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11 protocols using rabbit anti flag f7425

1

HA-tagged Protein Immunoprecipitation and Detection

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Cells were lysed with lysis buffer (20 mM Tris-HCl, pH 7.5, 150 mM NaCl, 1 mM Na2EDTA, 1 mM EGTA, 1% TritonX-100, 2.5 mM sodium pyrophosphate, 1 mM -glycerophosphate, 1 mM Na3VO4) on ice for 15 min. Cell lysates were then centrifuged at 20,000 g for 30 min. The supernatant was immunoprecipitated with 20 µl of mouse anti-HA-agarose beads (A2095, Sigma) at 4 °C for 3 h or overnight. After the immunoprecipitation, the beads were washed four times in lysis buffer, and the immunoprecipitated proteins were subsequently eluted by 1× SDS sample buffer at room temperature for 10 min. The supernatant was collected and denatured at 100 °C for 2 min. The samples were subjected to western blotting with the corresponding antibodies. Rabbit anti-Flag (F7425, dilution 1:1000), mouse anti-α-tubulin (T5168, 1: 5000), and mouse anti-HA antibodies (H3663, dilution 1:1000) were purchased from Sigma. Rabbit anti-HA (ab9110, dilution 1:1000) and mouse anti-KAP1 (ab22553, dilution 1:1000) were from Abcam. The uncropped western blot images are provided in Supplementary Figure 6.
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2

Hsp90 Immunoprecipitation and Western Blot

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HeLa cells were grown in 10-cm tissue culture dishes. Mock infections and infections were carried out according to a standard protocol. At 17 hpi, the cells were treated with DMSO or 300 nM geldanamycin for 1 h prior to harvesting. Cell lysates (1 ml) were incubated with 100 μl of a protein A-Sepharose bead slurry (P3391; Sigma-Aldrich) conjugated to isotype control (rabbit anti-FLAG [F7425; Sigma-Aldrich]) or Hsp90 antibody (rabbit anti-HSP90AB1 [11405-1-AP; Proteintech]). Lysate and beads were gently mixed overnight on ice. Subsequently, the mixture was centrifuged at 2,000 × g for 2 min at 4°C, and the supernatant was discarded. The beads were washed four times with lysis buffer. The beads were resuspended in 50 μl of 2× SDS sample buffer and heated at 100°C for 5 min, followed by centrifugation at 2,000 × g for 3 min. The proteins were separated by electrophoresis through SDS-PAGE gels, and Western blot analysis was carried out as described above.
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3

Sulforaphane and Zidovudine Treatment Protocol

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Sulforaphane (SFN) (S8044) and Zidovudine (AZT) (L0350) were bought from LKT Laboratories. The mouse anti-actin (A1978), mouse anti-Flag (F1804), and mouse anti-HA (H9658) monoclonal antibodies; the rabbit anti-Flag (F7425), rabbit anti-HA (H6908), and anti-Mouse IgG-FITC antibodies were purchased from Sigma. Rat anti-Myc (ab206486), mouse anti-Tubulin (TA503129) monoclonal antibodies, Rabbit anti-Lamin (EPR8985), Alexa Fluor 568-conjugated (ab175476) and Alexa Fluor 647-conjugated (ab190565) antibodies were purchased from Abcam (Cambridge, UK). The rabbit anti-GST (10000-0-AP) antibodies were purchased from Proteintech. DyLight 800-labeled goat anti-mouse (5230–0415) and DyLight 508 680-labeled goat anti-rabbit (5230–0403) secondary antibodies were purchased from KPL. Anti-eqNrf2, anti-eqKeap1 and anti-P26 antibodies were prepared in our laboratory. The nuclear extraction kit was purchased from Invent Biotechnologies (SC-003). Non-cytotoxic dosages were used in this study.
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4

