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81 protocols using phospho histone h3

1

Immunohistochemical Analysis of Apoptosis and Mitosis

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For immunohistochemical analysis, anti-cleaved caspase 3 (monoclonal, Cell Signaling Technology, Inc., Danvers, MA, USA) and phospho-histone H3 (polyclonal, Cell Signaling Technology, Inc., Danvers, MA, USA) were used as primary antibodies. Immunohistochemical analysis was performed using a universal second antibody kit that uses a peroxidase-conjugated labelled dextran polymer (Envision Plus, Dako, Glostrup, Denmark). The following primary antibodies were used: anti-cleaved caspase 3 (monoclonal, Cell Signaling Technology, Inc., Danvers, MA, USA) and phospho-histone H3 (polyclonal, Cell Signaling Technology, Inc., Danvers, MA, USA).
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2

Fetal Erythrocytes Immunohistochemistry

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Analysis of foetal erythrocytes from cord blood samples was carried out by Wright-Giemsa staining. For immunohistochemical analysis, anti-cleaved caspase 3 (monoclonal, Cell Signaling) and phospho-histone H3 (polyclonal, Cell Signaling Technology, Inc) were used as primary antibodies. Immunohistochemical analysis was performed using a universal second antibody kit that uses a peroxidase-conjugated labelled dextran polymer (Envision Plus, Dako, Glostrup, Denmark). The following primary antibodies were used: anti-cleaved caspase 3 (monoclonal, Cell Signaling Technology, Inc) and phospho-histone H3 (polyclonal, Cell Signaling Technology, Inc).
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3

Proliferation and Apoptosis Assays

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Triplicate samples of 5,000 cells were seeded in 96-well plates in medium containing puromycin for 48 h before proliferation was assessed using CellTiter 96 (Promega) at 570 nm absorbance using a Synergy-2 multi-detection plate reader (BioTek). Alternatively, cells were incubated with 10 µM bromodeoxyuridine (BrdU) for 2 h, washed in PBS, and fixed in 70% ethanol. DNA was denatured in 2 N HCl at room temperature for 15 min and resuspended in 0.1 M Na2B4O7, followed by staining with FITC-conjugated BrdU Ab (BD Pharmingen), washing in PBS, additional staining with 10 mg/ml propidium iodide for 30 min, and analysis on a FACScan instrument (Becton-Dickinson). For analysis of apoptosis, we used a FITC Annexin V Apoptosis detection kit I (BD Pharmingen) and analyzed cells on a FACScan instrument (Becton-Dickinson). Phospho-Histone H3 was analyzed as described previously34 (link), using Histone H3 (Cell Signaling, cat. no. 9715) and Phospho-Histone H3 (Cell Signaling, 3377) Ab.
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4

Immunohistochemical Analysis of Cell Markers

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IHC was carried out in the Bond stainer (Leica). In brief, slides were dewaxed in Bond Dewax solution) and hydrated in bond wash solution. Antigen retrieval for antibodies was performed for 30 min at 100°C in bond-epitope retrieval solution 1 (pH 6.0). Slides were incubated with primary antibody for 1 hr. Primary antibodies used were Dicer 13D6 (Abcam), cleaved caspase-3 (Cell Signaling Technology), γH2AX (Cell Signaling Technology), p27-Kip1 (Dako), PCNA (Cell Signaling Technology), BrdU (AbD Serotec), Ki-67 (Leica), phospho-histone H3 (Cell Signaling Technology), and NeuN (Millipore). Nuclei were counterstained with hematoxylin or DAPI. Antibody detection was performed using the Bond Polymer Refine Detection System (DS9800). Stained slides were dehydrated and coverslipped. Stained slides were digitally imaged at 20× magnification using the Aperio ScanScope XT (Aperio Technologies), and digital images were stored in the Aperio eSlide Manager Database at Translation Pathology Laboratory (TPL).
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5

Immunostaining Protocol for Epithelial Markers

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Mouse monoclonal antibody against IL-33 (clone Nessy-1) (#ALX-804-840-C100) was purchased from Enzo. Rabbit polyclonal antibodies against KRT5 (#ab24647) and Ki-67 (#ab15580) were purchased from Abcam (Abcam, Cambridge, MA). Rabbit polyclonal antibody against KRT14 (#PRB-155P) was purchased from Covance (Covance, Princeton, NJ). Rabbit polyclonal antibody against KRT4 (#HPA034881) was purchased from Sigma (Sigma-Aldrich Corp, St. Louis, MO). Rabbit monoclonal antibodies against E-cadherin (#3195), p75 (#8238), and phospho-histone H3 (#3377) were purchased from Cell Signaling (Cell Signaling Technology, MA). Mouse monoclonal antibody against p63 (#sc-8431) was purchased from Santa Cruz (Santa Cruz Biotechnology, TX). Mouse monoclonal antibody against PCNA (#MAB424) was purchased from Millipore (Billerica, MA). Goat polyclonal antibody against IL-33 (#AF3625) was purchased from R&D (R&D Systems, Minneapolis, MN). Donkey anti-goat Alexa Fluor 488 (A11055), anti-rabbit Alexa Fluor 568 (A10042), and anti-mouse Alexa Fluor 647 (A31571) secondary antibodies were purchased from Life Technologies (Carlsbad, CA). Mouse anti-HSP90 (TA500494) and mouse anti-GAPDH (TA310153) primary antibodies were purchased from Origene (Rockville, MD).
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6

