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6 protocols using anti rad50

1

ATM/DNA-PK Regulation of DDR Signaling

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HCT116 Flp-In T-REx cells were treated with 10 μg/mL doxycycline (Dox) for 16 hr to induce the expression of homeodomain proteins. KU-55933 (EMD Millipore) and NU-7441 (R&D Pharmaceuticals; 3712) were used to treat cells for 1 hr for ATM or DNA-PK inhibition, respectively. DNA-damaging agents and hydrogen peroxide treatments were used to treat cells as indicated in figure legends. After treatment, cells were scraped into PBS and centrifuged at 800 × g for 2 min. Cells were lysed with cell lysis buffer, and lysates were clarified at 10,000 × g for 10 min. The protein concentrations of the lysates were quantified using Bradford assay, and protein levels were normalized for all samples. Primary antibodies used were anti-ATM (Santa Cruz), anti-phospho-Ser1981-ATM (Abcam), anti-Kap1 (Abcam; ab22553), anti-phospho-Ser824-Kap1 (Bethyl Laboratories; A300–767A), anti-Nbs1 (Genetex; GTX70224), anti-Rad50 (Genetex; GTX70228), anti-Mre11 (Genetex; GTX70212), anti-MBP (Rockland; 200–401–385), anti-Flag (Sigma; A1205), anti-β-actin (Cell Signaling; 4970), anti-Chk2 (Genetex; GTX70295), anti-phospho-Thr68-Chk2 (Cell Signaling; 2661S), anti-phospho-Ser15-p53 (Abcam; ab1431), and anti-phospho-Ser15-p53 (mouse) (Assay Biotech; A7180). Alexa Fluor 68-anti-rabbit and IRDye 800 anti-mouse were the secondary antibodies used. Membranes were scanned and quantified using the Odyssey system (Li-Cor).
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2

ATM/DNA-PK Regulation of DDR Signaling

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HCT116 Flp-In T-REx cells were treated with 10 μg/mL doxycycline (Dox) for 16 hr to induce the expression of homeodomain proteins. KU-55933 (EMD Millipore) and NU-7441 (R&D Pharmaceuticals; 3712) were used to treat cells for 1 hr for ATM or DNA-PK inhibition, respectively. DNA-damaging agents and hydrogen peroxide treatments were used to treat cells as indicated in figure legends. After treatment, cells were scraped into PBS and centrifuged at 800 × g for 2 min. Cells were lysed with cell lysis buffer, and lysates were clarified at 10,000 × g for 10 min. The protein concentrations of the lysates were quantified using Bradford assay, and protein levels were normalized for all samples. Primary antibodies used were anti-ATM (Santa Cruz), anti-phospho-Ser1981-ATM (Abcam), anti-Kap1 (Abcam; ab22553), anti-phospho-Ser824-Kap1 (Bethyl Laboratories; A300–767A), anti-Nbs1 (Genetex; GTX70224), anti-Rad50 (Genetex; GTX70228), anti-Mre11 (Genetex; GTX70212), anti-MBP (Rockland; 200–401–385), anti-Flag (Sigma; A1205), anti-β-actin (Cell Signaling; 4970), anti-Chk2 (Genetex; GTX70295), anti-phospho-Thr68-Chk2 (Cell Signaling; 2661S), anti-phospho-Ser15-p53 (Abcam; ab1431), and anti-phospho-Ser15-p53 (mouse) (Assay Biotech; A7180). Alexa Fluor 68-anti-rabbit and IRDye 800 anti-mouse were the secondary antibodies used. Membranes were scanned and quantified using the Odyssey system (Li-Cor).
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3

Western Blot Analysis of DNA Repair Proteins

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Western blots were performed with primary antibodies anti-RAD50 (GTX70228, Genetex, Irvine, CA, USA), anti-MRE11 (GTX70212, Genetex, Irvine, CA, USA), anti-NBS1 (GTX70224, Genetex, Irvine, CA, USA), anti-6xHIS (#12698, Cell Signaling Technology, Danvers, MA, USA), anti-α-tubulin (GTX112141, Genetex, Irvine, CA, USA), and anti-P84 (GTX70220, Genetex, Irvine, CA, USA), as described previously [36 (link),37 (link)].
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4

Characterization of Telomeric Protein Complexes

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Whole cell and nuclear extracts were prepared as described previously63 (link). Western blot analysis was performed as described64 (link) with the following primary antibodies: anti-TRF1 (#5745, 0.5 μg/ml)63 (link), anti-TRF2 (4A794, 2.5 μg/ml, Novus Biologicals, Littleton, CO, USA), anti-POT1 (#978, 1:1,000, provided by Dr. Titia de Lange), anti-TIN2 (1:1,500, provided by Dr. Zhou Songyang), anti-TPP1 (#467, 1:1,000, provided by Zhou Songyang), anti-RAP1 (1:1,000, provided by Zhou Songyang), anti-RIF1 (#1060, 1:1,000, provided by Titia de Lange), anti-dyskerin (H-300, 2 μg/ml, Santa Cruz Biotechnology, Dallas, TX, USA), anti-MRE11 (12D7, 1:500, GeneTex, Irvine, CA, USA), anti-RAD50 (13B3, 1:1,000, GeneTex), anti-NBS1 (#3002, 1:1,000, Cell Signaling Technology, Danvers, MA, USA), anti-BLM (ab476, 1:2,000, Abcam, Cambridge, UK), anti-WRN (ab200, 1:2,000, Abcam), anti-ATM (2C1, 2 μg/ml, Santa Cruz Biotechnology), anti-PARP-1 (C2-10, 1:2,000, Pharmingen, Franklin Lakes, NJ, USA), anti-tankyrase-1 (H-350, 2 μg/ml, Santa Cruz Biotechnology), anti-glyceraldehyde-3-phosphate dehydrogenase (GAPDH; RDI-TRK5G4-6C5, 0.5 μg/ml, Research Diagnostics, Flanders, NJ, USA), anti-α-tubulin (B-5-1-2, 1:1,000, Sigma), anti-lamin A/C (636, 2 μg/ml, Santa Cruz Biotechnology) and anti-hTERT (1531-1/Y182, 1:1,000, Abcam). Images were processed with Photoshop CS5 (Adobe).
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5