Antibody Characterization for Molecular Studies

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The following antibodies were used: mouse anti-Flag (M2, Sigma-Aldrich, St. Louis, MO), rabbit anti-Flag (F7425, Sigma-Aldrich, St. Louis), mouse anti-RTA (mouse hybridoma), mouse anti-LANA (mouse hybridoma), mouse anti-Myc (mouse hybridoma), rabbit anti-HA (6908, Sigma-Aldrich, St. Louis, MO), mouse anti-HA12CA5 (sc-57592, Santa Cruz Biotechnology), mouse anti-GFP (G1546, Sigma-Aldrich, St. Louis), mouse anti-GAPDH (G8140, US Biological, Salem MA), and rabbit anti-Myc (SAB4300605, Sigma-Aldrich, St. Louis, MO), goat anti-PRMT5 (C-20, sc-22132, Santa Cruz Biotechnology), mouse anti-ORF59 (generous gift from Dr. Bala Chandran), rabbit anti-Control IgG (sc-2027, Santa Cruz Biotechnology), mouse anti-Control IgG (sc-2025, Santa Cruz Biotechnology), rabbit anti-H4R3me2s (61187, Active Motif, Carlsbad CA), rabbit anti-Histone H4 (#61299 Active Motif), rabbit-anti-PRMT5 antibody (#61001 Active Motif), rabbit anti-control IgG (ChIP grade—Cell Signaling Technology #2729, rabbit anti-COPR5 antibody (Novus Biologicals #NBP2-30884), and additional rabbit-anti ORF59 antibody custom synthesized for our lab by GenScript.
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5

Antibody Characterization for DNA Damage Response

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Antibodies were as follows: rabbit anti-FANCD2 (NB100-182; Novus) at 1:10,000; rabbit anti-FANCI (A301-254A; Bethyl) at 1:1,000; rabbit anti-SF3B1 (A300-996A; Bethyl) at 1:2,000; rabbit anti-SF3B1 (Eurogentec) at 1:1,000; rabbit anti-SF3A3 (A302-507A; Bethyl) at 1:2,000; rabbit anti-FLAG (F7425; Sigma-Aldrich) at 1:1,000; rabbit anti-DHX15 (A300-389A; Bethyl) at 1:5,000, mouse anti-SC35 (556363; BD Pharmingen) at 1:500; rabbit anti-U2AF65 (ab37530; Abcam) at 1:250; rabbit anti-pSer345(Chk1) (2348L, rabbit; Cell Signaling Technology) at 1:1,000; mouse anti-Chk1 (Sc-8408; Santa Cruz Biotechnology) at 1:1,000; mouse anti-tubulin (T5168; Sigma-Aldrich) at 1:10,000; anti-rabbit HRP-linked (7074; Cell Signaling Technology) at 1:2,500; anti-mouse HRP-linked (7076; Cell Signaling Technology) at 1:2,500; rabbit anti-Nbs1 (NB100-143; Novus Biologicals) at 1:1,000; mouse anti-PCNA (P8825; Sigma-Aldrich) at 1:3,000; rabbit anti-TopBP1 (A300-111A; Bethyl) at 1:1,000; rabbit anti-RNA-PolII (N-20) (sc-899; Santa Cruz Biotechnology) at 1:1,000; rabbit anti-TFIP11 (A302-548A; Bethyl) at 1:1,000; rabbit anti-SPF45 (A302-548A; Bethyl) at 1:1,000; rabbit anti-FANCA (A301-980A; Bethyl) at 1:2,000; and rabbit anti-PRP8 (GTX108046; GeneTex) at 1:1,000.
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6

Antibody Identification for Biomarker Analysis

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Mouse anti-BRCA1 (MS110; OP92), mouse anti-R-loop (S9.6; MABE1095), mouse anti-dsDNA (AE-2; MAB1293), and mouse anti-dsRNA (rJ2; MABE1134) were purchased from EMD Millipore. Mouse anti-BRCA2 mAb (OP95) was purchased from Calbiochem. Rabbit anti-nucleolin (D4C70; 14574), rabbit anti-β-actin (13E5; 4970), and rabbit anti-β-tubulin (9F3; 2128) were purchased from Cell Signaling Technology. Mouse anti-GAPDH (AC002) was purchased from ABClonal. Rabbit anti-FLAG (F7425) was purchased from Sigma-Aldrich.
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7

