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8 protocols using histone h2a

1

Antibody Characterization Protocol for DNA Damage Response

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Antibodies used in this study included: UBR5 (#8755, CST®, 1:1000); anti-mouse-BrdU (Becton Dickinson, different dilutions); anti-rat-BrdU (ab6326, Abcam; 1:500); PCNA-PC10 (Cancer Research, UK, 1:1000); Vimentin (V6389, Sigma-Aldrich, 1:1000); RNF8 (ab15850, Abcam; 1:2000); RNF168 (#ABE367, Millipore; 1:500); Tubulin (clone B-5-1-2, Sigma-Aldrich); Anti-Flag M2 (F3165, Sigma-Aldrich); 53BP1 (NB100-305, Novusbio, 1:2000); Chk1-PhosphoS345 (#2341 CST®,1:1000); Chk1 (#2360 CST®,1:1000); Chk2-PhosphoT68 (#2661 CST®, 1:500); Chk2(#2662 CST®, 1:1000); TRIP12 (ab86220, Abcam; 1:500); Histone H2A(ab18255, Abcam; 1:1000); polη (custom made, raised against the peptide: VQVEQRQNPHLRNKPC, 1:1000); polη-PhosphoS601(Eurogentec,(15 (link))); Histone H2A.X-PhosphoS139 (Upstate), RPA2 (1:1000, Millipore).
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2

Antibody and Inhibitor Protocol for Protein Analysis

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Antibodies (dilutions are indicated in brackets for western blot (WB), immunofluorescence (IF), or immunoprecipitation (IP)) against FLAG (Sigma, clone M2; Sigma, produced in Rabbit, IP 3 μl/sample, IF 1:100, WB 1:1000), FLAG (Sigma, clone M2; Sigma, M, Wb 1:1000, IF 1:200), ubiquityl-histone H2A (Millipore, clone E6C5), ubiquitin (Norvus Biologicals, FK2, M, WB 1:1000, IF 1:1000; Dako WB), K48-linkage specific polyubiquitin (Enzo lifesciences, WB 1:1000), K63-linkage specific polyubiquitin (Cell Signaling, clone D7A11, 1:1000), myc (MBL, clone PL14, WB 1:3000, IF 1:100), HSC70 (Stressgen, WB 1:5000, IF 1:100), LC3B (Novus Biologicals, NB100-220), GFP (clonetech, 632381), p62 (Enzo Life Sciences, BML-PW9860), Lamin A/C (Santa Cruz, 4A58), HSC70 (Stressmarq biosciences), HSP70 (Stressgen, clone SPA-810, WB 1:1000, IF 1:50), HSPA1A (Enzo life sciences, Rb, WB 1:1000), HSPB1 (Stressmarq biosciences), GAPDH (Fitzgerald, clone 6C5, WB 1:50,000), histone H2A (Abcam, WB 1:5000), MYC (Clonetech, Mountain View, CA, USA), and DNAJB1/Hsp40 (Stressgen, San Diego, CA, USA, Rb, 1:1000) were used.
MG132 (20 µM for 3–6 h), rapamycin, Pepstatin A (10 μg/ml), E64d (10 μg/ml), 3-methyladenine (3-MA, 10 mM) ammonium chloride (NH4Cl, 20 mM) were from sigma.
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3

Western Blot Analysis of Death Receptors

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Cells were harvested and lysed with RIPA buffer supplemented with EDTA-free proteinase inhibitor cocktail (Roche, Basel, Switzerland). Samples were loaded on precast 4 to 12% sodium dodecyl sulfate–polyacrylamide gel electrophoresis gels (Thermo Fisher Scientific) and transferred onto 0.45 μm nitrocellulose membrane. Next, the membranes were blocked for 1 h at room temperature in 5% non-fat milk and probed overnight at 4°C. The following primary antibodies were used: DR5 (Sigma, Zwijndrecht, Netherlands), DR4 (Imgenix, Cambridge, United Kingdom), histone H2A (Abcam, Cambridge, United Kingdom), and CD63 (Pharmingen, San Diego, CA, United States). After incubating with secondary antibodies, membranes were detected using Pierce ECL kit (Thermo Fisher Scientific).
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4

