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30 protocols using m1404

1

Mitotic Synchronization and Post-Mitotic Analysis of ES Cells

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ES cells—E14Tg2a, EKOiE5 (link), EKOie–NrKO14 (link), FLAG–Nr5a2 (ref. 14 (link)), NR5A2–GFP/ESRRB–mCherry14 (link), ESRRB/NR5A2–GFP lines and ESRRB/NR5A2–IAA ESCs (see details below)—were cultured on serum and leukemia inhibitory factor conditions as previously described11 (link). Mitotic ES cells (>95% purity as assessed by 4′,6-diamidino-2-phenylindole staining and microscopy) were obtained using a double synchronization method based on the CDK1 inhibitor RO-3306 (10 μM; Sigma, SML0569), nocodazole (50 ng ml−1; Sigma, M1404) and shake-off, as previously described9 (link). For post-mitosis analyses, cells were seeded in separate dishes (one per time point), purposely uncoated with gelatin and lysed in cold TRIzol (ThermoFisher, 15596026) 20, 30, 40, 50, 60, 90 and 120 min after release from the mitotic block9 (link). ESRRB/NR5A2 depletion was achieved with 0.5 mM auxin (5-Ph-IAA BioAcademia, 30-003), added during the 5 h of nocodazole block and maintained during the whole post-mitotic release. Asynchronous cells were treated in parallel during 5 h.
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2

FA Disassembly/Reassembly Assays in Keratinocytes

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FA disassembly/reassembly assays were performed as previously described (Ezratty et al., 2005 (link), 2009 (link); Nader et al., 2016 (link)). Briefly, keratinocytes were grown on fibronectin-coated coverslips until confluent and then serum starved for 18–24 h in serum-free low calcium E media. The keratinocytes were then treated with 10 μM NZ (Sigma-Aldrich M1404) in serum free low calcium E media for 3–4 h, washed with PBS, and placed in fresh serum-free low calcium E media. At the desired time points, the cells were then either fixed for 10 min with 4% PFA for subsequent IF or scraped off the cell coverslip with a cell scraper and incubated with antibodies for subsequent flow cytometry.
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3

Inducing Mitotic Slippage and Cytokinesis Failure

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Cells were seeded to 60–70% density. For mitotic slippage induction, 0.1 μg ml–1 nocodazole (Sigma-Aldrich, M1404) was added to the growth medium and CP-A and K562 cells were incubated for 72 and 48 h, respectively. For cells with an elongated G1 phase after tetraploidization, WGD in  CP-A TP53−/− cells was induced with 0.1 μg ml–1 nocodazole for 72 h and treated with 0.5 μM of the CDK4/6i palbociclib (Sigma-Aldrich, PZ0383) for the last 16 h of the WGD induction protocol. For cytokinesis failure inductions, RPE cells were incubated for 24 h with 0.1 μg ml–1 nocodazole-containing medium. Following nocodazole treatment, the cells were exposed for an additional 24 h to 4 μM dihydrocytochalasin B (Cayman Chemical, 20845). The treatment was removed and cells were allowed to recover for 48 h to allow transition from a binucleated to a mononucleated state. Alternatively, WGD was induced through cytokinesis failure in RPE TP53−/− cells by incubation for 24 h with 9 μM of the CDK1 inhibitor RO-3306 (Sigma-Aldrich, SML0569) for G2 synchronization. The compound was washed off and cells were then treated with 4 μM dihydrocytochalasin B for 24 h. Cells were allowed to recover for 48 h, and tetraploid cells were sorted on the basis of cell cycle staining with 1 μg ml–1 Hoechst 33342 (Thermo Fisher Scientific, H1399).
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4

Cell Cycle Synchronization and Immunoprecipitation

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For immunoprecipitation, MCF7 cells and 293T cells were treated with thymidine (2 mm, #T1895; Sigma‐Aldrich, St. Louis, MO, USA) for 18 h and released into fresh medium for 10 h and then blocked with 2 mm thymidine again for 18 h. After that, the cells were released into fresh medium for 2 h and treated with nocodazole (0.1 μg·mL−1, #M1404; Sigma‐Aldrich) for 10 h. Then the mitotic cells were collected for immunoprecipitation.
For analysis of flow cytometry and western blot, SUM159PT cells, MCF7 cells, and 293T cells were treated with nocodazole (0.1 μg·mL−1, #M1404; Sigma‐Aldrich) for 10 h and released into nocodazole‐free medium; then the cells were collected at the indicated time for further analysis.
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5

Cell Synchronization Using Nocodazole and Thymidine

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We first prepared stock solution of nocodazole (M1404; Sigma-Aldrich, St. Louis, MO) with DMSO (5 mg/mL) and then added it to cell culture medium to make the final solution (100 ng/mL). The control solution was prepared by adding the equivalent volume of DMSO to cell culture medium without nocodazole. The solution of thymidine (T1895; Sigma-Aldrich) was prepared with cell culture medium (2 mM). The control solution for thymidine was fresh cell culture medium Cell synchronization was achieved with two methods. In the first method, cells were incubated with nocodazole at a concentration of 100 ng/mL for 16 hr. Thereafter, the synchronized cells were collected via trypsinization followed by neutralization with medium and then washed with PBS (without calcium or magnesium) to remove nocodazole. In the second method,68 (link), 69 (link) cells were first incubated with 2 mM thymidine for 16 hr and then briefly washed three times with fresh medium, followed by incubation at 37°C in fresh medium containing no thymidine for 8 hr. Thereafter, the cells were treated again with thymidine for an additional 16 hr and released for 8 hr in fresh cell culture medium at 37°C. In the no treatment control group, the cells were treated with the control solutions, and all other experimental steps were the same as those in the treatment group.
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6

