S345‐Chk1 (#2348) and Phospho‐S10‐Histone H3 (#53348) was purchased from Cell Signaling Technology (Danvers, MA, USA); BRCA1 (sc‐6954), Cyclin A (sc‐2712682), Chk1 (sc‐8408), and ATR (sc‐1887) from Santa Cruz (Dallas, TX, USA); p53 (Ab‐6, Clone DO‐1, MS‐187‐P0) from Thermo Fisher Scientific; 53BP1 (MAB3802) and γH2AX S139 (05‐636) from MilliporeSigma (Burlington, MA, USA); and FANCD2 (NB100‐182) from Novus Biologicals (Centennial, CO, USA). The polyclonal anti‐Timeless antibody was generated previously [28 (link)].
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