Protein Extraction and Western Blotting

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Normal rabbit IgG and rabbit polyclonal antibodies to INTS3, Actin, NABP2, INTS9, INTS11, CUL9, COBRA1 (NELFB), JunB, and HA were obtained from Bethyl Laboratories, Inc. Other rabbit antibodies used include NABP2, NABP1 (Proteintech), Pol II (N-20, Santa Cruz), Spt5 (N-20, Santa Cruz), Histone H2A (Abcam), Histone H3 (Abcam), Histone H2B (Millipore), Histone H4 (gift from CD Allis), INIP (gift from W Wang), Lamin A/C (Cell Signaling), and Cyclin A. The mouse monoclonal Pol II antibody 8WG16 (Millipore) was also used (Supplementary information, Figure S1). Cell lysates were generated in lysis buffer (50 mM Tris, pH 8.0, 1 mM EDTA, 50 mM NaF, 0.5% Triton X-100, and either 150 or 250 mM NaCl, as indicated) supplemented with protease and phosphatase inhibitors. CSK (100 mM NaCl, 300 mM Sucrose, 3 mM MgCl2, and 10 mM PIPES, pH 6.8) extractions were generated as indicated. Select samples were generated by sonication (Bioruptor; Diagenode) in buffer containing 1 U/μl benzonase. Western blotting was performed as described previously32 (link).
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5

Immunoblotting of Protein Samples

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Protein samples were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and analyzed by immunoblotting as described previously [25 (link)]. The separated proteins were transferred onto the PVDF membrane and probed with antibodies against p-Ser, p-Thr, HMGB1, RPS3, GFP, α-tubulin (Cat. No. ab15246, Abcam), and histone H2A (Cat. No. 7631, Cell Signaling Technology, Danvers, MA, USA). The antibodies bound on the membrane were detected with secondary antibodies conjugated with horseradish peroxidase (Cat. No. HS-101, HS-201, Transgen, Beijing, China), followed by revealing with a chemiluminescence substrate. The luminescence signal was recorded digitally by using a Chemi-Doc XRS imaging system (Bio-Rad, Hercules, CA, USA). Digital image acquisition and analysis were conducted using the Quantity One program (Bio-Rad).
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6

Antibody Detection in Cellular Processes

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The following antibodies were used in this study: β-actin (Sigma-Aldrich, A5441), ASF1 and NASP (from Genevieve Almouzni), Calreticulin (Cell Signaling Technologies, 2891), FLAG (Sigma, F1804), HIRA (Abcam, ab20655), Histone H2A (Abcam, ab18255), Histone H3 (Abcam, ab1791), Histone H4 (Abcam, ab10158), HSC70 (Abcam, 19136), HSP90 (Abcam, ab13492), Importin 5 (Santa Cruz, sc11369), GAPDH (Santa Cruz Biotech, 365062), LAMP1 (Abcam, ab25630), LAMP2A (ThermoFisher Scientific, 512200), LC3B (Cell Signaling, 2775), TopoI (Santa Cruz, sc32736), VDAC (Abcam, ab15895), Alexa 488 goat anti-mouse IgG (H + L) (ThermoFisher Scientific, A11001), anti-Mouse IgG HRP (Rockland, 610–1302), anti-Rabbit IgG HRP (Rockland, 611–1322), anti-Rat IgG HRP (Rockland, 612-703-002).
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7

Western Blot Analysis of Pluripotency Markers

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Western blot analysis was performed as described previously.47 (link) The following primary antibodies were used: macroH2A1 (ab-37264, Abcam, Cambridge, MA, USA), Histone H3 (ab1791, Abcam), Histone H2A (Abcam), OCT4 (611203, BD Biosciences, San Jose, CA, USA), SOX2 (SC-20088, Santa Cruz, Santa Cruz, CA, USA), C-Myc (SC-40, Santa Cruz), KLF4 (ab75486, Abcam), HMGA2 (ab52039, Abcam), AURKA (610939, BD Biosciences), H-RAS (18295-1-ap, Proteintech, Chicago, IL, USA), Lin28B (#4196, Cell Signaling, Beverly, MA, USA), CHK1 (#2360, Cell Signaling), pCHK1 (#2348, Cell Signaling), CHK2 (#2662, Cell Signaling), pCHK2 (#2662, Cell Signaling) and β-actin (A5316, Sigma, St. Louis, MO, USA).
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8

Western Blot Antibody Optimization

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Human THP-1 and HEK 293T cells were obtained from the 1:1,000); TLR4 (ABCAM, 1:500); CtBP1 (ABCAM, 1:100); CAV1 (Beyotime, 1:500); ABCA1 (ABCAM, 1:200); Histone H2A (ABCAM, 1:500); and β-actin, (Proteinteck, 1:2,000). Secondary antibodies were: HRP-labelled Goat Anti-Mouse IgG(H+L) (Beyotime, 1:1,000) and horseradish peroxidase (HRP)-labelled Goat Anti-Rabbit IgG(H+L) (Beyotime, 1:1,000). Immunoreactive bands were visualized with Tanon 5500 (China) and BeyoECL Plus (Beyotime, China).
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