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6 protocols using anti mdc1

1

Antibody Panel for DNA Damage Response

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Following antibodies were used in this study at the indicated concentration. Anti-phospho histone H2AX (Ser139) (γH2AX) (clone JBW301, EMD Millipore, 05–636, 1:1500 IF) (Cell Signaling Technologies, 2577, 1:1000 IF), anti-TOPBP1 (Bethyl Laboratories, A300–111A, 1:2000 IF, 1:2000 IB) (Abcam, ab2402, 1:1000 IF), anti-MDC1 (Abcam ab11171, 1:1000 IF, 1:1000 IB), anti-CIP2A (clone 2G10–3B5; Santa Cruz sc80659, 1:500 IF, 1:1000 IB), anti-GAPDH (clone 14C10, Cell Signaling Technologies, 1:5000 IB), anti-PolD3 (clone 3E2, Abnova, H00010714-M01, 1:1000 IB), anti-Lig4 (clone N2C2, GeneTex, GTX100100, 1:1000 IB), anti-Mre11 (clone 12D7, GeneTex, GTX70212, 1:1000), anti-Rad50 (Cell Signaling Technologies, 3427, 1:1000 IB), anti-HA-tag (Novus biologicals, NB600–363, 1:2000 IB), anti-Lamin A/C (clone E-1, Santa Cruz, sc-376248, 1:200 IF), anti-Lamin B1 (clone C-5, Santa Cruz, sc-365962, 1:200 IF), anti-53BP1 (Thermo Fisher Scientific, PA1–16565, 1:1000 IF), anti-BRCA1 (clone D-9, Santa Cruz, sc-6954, 1:1000 IF).
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2

Antibody Panel for Epigenetic Study

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The antibodies used in this study were: anti-Flag (M2 or rabbit, Sigma), anti-trimethyl H3-K9, anti-AcH3, anti-AcH4, anti-trimethyl H3-K27, anti-AcH4-K16, anti-AcH3-K9 (Upstate Biotechnology), anti-HP1 C1A9 (Developmental Studies Hybridoma Bank at the University of Iowa), anti-GCN5, anti-AR (N-20) (Santa Cruz Biotechnology), anti-MDC1 (Abcam), anti-MYST1 (Bethyl laboratories), anti-AR 441, anti-p21WAF1 Ab-11 (Thermo scientific), anti-GAPDH (Shanghai Kangchen).
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3

Immunoblotting and Immunofluorescence Protocols

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The following primary antibodies were used: anti-COMMD1 (Abcam, ab224727), (Invitrogen, MA5-26010), anti-β-actin (BD Biosciences, 612656), anti-gamma H2AX (Abcam, ab26350), anti-p53 Serine 15 (Cell Signaling, 9284), anti-p53 clone D0–7 (Sigma-Aldrich, p8999), anti-Chk2 Threonine 68 (Cell Signaling, 2661), anti-Chk2 (Cell Signaling, 2662), anti-ATM Serine 1981 (Cell Signaling, 13050), anti-ATM (Cell Signaling, 2873), anti-H2AX (Cell Signaling, 7631) anti-MDC1 (Abcam, 11169). The following secondary antibodies from LI-COR, Inc, were used for immunoblotting; IRDye® 800CW Donkey anti-mouse (926-32212) and IRDye® 680CW Donkey anti-rabbit (926-68073). The following secondary antibodies from Life Technologies were used for immunofluorescence; Alexa Fluor® 594 donkey anti-rabbit (A21207), Alexa Fluor® 594 donkey anti-mouse (A21203), Alexa Fluor® 488 donkey anti-rabbit (A21206) and Alexa Fluor® 488 donkey anti-mouse (A21202).
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4

Immunoprecipitation and Western Blotting for Protein Interactions

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Cells harvested by trypsinization were lysed in RIPA buffer and incubated with anti-GFP (Living Colors A.V., 1:1,000) primary antibody and anti-mouse IgG-conjugated beads overnight at 4 °C. Immunoprecipitates or whole protein lysates were separated by electrophoresis and transferred to polyvinylidene difluoride membranes, which were blocked in 5% skim milk dissolved in Tris-buffered saline (TBS)-Tween and incubated with a primary antibody (anti-mCherry (Novus Biological (NBP1-96752), 1:1,000), anti-Hsp90 (Cell Signaling (4877-1:5,000), 1:5,000), anti-Mdc1 (Abcam (ab11169), 1:1,000) or anti-phospho-threonine (Cell Signaling (9381), 1:1,000)) followed by anti-mouse IR800 CW or IR680 RD (Li-Cor, 1:5,000) secondary antibody. Membranes were scanned using an Odyssey infrared imaging system (LI-COR).
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5

Immunofluorescence analysis of oocyte markers

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Oocytes were fixed with 4% paraformaldehyde in phosphate-buffered saline (PBS) for 10 min and permeabilized with 0.1% Triton X-100 and 0.01% Tween-20 for 20 min at room temperature. They were then blocked with 3% bovine serum albumin (BSA)-supplemented PBS for 1 h and incubated with anti-acetylated a-tubulin (1:1,000), anti-γ-H2AX (1:250, Abcam), anti-p-ATM (1:100, Abcam), or anti-MDC1 (1:250, Abcam) antibodies overnight at 4°C. After they were washed three times, the oocytes were incubated with Alexa Fluor–conjugated 488 secondary antibodies (1:500, Jackson ImmunoResearch) at room temperature for 2 h. Finally, the oocytes were counterstained with DAPI, mounted on glass slides, and observed under an LSM 700 laser scanning confocal microscope (Zeiss) with a C-Apochromat 63×/1.2 water immersion objective. To measure the fluorescence intensity, images were captured with the same laser power, and the mean intensity of the fluorescence signals was measured. Data were analyzed using ZEN 2012 Blue (Zeiss) and ImageJ software (National Institutes of Health) under the same processing parameters.
For mitochondrial staining, oocytes were incubated with Mitochondrial Staining Reagent-Red-Cytopainter (Abcam) for 1 h at 37°C and observed under confocal microscopy.
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6

Immunofluorescence Assay for DNA Damage

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Cells were plated onto sterile glass coverslips and fixed with PBS-PFA 4% (wt/vol) for 15 min at room temperature (RT) and washed twice in PBS. Cells were permeabilized with lysis buffer (sucrose 300 mM, MgCl 2 3 mM, Tris pH 7.0 20 mM, NaCl 50 mM, Triton X-100 0.5%) for 3-5 min at RT under slow agitation. The following antibodies were diluted in PBS-BSA 4% and applied to the coverslips for 40 min at 37°C: anti-γH2AX (JBW301, 1:800), P-ATM Ser1981 (10H11.E12, 1:200), and 53BP1 (1:500) from Millipore, and anti-MDC1
(1:200) from AbCam. For NLRP3 labeling, cells were fixed with PBS-PFA 4% (wt/vol) for 15 min at RT, washed twice in PBS and permeabilized with 1% triton X100. Anti-flag was diluted in saturation buffer (PBS, 1% BSA; NaCl 0.02%; Tween 20 0.5%; SVF 3%) and incubated on cells for 1 h. Cells were then incubated with Alexa-Fluor 488-conjugated antimouse or Alexa-Fluor 555-conjugated anti-rabbit (1:800; Life Technologies) for 20 min at 37°C and in Hoechst (500 ng/mL in PBS) for 10 min at RT. Fluorescence microscopy pictures were taken using a Nikon Eclipse Ni-E microscope, and confocal Zeiss LSM 780.
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