Genetic Engineering of Cellular Models

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HeLa and HEK293T cells were maintained in DMEM (Hyclone) medium supplemented with 10% fetal bovine serum (Hyclone) and 1% pen-strep (Gibco 15140-122). The CHK2 knockout (KO) HeLa cell line was generated as described previously [17 (link)]. The CHK2 KO cells were transfected with constructs expressing myc-CHK2 (WT or Y156F)-FLAG to establish G418-resistant stable cell lines. These cells were regularly maintained in a medium containing 400 μg/mL G418. The normal human fibroblasts MRC5 and WI38 were maintained in MEM (Gibco) supplemented with 10% fetal bovine serum and 1% pen-strep. All cell lines were from ATCC.
For ionizing radiation treatment, cells were exposed to 8 Gy X-ray using the Torrex 150D inspection system (EG&G) and then incubated for 2 h. Where indicated, cells were treated with CHK2 inhibitor II (C3742, Sigma Aldrich) and JAK2 inhibitor IV (#420139, Calbiochem) at concentrations of 5 and 2.5 μM, respectively. For nocodazole treatment of HeLa and HEK293T (M1404, Sigma Aldrich), either 50 ng/ml (for protein analysis) or 25 ng/ml (for confocal microscopy) was used. For the mitotic arrest of normal fibroblasts WI38 and MRC5, 600 ng/ml of nocodazole was used for protein analysis and 500 n/ml was used for confocal microscopy. Turbofect (Thermo Scientific) and calcium phosphate method were used for transfection of HeLa and HEK293T cells, respectively.
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7

Cell Cycle Synchronization Protocols

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For cell cycle synchronization using double thymidine (DOT scientific, DST18050), 5×105 HEK 293T cells were seeded in 6-well plates and treated with 2 mM thymidine for 16 h, followed with two PBS washes, and incubated with fresh medium for 8 h before the second 2 mM thymidine block for 14 h, following a previously published protocol.60 (link) Cells were washed with PBS twice, then incubated with fresh medium to release from the G1/S boundary, then either fixed in 10% formalin for immunostaining, harvested for western blotting, or trypsinized and harvested for flow cytometry analysis (FACS) at specific time points after release.
For cell cycle synchronization using thymidine and nocodazole (Sigma, M1404), 5×105 HEK 293T cells were seeded in 6-well plates and treated with 2 mM thymidine for 18 h, followed by two PBS washes, and incubated with fresh medium for 3 h before the second 100 ng/mL nocodazole block for 13 h following a previously published protocol.61 (link) Cells were washed with PBS twice, then incubated with fresh medium to release from G2/M phase, and fixed in 10% formalin for immunostaining or harvested for western blotting.
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8

Mitochondrial Dynamics in Cell-Cell Interactions

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The mitochondria in living cells were transfected for 24 h with Ad-Mito-EGFP, which contained the mitochondria-specific targeting sequence 5′-ATGTCCGTCCTGACGCCGCTGCTGCTGCGGGGCTTGA-3′. Then, cocultured CMs and MFs were treated with microtubule depolymerisation reagents nocodazole (30 μM, 4 h; M1404, Sigma, St. Louis, MO, USA) or colcemid (4 μM, 4 h; 10295892001, Sigma), followed by mitochondrial tracking.
Mitochondrial movement in MNTs between CMs and MFs was tracked in 30 s intervals for 15–20 min using a confocal fluorescence microscope with a 63X/1.4NA oil immersion objective lens (Zeiss Laser Scanning Microscope, LSM780, Zeiss, Oberkochen, Germany). A cell incubation system (Incubator PM S1) was used to ensure that the cells were imaged under 37 °C and 5% CO2 conditions. For living cells, we were able to distinguish between CMs and MFs because only CMs can beat. AxioVision 4 Tracking Module (Zeiss) and ImageJ (NIH, Bethesda, MA, USA) were used to track and analyse mitochondrial movement velocity in MNTs.
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9

Jurkat Cell Nocodazol Synchronization

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Jurkat cells were washed, resuspended at 1 × 106 cells/mL and incubated 4 h with nocodazol (5 μg/mL, M1404, Sigma-Aldrich, St. Louis, MO, USA) in RPMI containing 10% of FCS at 37 °C. 150,000 Jurkat cells were then incubated on coverslip for 30 min, washed once with cold PBS and fixed.
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10

Quantifying Centriole Localization in Sperm

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Rhodamine-labelled tubulin was added to the XEE to visualise the nucleation of microtubules. Centrioles of the bipolar spindles were detected by adding Nocodazole (0.5 uM, 20 min at 20 °C, M1404 Sigma) to the XEE before spinning them down11 (link). Briefly, right after the pelleting of the samples, they were blocked with 5% BSA 0.1% Triton X-100 in PBS for 50 min at room temperature, and the monoclonal mouse anti-centrin antibody (20H5, Millipore, 1:2,000) was then used to immunodetect the centrosomes. The percentage of detected centrioles at both poles, one pole and no centrioles was quantified for Xenopus, human normozoospermic and asthenozoospermic sperm samples in four independent experiments.
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