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8 protocols using p histone h3 ser10

1

Comprehensive Antibody Characterization Protocol

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Chemical reagents, such as DMSO, NaCl, SDS, and Tris base for buffer preparation were obtained from Sigma-Aldrich (St. Louis, MO). The FBS, cell culture media, and antibiotics were purchased from Invitrogen (Grand Island, NY). Antibodies against Skp2 (#2652, IB:1:2000, IHC: 1:100), HK1 (#2024, IB: 1:2000), HK2 (#2867, IB: 1:2000, IHC:1:200), p-Akt (#4060, IB: 1:1000), Akt (#4691, IB: 1:2000), p-S6 (#4858, IB: 1:4000), p-Histone H3 (Ser10) (#53348, IF: 1:200), ubiquitin (#3936, IB: 1:1000), β-actin (#4970, IB: 1:5000), p27 (#3686, IB: 1:1000), anti-rabbit IgG HRP (#7074), and anti-mouse IgG HRP (#7076) were obtained from Cell Signaling Technology, Inc. (Beverly, MA). HK2 (LS‑C404653) antibody for IHC staining was obtained from LifeSpan BioSciences, Inc. Antibodies against Ki67 (ab16667, IHC: 1: 250) and donkey anti-rabbit IgG H&L (Alexa Fluor® 488) (ab150073, IF: 1:800) were purchased from Abcam (Cambridge, UK).
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2

Comprehensive DNA Damage Response Assay

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ATR, p-CHK1 (S345), RPA70, and p-histone H3 (Ser10) antibodies were obtained from Cell Signaling; ATRIP, NUP153, and RPA32 were obtained from Abcam; TPR, γH2AX (S139), and lamin A Abs were obtained from Sigma and Millipore; and Chk1 was obtained from Leica. EdU (click-IT), RPA70-, TopBP1-, and RAD17-small hairpin RNAs (shRNAs) were obtained from Invitrogen and Origene Technologies, respectively. ATR-specific inhibitor and ATR shRNA were from Dr. Oscar Capetillo (Centro Nacional de Oncologia [CNIO]) (Toledo et al., 2011 (link)); the GFP-ATR plasmid was from Dr. Randal Tibbetts (Tibbetts et al., 2000 (link)); RFP-Lamin was from Prof. Howard J. Worman (Columbia University) (Ostlund et al., 2006 (link)); and RFP-Nucleophosmin was a gift by Dr. Michelle Hill (University of Queensland). GFP-H2B and m-cherry-H2B were from IFOM. Colchicine, α-tubulin Ab, Leptomycin B, Hydroxy Urea, sorbitol, Aphidicholine, and R3306 CDK1-specific inhibitor were obtained from Sigma.
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3

Quantitative Analysis of Angiogenesis, Proliferation, and Apoptosis

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IHC was performed according to a previously described protocol [64 (link)]. The slides were stained with antibodies against CD31 (Cell Signaling Technology, Beverly, MA, USA, #77699), p-histone H3 Ser10 (Cell Signaling Technology, Beverly, MA, USA, #9701), and cleaved PARP (Cell Signaling Technology, Beverly, MA, USA, #5625) to assess the microvessel density, cell proliferation, and apoptosis, respectively. At least 10 fields were randomly captured at a magnification of 100× on each IHC-stained slide using an Olympus BX60 microscope (Olympus, Tokyo, Japan). To quantify the mean of the microvessel density, the p-histone H3 Ser10, and the cleaved PARP cells, all the positively stained cells in the captured images were counted and expressed as a percentage value compared with the total number of cells in that region.
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4

Quantifying Tumor Microenvironment Markers

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IHC was performed according to a previously described protocol [62 (link)]. The slides were stained with antibodies against CD31 (Cell Signaling Technology, #77699); p-histone H3 Ser10 (Cell Signaling Technology, #9701); and cleaved PARP (Cell Signaling Technology, #5625) to assess the microvessel density, cell proliferation, and apoptosis, respectively. At least 10 fields were randomly captured at a magnification of 100× on each IHC-stained slide using an Olympus BX60 microscope (Olympus, Tokyo, Japan). To quantify the mean of the microvessel density, the p-histone H3 Ser10, and the cleaved PARP cells, all the positively stained cells in the captured images were counted and expressed as a percentage value compared with the total number of cells in that region.
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5

Nuclear Fractionation and Immunoblotting

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The cultured cells were lysed and kidney tissues homogenized in radioimmunoprecipitation assay buffer containing protease inhibitors. Nuclear fractions were prepared with the NE-PER kit (Thermo Scientific, Rockford, Illinois, USA) according to the manufacturer's instruction. Protein samples were processed for immunoblot analysis as previously described [40 (link)]. The antibodies against Nrf2 and lipocalin-2 were purchased from Abcam, those against GSK3β, p-GSK3β (S9), β-Tubulin and p-Histone H3 (Ser10) were purchased from Cell Signaling Technology, and those against HO-1, nitrotyrosine and histone H3 were acquired from Santa Cruz Biotechnology.
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6

Multiplex Immunoblotting of Cell Signaling

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Primary Abs against PLK1, PLK2, PLK3, cleaved caspase‐3, p‐Histone H3 (Ser10), PCNA, and β‐actin were acquired from Cell Signaling Technology. Alpha‐tubulin Ab was purchased from Sigma.
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7

Molecular Mechanism of Vemurafenib Response

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Vemurafenib was purchased from ChemieTek. Sunitinib, imatinib, crenolanib and LDE225 were purchased from Selleck Chemicals LLC. MTT was purchased from Sigma. p-AKT (Ser473)-, AKT-, p-PI3K p85 (γ458)-, p-CRAF(S289/296/301)-, p-MEK 1/2 (S217/221)-, p-ERK 1/2 (Thr202/Tyr204)-, ERK1/2-, PDFGRβ-, p-PDGFRα-, PDGFRα-, PTEN-, VEGFR2-, Cleaved Caspase-3 (Asp175)-, p-Histone H3 (Ser10)-, Gli1- and β-actin-specific monoclonal antibodies (mAbs) were purchased from Cell Signaling Technology. The calnexin-specific mAb TO-5 was developed and characterized as described [55 (link)]. PDGFRα-specific shRNA and GFP-shRNA were provided by the- Vector Core Facility of the University of Pittsburgh Cancer Institute.
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8

Antibody Validation for Cell Cycle Analysis

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All primary monoclonal antibodies (mAb) were purchased from commercial vendors: pS343-Nbs1 (rabbit mAb, Abcam), γH2AX (mouse mAb, Millipore), and Rad51 (rabbit mAb, Epitomics; mouse mAb, Novus Biologicals). Certificates of Analysis were provided for all antibodies. Antibodies were custom-conjugated to fluorescent dyes or haptens: anti-γH2AX-biotin (Millipore), anti-γH2AX to Alexa Fluor 790, anti-pS343-Nbs1 to Digoxigenin (DIG) and anti-Rad51 to Dinitrophenol (DNP) (Molecular Probes, Inc.). New and previously qualified lots of antibodies were compared side-by-side. Validation details can be found in the Supplemental Methods and Supplemental Figs. S1 and S2, and in LoRusso, et al. for pS343-Nbs1 (6 (link)). Cell cycle and apoptosis antibodies used were: p21 Waf1/Cip1 (12D1), cyclin B1 (D5C10), p-histone H3-Ser 10 (rabbit mAb, Cell Signaling Technologies, Danvers, MA), cyclin B1-Alexa-647 (rabbit mAb, [EPR17060] Abcam), geminin (mouse mAb, Abcam), and cleaved caspase-3 rabbit antibody (R&D Systems).
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