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8 protocols using ab5168

1

Western Blotting and Immunostaining of Meiotic Proteins

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Anti-myc (9E10, sc-40, Santa Cruz), anti-tubulin (MCA77G, Bio-Rad/Serotec, Ltd), anti-Cdc5 (sc-33625, Santa Cruz), and histone H3 phospho-T11 (ab5168, Abcam) were used for western blotting. Rabbit anti-Rad5121 (link) and guinea pig anti-Rad5173 (link), rabbit anti-Hop174 (link) and rabbit anti-Rfa275 (link) were home-made and used for staining. Rabbit anti-Ndt80 was a gift by M. Lichten. The secondary antibodies for immuno-staining were Alexa Fluor 488 (Goat, A-21206, Thermo Fisher Scientific) and 594 (Goat, A-211012, Thermo Fisher Scientific) IgG used at a 1/2000 dilution. For western blotting, alkaline phosphatase-conjugated secondary antibodies (Promega) were used.
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2

Antibody Usage in Molecular Biology

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All antibodies used in this study were listed in Supplementary Table 3. Antibodies against anti-H3 (1: 5000; ab1791) and H3T11 phosphorylation (1:5000; ab5168) were purchased from Abcam; antibodies against Sir2 (1:500; sc-6667), and Sir3 (1:500; sc-101612) were purchased from Santa Cruz Biotechnology; antibodies against GAPDH (1:10000; 10494-1-AP), GFP (1:5000; 66002-1-1g), Myc (1:5000; 60003-2-1g), goat polyclonal anti-mouse IgG (1:5000; SA00001-1), and goat polyclonal anti-rabbit IgG (1:5000; SA00001-2) were obtained from proteintech; antibody against histone H3 (1:3000; 9715S) was purchased from Cell Signaling Technology; antibody against FLAG M2 (1:3000; F1804-1MG) was obtained from Sigma-Aldrich; antibody against H4K16ac (1:2000; 07-329) was obtained from EMD Millipore.
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3

Immunofluorescence Staining of p-H3 and cMYC

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The cells were cultured on coverslips or in microwells (154534, Thermo Scientific). The cells were fixed in 4% PFA for 10 min at room temperature. After washing with PBS for three times, the cells were permeabilized with 0.5% Triton X-100 in PBS for 10 min at room temperature. After washing with PBS for three times, cells were blocked with 5% BSA in PBS for 30 min at 37°C. The cells were incubated with the primary antibody against p-H3 (T11) (1 : 100, ab5168, Abcam) or cMYC (1 : 800, 5605, Cell Signalling) diluted in 3% BSA in PBS for 30 min at 37°C. After washing with PBS for three times, the cells were incubated with anti-rabbit FITC secondary antibody (711-095-152, Jackson ImmunoResearch) diluted 1 : 200 in BSA 1% in PBS for 30 min at 37°C. One drop of Vectashield antifade mounting medium, containing DAPI, (H-1200, Vector Laboratories) was added to each sample before analysis. Fiji software was used for the quantification of the intensity.
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4

Antibody Verification for Histone Modifications

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Antibodies against anti-H3 (1:5000; ab1791), anti-H4 (1:5000; ab10158) and H3pT11 (1:5000; ab5168) were purchased from Abcam; antibodies against H3K79me1 (1: 1000; A2367), H3K79me2 (1: 5000; A2368), H3K79me3 (1:5000; A2369), anti-His (1:5000; AE0039) and anti-FLAG (1:5000; AE024) were purchased from Abclonal; antibody against Sir2 (1:500; sc-6667) was purchased from Santa Cruz Biotechnology; antibodies against GAPDH (1:10,000; 10494-1-AP), GFP (1:5000; 66002-1-1 g), Myc (1:5000; 60003-2-1 g), goat polyclonal anti-mouse IgG (1:5000; SA00001-1) and goat polyclonal anti-rabbit IgG (1:5000; SA00001-2) were obtained from Proteintech; antibody against FLAG M2 (1:3000; F1804-1MG) was obtained from Sigma-Aldrich; antibody against H4K16ac (1:2000; 07-329) was obtained from EMD Millipore; antibody against CBP (1:2000; Abs130593) was purchased from Absin Bioscience Inc. The custom-made antibodies against Acs2, Pyk1, Sam1 and Shm2 were produced by Covance Inc. and their specificity was verified by immunoblots of cell lysates of the corresponding histone point mutants, gene deletion or knockdown mutants31 (link).
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5

