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32 protocols using anti phospho histone h3 ser10

1

Multimodal Characterization of Craniofacial Development

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Single- or dual-color fluorescent in situ hybridizations were carried out as previously detailed (Barske et al., 2018 (link)). Published probes used in this study include barx1 (Barske et al., 2016 (link)), dlx2a (Akimenko et al., 1994 (link)), jag1b (Zuniga et al., 2010 (link)), and sox9a (Yan et al., 2002 (link)). The fgfr2 probe was a gift from S. Paul (UCLA). Partial cDNAs for cdh2, lhx6, lhx8a, ncam1a, and pax9 were amplified and cloned into pCRBlunt-II-TOPO (Life Technologies), then sequence-verified, linearized, and used as templates for in vitro transcription with Sp6 or T7 polymerase (Roche) (Table S1). Immunostaining was performed separately or following in situ hybridization, using chick anti-GFP (Abcam ab13970, 1:300), anti-phospho-Histone H3 (Ser10) (Sigma 06–570, 1:500), or anti-Alcama (DSHB Zn8, 1:2000) with Alexa dye-conjugated secondary antibodies (1:300, Thermofisher). Alcian Blue and Alizarin Red staining of larvae and adult facial skeletons was performed as described (Ullmann, 2011 ; Walker and Kimmel, 2007 (link)). For all mutant/transgenic analyses, a minimum of n = 2 or 3 individuals with the genotype in question were imaged and evaluated.
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2

Immunofluorescence and Western Blotting Protocols

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Immunofluorescence and Western blotting were performed essentially as previously described [84 (link)]. For immunofluorescence, the following antibodies were used. Primary antibodies: anti-Lamin A (1:1000; Sigma-Aldrich), anti-centromere protein (ACA, CREST, 1:400; Antibodies Incorporated), anti-phospho-Histone H3 (Ser10, 1:300; Sigma-Aldrich), anti-α-tubulin DM1A (1:500; Sigma-Aldrich), anti-CENP-A (3–19, 1:300; Invitrogen). Secondary antibodies: Alexa Fluor 647 Goat Anti-Rabbit IgG (H+L, 1:200; Invitrogen), Alexa Fluor 647 IgG (H+L) Cross-Adsorbed Goat anti-Human (1:200; Invitrogen), Alexa Fluor 488 goat anti-rabbit (1:200; Invitrogen), Texas Red-X goat anti-mouse IgG (1:200; Invitrogen) and Alexa Fluor 488 Phalloidin (to label F-actin, 1:1000; Invitrogen). For Western blotting, the following primary antibodies were used: anti-α-tubulin DM1A (1:5000; Sigma-Aldrich), anti-KIF18A (1:1000; Bethyl Laboratories Inc.), anti-CENP-A (3–19, 1:2000; Invitrogen) and anti-Histone H3 (3H1, 1:1000; New England BioLabs).
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3

Pancreatic Immunohistochemistry of Mouse

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Mouse pancreases were dissected and fixed in 4% formaldehyde at 4 °C for 12 h before embedding in paraffin62 (link). Two-four-micrometer sections were deparaffinized, rehydrated, and incubated overnight at 4 °C with anti-PDX-1 (Abcam; #47267), anti-Glut2 (Chemicon; #07-1402), anti-Ki67 (Dako; #M7249), anti-phospho-Histone H3 (Ser10; Merck #06-570), and anti-NKX6.1 (DSHB, University of Iowa #F55A1266 (link)) in combination with TSA (Invitrogen #T30955), or for 2 h at room temperature with anti-insulin (Dako; A0546) antibodies (all at a dilution of 1:100, except anti-PDX-1, which was diluted 1:400) followed by fluorescein isothiocyanate (FITC)- or Cy3-conjugated secondary antibodies (Jackson ImmunoResearch Laboratories, West Grove, PA). Slides were mounted with Vectashield with 4′6-diamidino-2-phenylindole (DAPI) (Vector Labs). β-cell apoptosis was analyzed by the terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling (TUNEL) technique according to the manufacturer’s instructions (In Situ Cell Death Detection Kit, TMR red; Roche) and double stained for insulin. Fluorescence was analyzed by using a Nikon MEA53200 (Nikon GmbH, Dusseldorf, Germany) microscope, and images were acquired by using NIS-Elements software (Nikon).
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4