Immunoblotting and Immunofluorescence Analysis of Autophagy Markers

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Commercial antibodies include: phospho-Histone H3 (Cell Signaling Technology (CST) 9701), cleaved caspase-3 Alexa Fluor 488 (CST 9669S), phospho-p44/42 MAPK (P-ERK) (Invitrogen 44–680G), p44/42 MAPK (ERK1/2) (Invitrogen 13–6200), ATG12 (CST 2010), ATG7 (Santa Cruz Biotechnology sc8668), p62 (Progen Biotechnik GP62C), tubulin (Sigma T6199), p53 (DO1, Calbiochem OP43), cleaved PARP (CST 9451), G6PD (Abcam ab993) LC3 5F10 for IF (Axxora NT0231-00). For immunobloting, we utilized an LC3 antibody which has been described previously and is now commercially available (EMD Millipore ABC232) (35 (link)). Chemicals include: chloroquine (CQ), quinacrine (Q), 6-aminonicotinamide (6-AN), N-acetyl Cysteine (NAC), etoposide (Et) and doxorubicin (DX), all from Sigma-Aldrich, staurosporine (STS, EMD Chemicals), 1-13C glucose (Cambridge Isotopes), 1-14C glucose and 6-14C glucose (Perkin Elmer), and Hoechst (Invitrogen).
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7

Visualizing Retinal Cell Proliferation

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Click-iT EdU imaging kit (Invitrogen, C10337) was used according to the manufacturer's protocol in order to visualize cells undergoing S-phase during the time-window under study. 3-D RCs were incubated with 50 µg of EdU diluted in PBS for 1hr or 20 hr, then collected and processed for microscopic imaging. An antibody against the DNA replication licensing factor MCM2 (rabbit, 1:1000, Abcam, ab4461) was used to identify proliferating retinal progenitors, whereas an antibody against Phospho-Histone H3 (PH3, rabbit, 1: 250, Cell Signaling, #9701L) was used to identify cells in M phase by immunohistochemistry as described above.
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8

Immunofluorescence and TUNEL Staining Protocol

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Immunofluorescence and TUNEL staining were performed as described previously (Dai et al., 2013 (link)). The following primary antibodies were used: RPGRIP1L, 1:100 (Origene, Rockville, MD); p63, 1:100 (Santa Cruz Biotechnology, Santa Cruz, CA); KRT14, 1:1,000 (Covance, Princeton, NJ); KRT1, 1:500 (Roop et al., 1987 (link)); KRT17, 1:1,000 (Abcam, Cambridge, MA); LOR, 1:100 (Covance); NGFR, 1:100 (Promega); LEF1, 1:100 (Cell Signaling, Danvers, MA); BrdU, 1:50 (Life Technologies); acetylated α-tubulin, 1:1,000 (Sigma, St. Louis, MO); γ-tubulin, 1:1,000 (Abcam); ARL13B, 1:1,000 (#73-287, NeuroMab, Davis, CA); phospho-histone H3, 1:100 (Cell Signaling). AlexaFluor-conjugated secondary antibodies (1:250) were from Life Technologies. Sections were sealed in mounting medium with DAPI (Vector Laboratories, Burlingame, CA). Images were acquired by Nikon 80i fitted with Nikon DS-Qi1Mc camera and processed with Photoshop 5.5 CS.
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9

Drosophila Experiments: Developmental and Genetic Analyses

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Fly experiments were conducted as previously described (Ferguson and Martinez-Agosto 2014 (link)). Fly stocks were maintained at 25°C on standard food containing 0.7% agar, 5% glucose and 7% dry yeast. Canton-S was used as the wild type (wt) strain for all performed experiments. The strains apterous-gal 4(II)/Cyo, GFP, UAS-Mes-4/NSD (BL 22044, BL 15384), and UAS-IRwt were obtained from the Bloomington Drosophila Stock Center. We generated a UAS-Mes-4/NSD; UAS-IRwt stock using standard methods.
Brightfield images of third instar larvae and adult flies were obtained using a Leica light microscope. Larvae images were obtained at a magnification of 2.0X, adult flies at 1.6X and adult wings at 3.2X. Third instar larvae tissues were dissected then fixed at room temperature in 3.7% formaldehyde. Tissues were washed in 0.4% Triton X-100 in primary antibody overnight at 4°C, washed, stained in secondary antibody for 2 hours, mounted using Vectashield (Vector Laboratories) and imaged using a Zeiss LSM5. Antibodies used include: Cleaved Caspase-3 (Cell Signaling; 1:50), Phospho Histone H3 (Cell signaling; 1:50), Gigas (DHSB, 1:20), and H3K36me2 (EMDMillipore, 1:100).
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10

Anticancer Compound Stock Preparation

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Hydroxyurea was purchased from Tokyo Chemical Industry Co., Ltd. (Tokyo, Japan) and dissolved in distilled water to prepare a 1 M stock solution. Gemcitabine, irinotecan, carboplatin and doxorubicin were purchased from Wako Pure Chemical Industries, Ltd. (Osaka, Japan) and dissolved in dimethylsulfoxide (DMSO) to prepare 1 mM, 20 mM, 25 mM and 10 mM stock solutions, respectively. Methotrexate was also purchased from Wako and dissolved in 1 M NaOH to prepare a 10 mM stock solution. Sunitinib, 5-fluorouracil, paclitaxel and cisplatin were purchased from Sigma (St. Louis, MO, USA) and dissolved in DMSO to prepare 10 mM, 10 mM, 1 mM and 100 mM stock solutions, respectively. Temozolomide was purchased from LKT Laboratories, Inc. (St. Paul, MN, USA) and dissolved in DMSO to prepare a 50 mM stock solution. Antibodies such as Cleaved Caspase-3 (Asp175, #9661), Cleaved PARP (Asp214, #9541), Merlin (#12888), Vimentin (#5741), phospho-Histone H3 (S10, #9706), Cleaved PARP (Asp214, Fluorescein conjugate, #9547), and GAPDH (#5174) were purchased from Cell Signaling Technology, Inc. (Danvers, MA, USA).
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