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3 protocols using brca2

1

Antibody Panel for DNA Damage Signaling

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The following antibodies were used for western blot analysis: 53BP1 (Bethyl Laboratories, A300-272A, 1:3000), LIN37 (Santa Cruz Biotechnology, sc-515686, 1:200), BLM (Bethyl Laboratories, A300-572A, 1:2000), BRCA1 for mouse (R and D Systems, gift from Dr. Andre Nussenzweig, NCI, 1:1000) (Zong et al., 2019 (link)), BRCA1 for human (Millipore Sigma, 07-434, 1:1000), RAD51 (Millipore Sigma, ABE257, 1:2000), BARD1 (Thermo Fisher Scientific, PA5-85707, 1:1000), CtIP (gift from Dr. Richard Baer, [Columbia University, New York], 1:1000), MRE11 (Novus Biologicals, NB100-142, 1:2000), RIF1 (Abcam, ab13422, 1:500), SHLD1/C20orf196 (Thermo Fisher Scientific, PA5-559280, 1:200), GAPDH (Sigma, G8795, 1:10,000), KAP1 (Genetex, GTX102226, 1:2000), FANCD2 (R and D Systems, MAB93691, 1:1000), BRCA2 for human (Proteintech, 19791-1-AP, 1:500), Rb1 (Thermo Fisher Scientific, LF-MA0173, 1:1000), Phospho-Rb (Ser780) (Cell Signaling Technology, 8180T, 1:1000), Phospho-Rb (Ser807/811) (Cell Signaling Technology, 8516T, 1:1000), PCNA (Bethyl Laboratories, A300-276A, 1:3000), CDK4: (Novus Biologicals, NBP1-31308, 1:1000), CDK4 (phosphor Thr 172) (GeneTex, GTX00778, 1:1000), and RPA (Cell Signaling Technology, 2208S, 1:1000).
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2

Protein Extraction and Western Blot Analysis

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Protein extraction was conducted using RIPA Lysis Buffer (Beyotime Biotechnology, Shanghai, China) containing a protease inhibitor cocktail (Thermo Fisher Scientific, USA). Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) assay was performed as in previous reports.52 (link) Primary antibodies used in this study were β-actin (cat. 200068-8F10; ZEN-bioscience), H3 (cat. ASO71; ABclonal), Cyclin D1 (cat. 55506 T; CST), CDK4 (cat. 12790 T; CST), Cyclin A2 (cat. ab181591; Abcam), Cyclin E1 (cat. 20808 S; CST), CDK1 (cat. ab32094; Abcam), Cyclin B1(cat. 55004-1-AP; Proteintech), H3K9me1 (cat. A2358; ABclonal), H3K9me2 (cat. A2359; ABclonal), H3K9me3 (cat. ab176916; Abcam), MDIG (cat. 12214-1-AP; Proteintech), OTX2 (cat. 13497-1-AP; Proteintech), Myc (cat. 10828-1-AP; Proteintech), BRCA2 (cat. AF7817; Affinity), Junb (cat. 10486-1AP; Proteintech), E2F2 (cat. AF4100), ATAD5 (cat. Bs-7656R; Bioss). Western blots were quantified using ImageJ software (Version 1.51n, National Institutes of Health, Bethesda, MD, https://imagej.net/ij/index.html), as previously described.53 (link) The original and uncropped films of Western blots were provided as Supplementary Figs. S19S21.
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3

Immunohistochemical Analysis of DNA Repair Proteins

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Slides were baked at 60°C for one hour. After deparaffinization and rehydration, tissue sections were treated with either citrate buffer or Borg Decloaker for five minutes in a pressure cooker for antigen retrieval. Hydrogen peroxide (3%) was applied to the sections for 10 minutes. Sections were incubated with primary antibodies against BRCA1 (Biocare Medical), BRCA2 (Proteintech), PCNA, RAD51 (Abcam), RAD6, RAD18 or RPA1/RPA70 (Abcam) for 30 minutes. After buffer rinsing, sections were incubated with anti-mouse HRP-labeled polymer (EnVision) or anti-HRP-labeled polymer (Mach2) for 30 minutes and buffer rinsed twice. Finally, the staining was visualized by DAB+ (Dako). IHC staining was performed using the IntelliPATH FLX Automated Stainer at room temperature.
A light hematoxylin counterstain was performed, then slides were dehydrated, cleared, and mounted using permanent mounting media.
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