Immunostaining of DNA Repair Proteins

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For phospho-Histone H2AX, 53BP1, Lamin B and phospho-Histone H3, cells were fixed with 4% formaldehyde and permeabilised with 0.2% Triton X-100 for 5 min. For RAD51 foci, cells were pre-extracted with 0.2% Triton X-100 for 1 min. For colocalisation with replication foci, antibodies were fixed with 4% formaldehyde before DNA denaturation with HCl and immunostaining for thymidine analogues. Primary antibodies were rat monoclonal anti-BrdU (BU1/75, AbD Serotec, 1:400) to detect CldU, mouse monoclonal anti-BrdU (B44, Becton Dickinson, 1:50) to detect IdU, mouse monoclonal anti-phospho-Histone H2AX (Ser139) (JBW301, Merck Millipore, 1:1000), rabbit polyclonal anti-RAD51 (H-92, Santa Cruz Biotechnology, 1:500), rabbit polyclonal anti-53BP1 (Bethyl, 1:3000), goat polyclonal anti-Lamin B (Santa Cruz Biotechnology, 1:400) and rabbit polyclonal anti-phospho-Histone H3 (Ser10) (Merck Millipore, 1:500).. Secondary antibodies were anti-Rat IgG AlexaFluor 555, anti-mouse IgG AlexaFluor 488, anti-rabbit IgG AlexaFluor 555 or AlexaFluor 647 and anti-goat IgG Alexafluor 594 (Molecular Probes). DNA was counterstained with DAPI and images acquired as above.
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5

Multimodal Immunofluorescence Imaging

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Immunohistochemistry performed as described previously86 . The following antibodies and dilutions were used: anti-BrdU antibody (Abcam, ab6326, 1:250), anti-phospho-histone H3 (Ser10) (EMD Millipore, 06-570, 1:250), anti-GFP (Thermo Fisher Scientific, A-11122, 1:50), goat anti-rat Cy3 secondary (Jackson Immuno Research, 112-165-003, 1:500), goat anti-rabbit Cy3 secondary (Jackson Immuno Research, 111-165-144, 1:500), and goat anti-rabbit Cy5 secondary (Jackson Immuno Research, 711-035-152, 1:500). Nuclei were counterstained with DAPI using Vectashield with DAPI (Vector Laboratories, H-1200). F-actin was labeled using AlexaFluor 633 Phalloidin (Thermo Fisher Scientific, 1:33, A22284). TUNEL-labeling was accomplished using TMR-Red In situ Cell Death Detection Kit (Sigma Aldrich, 12156792910).
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6

Immunofluorescence Staining Protocol for Enteroid Monolayers and Organoids

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Enteroid monolayers and 3D organoids were fixed in 4% paraformaldehyde in PBS for 20 minutes followed by a block while permeabilizing in 5% BSA/ 0.2% Triton X-100/ PBS for 30 minutes at room temperature. The stainings were performed overnight at 4°C with the following primary antibodies: anti-Cleaved Caspase-3 (Asp175) (Cell Signaling, #9661), anti-phospho-Histone H3 (Ser10) (Merck-Millipore, #06-570), anti-GFP (Abcam, #ab6673), anti-Phospho-c-Jun (Ser73) (D47G9) (Cell Signaling, #3270), anti-Phospho-JNK1+JNK2 (T183 + Y185) (Abcam, #ab4821) and anti-Ly-6A/E (Sca-1) (Biolegend, cat#108101). Appropriate Alexa Fluor labeled secondary antibodies (ThermoFischer Scientific) were combined with DAPI and/or Phalloidin Alexa Fluor 647 (ThermoFischer Scientific, cat# A22287). For labeling of cells in S-phase, a pulse of 10 μm EdU (5-ethynyl-2′-deoxyuridine) was given one hour prior to fixation and detection was performed according to manufacturer’s guidelines before starting the immunofluorescence staining using Click-iT EdU Cell Proliferation Kit for Imaging Alexa Fluor 647 (ThermoFischer Scientific, cat# C10340).
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7