Antibody usage for western blotting

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Antibodies against H3 (1: 5000; ab1791), and H3pT11 (1:3000; ab5168) were purchased from Abcam; antibody against FLAG M2 (1:3000; F1804-1MG) was obtained from Sigma-Aldrich; antibodies against Myc (1:5000; 60003-2-1 g), PHGDH (1:3000; 14719-1-AP), GAPDH (1:10000; 10494-1-AP), PSAT1 (1:3000; 10501-1-AP), PSPH (1:3000; 14513-1-AP), PKM1 (1:2000; 15821-1-AP), p21 (1:3000; 10355-1-AP), PCAF (1:3000; 13983-1-AP), SIRT1 (1:2000; 13161-1-AP), 6×His (1:5000; HRP-66005), GST (1:5000; HRP-66001), beta-actin (1:10000; 20536-1-AP), and goat polyclonal anti-mouse IgG (1:5000; SA00001-1) were obtained from proteintech; antibodies against PKM2 (1:3000; 4053 S), p300 (1:5000; 54062), and ATF4 (1:1000; 11815) were purchased from Cell Signaling Technology; antibodies against mouse CDKN1A/p21 (1:3000; A11454), SOD1 (1:2000; A0274), SOD2 (1:1000; A19576), Caspase 3 (1:2000; A11040), PPARγ (1:1000; A11183), PGC1α (1:1000; A220995), and mouse PKM2 (1:5000; A19102) were purchased from Abclonal; antibody against SIRT6 (1:2000; 200499-6C9) was purchased from ZENBO; antibody against PKM2 K433ac (1:500) was custom-made in Abclonal. Antibody against PKM2K305ac was a gift from Dr. Qunying Lei (Fudan University). The specificity of the custom-made antibodies was confirmed by dot blots with peptides or immunoblots with cell extract of corresponding mutants.
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6

Antibody Immunoblotting and ChIP Protocol

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The antibodies used for immunoblotting or ChIP were Chk1 (sc8408 and sc56291; Santa Cruz), FLAG (M158‐3L; MBL), myc (sc789 and sc40; Santa Cruz), H3 (ab1791; Abcam), I‐2 (AF4719; R&D SYSTEMS), IKKα (sc7182; Santa Cruz), NIPP1 (612368; BD Biosciences; HPA027452; Sigma), normal goat IgG (sc2028; Santa Cruz), normal mouse IgG (sc2025; Santa Cruz), normal rabbit IgG (cs2729; Cell Signaling), PKAα (sc28315; Santa Cruz), PKA‐pThr197 (cs4781; Cell Signaling), pS/T‐PKA (cs9624; Cell Signaling), H2AX (ab11175; Abcam), γH2AX (05‐636; Sigma), H3 (17168‐1‐AP; Proteintech), H3‐pThr11 (ab5168; Abcam), PNUTS (611060; BD Biosciences), PP1‐pThr321 (2581; Cell Signaling; Thr321 corresponds to Thr311 of PP1γ), PP1γ (sc6108; Santa Cruz; 07‐1298; Millipore), and MYPT1 (ab59235; Abcam).
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7

Western Blot Antibody Validation Protocol

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Antibodies against H3 (1: 5000; ab1791), H3pT11 (1:3000; ab5168) and SETX (1:3000; ab243904) were purchased from Abcam; antibody against FLAG M2 (1:3000; F1804-1MG) was obtained from Sigma-Aldrich; antibodies against Sir2 (1:500; sc-6667) and LC3 (1:1000; sc-398822) were purchased from Santa Cruz Biotechnology; antibodies against Myc (1:5000; 60003-2-1 g), GAPDH (1:10000; 10494-1-AP), beta-actin (1:10000; 20536-1-AP), GFP (1:5000; 66002-1-Ig) and goat polyclonal anti-mouse IgG (1:5000; SA00001-1) were obtained from Proteintech; antibody against Rif1 (1:3000; 95558 S) was purchased from Cell Signaling Technology; antibodies against CDKN1A/p21 (1:3000; A11454), and PPP1CA (1:5000; A12468) were purchased from Abclonal; antibody against CBP (1:3000; abs130593) was purchased from Absin. Antibody against Glc7 (1:5000) was custom-made in Abclonal and its specificity was confirmed by dot blots with Glc7 peptide (Supplementary Fig. S11b). H3pT11 was validated for ChIP assay in H3T11A mutant and PKM2 knockdown HUVECs (Supplementary Fig. S11c, d).
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8

Immunostaining and Fluorescence Imaging of Amphibian Embryos

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For antibody staining embryos were embedded in fish gelatin as described previously (Chalmers et al., 2003) , except tadpole-stage (stage 30) embryos, which were incubated in 20% sucrose for 2 h, washed several times in PBS and then embedded in 15% fish gelatin for freezing. The embryos were cryosectioned and antibody stained as described (Chalmers et al., 2003) . The following antibodies were used: monoclonal anti-γ-tubulin produced in mouse clone GTU-88 (Sigma; T6557, 1 in 100), polyclonal rabbit anti-active caspase 3 (Abcam; ab13847, 1 in 100) rabbit polyclonal anti-histone H3 phospho S10 (Abcam; ab5168, 1 in 500). The following secondary antibodies were used: anti -mouse Alexa 568 (A-11004, Molecular Probes, Eugene, OR); anti-rabbit Alexa 568 (A-11011, Molecular Probes). All secondary antibodies were used at a 1 in 200 dilution. The nuclear stain, DAPI (Sigma, D9542, 1mg/mL) was used at 1 in 1000 dilution. Stained sections were mounted in Vectasheild (Vector Labroratories, Burlingame, CA) and imaged on a Zeiss LSM META confocal microscope (Thornwood, NY). GFP fluorescence was visualised directly without the use of antibody staining. All fluorescencent images were captured in the linear range of the confocal to allow quantification (see below).
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