Comprehensive Antibody Characterization Protocol

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The following antibodies were used: anti-SLFN5 (Sigma-Aldrich; Cat.HPA017760; Lot.B96361), anti-SLFN11 (Novus Biologicals; Cat.NBP1–92368; Lot.H96783), anti-PML (Bethyl Laboratory; Cat.A301–167A, Santa Cruz; Cat.sc-966; Lot.H1413), anti-IFI16 (Santa Cruz; Cat.sc-8023; Lot.C1312), anti-ATRX (Santa Cruz; Cat.sc-15408), anti-DNA-PKcs (Santa Cruz; Cat.sc-5282; Lot.G280), anti-SUMO2+3 (Abcam; Cat.ab3742; Lot.GR8249–1), anti-RNAP II (Santa Cruz; Cat.sc-56767), anti-GFP rabbit (Abcam; Cat.ab290; Lot.GR3251545–1), anti-GFP mouse (Millipore; Cat.MAB2510; Lot.2512480), anti-RAD50 (GeneTex; Cat.GTX70228; Lot.40186), anti-V5 (Santa Cruz; Cat.sc-271944; Lot.E2217), anti-HA (Abcam; Cat.ab9110; Lot.GR3217183–2), anti-GAPDH (GeneTex; Cat.GTX100118; Lot.42158), anti-α-Tubulin (Santa Cruz; Cat.sc-69969; Lot.DO412), anti-β-Actin (Sigma-Aldrich; Cat.a5441; Lot.064M4789V), anti-KU70 (Abcam; Cat.ab83501; Lot.GR3176811–2), anti-Histone H3 (Abcam; Cat.ab1791; Lot.GR3198176–1), anti-ICP0 (Santa Cruz; Cat.sc-53070; Lot. A0313), anti-ICP8 (gifted from David M. Knipe), anti-TK (Santa Cruz; Cat.sc-28037; Lot.K1813), anti-VP21 and anti-gD (gifted from Gary H. Cohen), anti-IE1/IE2 (Virusys; Cat.P1215; Lot.A1345070), anti-UL44 (Virusys; Cat.ca006–100; Lot.C1034151), adenovirus late protein antibody staining Hexon, Penton and Fiber (gift from James M. Wilson), and anti-DBP (gift from Arnold J. Levine).
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6

Antibody Characterization for SLFN5, SLFN11, and DNA Repair

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The following antibodies were used: anti-SLFN5 (Sigma-Aldrich; Cat.HPA017760; Lot.B96361), anti-SLFN11 (Novus Biologicals; Cat.NBP1-92368; Lot.H96783), anti-PML (Bethyl Laboratory; Cat.A301-167A, Santa Cruz; Cat.sc-966; Lot.H1413), anti-IFI16 (Santa Cruz; Cat.sc-8023; Lot.C1312), anti-ATRX (Santa Cruz; Cat.sc-15408), anti-DNA-PKcs (Santa Cruz; Cat.sc-5282; Lot.G280), anti-SUMO2+3 (Abcam; Cat.ab3742; Lot.GR8249-1), anti-RNAP II (Santa Cruz; Cat.sc-56767), anti-GFP rabbit (Abcam; Cat.ab290; Lot.GR3251545-1), anti-GFP mouse (Millipore; Cat.MAB2510; Lot.2512480), anti-RAD50 (GeneTex; Cat.GTX70228; Lot.40186), anti-V5 (Santa Cruz; Cat.sc-271944; Lot.E2217), anti-HA (Abcam; Cat.ab9110; Lot.GR3217183-2), anti-GAPDH (GeneTex; Cat.GTX100118; Lot.42158), anti-α-Tubulin (Santa Cruz; Cat.sc-69969; Lot.DO412), anti-β-Actin (Sigma-Aldrich; Cat.a5441; Lot.064M4789V), anti-KU70 (Abcam; Cat.ab83501; Lot.GR3176811-2), anti-Histone H3 (Abcam; Cat.ab1791; Lot.GR3198176-1), anti-ICP0 (Santa Cruz; Cat.sc-53070; Lot. A0313), anti-ICP8 (gifted from David M. Knipe), anti-TK (Santa Cruz; Cat.sc-28037; Lot.K1813), anti-VP21 and anti-gD (gifted from Gary H. Cohen), anti-IE1/IE2 (Virusys; Cat.P1215; Lot.A1345070), anti-UL44 (Virusys; Cat.ca006-100; Lot.C1034151), adenovirus late protein antibody staining Hexon, Penton and Fiber (gift from James M. Wilson), and anti-DBP (gift from Arnold J. Levine).
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