Detailed Antibody Protocol for Western Blotting

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Anti-HA (clone 3F10, Sigma-Aldrich), anti-α-Tubulin (clone DM1A, Sigma-Aldrich), anti-Cdk1 (ab18, Abcam, Cambridge, UK), anti-ERK1/ERK2 (9102, Cell Signaling, Danvers, MA), anti-xGLD2 (rabbit polyclonal antibody raised against KRRSDEGNSPYDVKC peptide, X. laevis), anti-4E-T (2297, Cell Signaling), anti-DDX6 (PD009, MBL, Nagoya, Japan), anti-hCPEB4 for WB (rabbit polyclonal antibody raised against amino acids 1–302), anti-hCPEB4 for IP (ab83009, Abcam), anti-phospho Histone H3 (Ser 10) (06–570, Merck Millipore, Billerica, MA), anti-Symplekin (610644, BD Transduction Laboratories, Franklin Lakes, NJ), anti-CPSF2 (ab126760, Abcam), anti-PARN (ab89831, Abcam), anti-hGLD2 (AP5092, Abgent, San Diego, CA), anti-S6 (2317, Cell Signaling), anti-Vinculin (ab18058, Abcam).
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8

Western Blot Analysis of Cell Cycle Regulators

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Cellular lysates were prepared using RIPA buffer (50 mM Tris pH 8.0, 150 mM NaCl, 1% NP-40, 0.5% Na-desoxycholate, 0.1% SDS, 1 mM NaF, 1 mM DTT, phosphatase and protease inhibitor cocktail tablets (Roche, Mannheim)). Western blot analysis was performed as previously described [53 (link), 63 (link)]. Following antibodies were used: Mouse monoclonal antibodies against cyclin B1, Plk1 and p53 (Santa Cruz). Rabbit monoclonal antibodies against p21 and rabbit polyclonal antibodies against PARP were purchased from Cell Signaling. Anti-phospho-histone H3 (Ser10) were obtained from Merck Millipore. Mouse monoclonal antibody against β-actin was from Sigma-Aldrich.
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9

Immunohistochemistry of Cardiac Tissues

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Tissues were fixed in 4% paraformaldehyde in PBS overnight at 4°C
and incubated in 30% sucrose in PBS at 4°C overnight. Tissues were
embedded in tissue freezing medium and cut 8 μm thicknesses. For antigen
retrieval, either 1 mM EDTA with 0.05% Tween 20 in boiling water or epitope
retrieval solution (IHC World) in a steamer (IHC-Tek Epitope Retrieval Streamer
Set) were used, then sections were blocked with 10% serum from the host animal
of secondary antibodies, and incubated with primary anti-bodies overnight at 4
°C. The sections were subsequently washed with PBS and incubated with
corresponding secondary antibodies conjugated to Alexa Fluor 488 or 555
(Invitrogen). The slides were mounted in antifade mounting medium (Vector
Laboratories, Burlingame, California). Primary antibodies used are as follows:
anti-phospho histone H3 Ser10 (Millipore 06–570, 1:100), anti-aurora B
(Sigma A5102, 1:100), anti-troponin T, cardiac isoform Ab-1, clone 13–11
(Thermo Scientific MS-295-P1, 1:100), anti-sarcomeric α-actinin (Abcam,
ab68167, 1:100), anti-8 hydroxyguanosine (Abcam ab62623, 1:50),
anti-phosphorylated ATM (Santa Cruz Biotechnology sc-47739, 1:100),
Anti-phospho-Histone gamma H2AX (Millipore-Sigma 05–636). DAPI was used
for the nuclear staining.
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10

Immunofluorescence Staining of Cell Markers

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Deparaffinization, antigen retrieval with 1 mM EDTA (pH 9.0) in boiling water, and blocking of nonspecific binding sites were performed. The sections were then incubated with primary antibodies overnight at 4°C, washed three times with PBS, and incubated with fluorescence-labeled secondary antibodies for 1 h at 25°C in the dark. The slides were washed three times in PBS, counterstained with DAPI (Sigma-Aldrich, St. Louis, MO, USA), and mounted with VECTASHIELD (Vector Labs, CA, USA). The primary antibodies used were as follows: anti-phospho Histone H3 Ser10 (Millipore #06-570, 1 : 100), anti-Ki67 (Abcam, ab16667, 1 : 200), anti-Aurora B (1 : 100; ab2254, Abcam), and anti-Sarcomeric Alpha Actinin (Abcam, ab9465, 1 : 500). The anti-rabbit Alexa Fluor 488-conjugated (1 : 500; A-21206) and anti-mouse Alexa Fluor 594-conjugated (1 : 500; A-21203) secondary antibodies were from Invitrogen. Fluorescence was observed under a ZEISS LSM800 confocal laser scanning microscope (Carl Zeiss, Inc., Jena, Germany).
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