Antibody Specifications for Protein Interactions

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The following are the specificities and sources of antibodies used: Against phosphotyrosine (PY20; GE Healthcare), the FLAG epitope (mouse monoclonal M2, F3165, and rabbit anti-FLAG, F7425; Sigma), the Myc epitope (rabbit anti-Myc, 600–401–381; Rockland, and mouse monoclonal 9E10; Sigma), GFP (mouse monoclonal anti-GFP, 11–814–460–001; Roche), Hic-5 (mouse monoclonal anti-Hic-5, 611164; BD Biosciences), paxillin (mouse monoclonal anti-paxillin, 610569; BD Biosciences, and rabbit anti-paxillin, sc-5574; Santa Cruz Biotechnology), and Git1 (rabbit anti-Git1, sc-13961; Santa Cruz Biotechnology, and mouse anti-Git1 monoclonal antibody, 611396; BD Biosciences). Rabbit antisera specific for the amino acid residues 251–555 of Git1 (anti-GIT1/Cat-1) [13 (link)], rabbit polyclonal antibodies against phospho-Tyr-554 on Git1 (anti-pY554-Git1) [12 (link)], and a rabbit anti-Ptprz-S serum [15 (link)] were prepared in our laboratory. Anti-pY554-Git1 antibodies were conjugated with horseradish peroxidase (HRP) using a peroxidase labeling kit (Dojindo Molecular Technologies).
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8

Antibody and RNA Synthesis Protocols

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The mouse anti-actin (A1978), mouse anti-FLAG (F1804), and mouse anti-HA (H9658) monoclonal antibodies and the rabbit anti-FLAG (F7425), rabbit anti-HA (H6908), and anti-Mouse IgG-FITC antibodies were purchased from Sigma. Mouse anti-tubulin (TA503129) monoclonal antibodies, rabbit anti-lamin (EPR8985), Alexa Fluor 568-conjugated (ab175476), and Alexa Fluor 647-conjugated (ab190565) antibodies were purchased from Abcam (Cambridge, UK). DyLight 800-labeled goat anti-mouse (5230-0415) and DyLight 680-labeled goat anti-rabbit (5230-0403) secondary antibodies were purchased from KPL. Anti-Grev and anti-p26 antibodies were prepared in our laboratory. The T7 quick high-yield RNA synthesis kit (E2050S) was purchased from NEB. The RNA 3′-end desthiobiotinylation kit (20163) and streptavidin magnetic beads (88816) were purchased from Thermo. Leptomycin B (LMB) was purchased from Beyotime Biotechnology.
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9

Antibody Validation for Protein Signaling

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Mouse anti-Myc (9E10), rabbit anti-HA (F-7), mouse anti-α-tubulin (B-7) and mouse anti-β-tubulin (3F3-G2) antibodies were purchased from Santa Cruz. Mouse anti-Flag (F3165), rabbit anti-Flag (F7425) and mouse anti-ubiquitin (P4D1) antibodies were purchased from Sigma-Aldrich. Rabbit anti-cGAS (D1D3G), rabbit anti-STING (D2P2F) and rabbit anti-TBK1 (D1B4) antibodies were from Cell Signaling Technology. Mouse anti-V5 (E10/V4RR) antibodies were from Invitrogen.
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10

Antibody Characterization for DNA Damage Response

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Antibodies used in this study were as follows: anti-USP15 (A300-923A, WB: 1:1000), anti-BARD1 (A300-263A, WB: 1:1000; IF: 1:200), and anti-RAP80 (A300-764A, WB: 1:1000; IF: 1:100) were purchased from Bethyl Laboratory. Anti-HP1γ (MABE656, WB: 1:2000). Mouse anti-γ-H2AX (05-636, IF: 1:500), mouse anti-MDC1 (05-1572, IF: 1:300) and mouse anti-FK2 (04-263, IF: 1:200) were purchased from Millipore. Anti-RPA 70 (#2267, IF: 1:200), rabbit anti-γ-H2AX (#9718, IF: 1:400), and rabbit anti-HA (#3724, WB: 1:2500; IF: 1:300) were from Cell signaling Technology. Anti-Rad51 (GTX100469, IF: 1:200) were from Genetex. Anti-BRCA1 (D9, IF: 1:50) and anti-His tag (sc8036, WB: 1:1000) were from Santa Cruz. Anti-poly PAR (4336-BPC-100, WB: 1:1000) were from Trevigon. Anti-53BP1 (NB100-304, WB: 1:1000; IF: 1:300) were from Novus Biologicals. Anti-RNF8 (14112-1-AP, IF: 1:100) were from Proteintech. Rabbit anti-FLAG (F7425, WB: 1:2500) and mouse anti-FLAG (F3165, WB: 1:2500) were from Sigma-Aldrich. Mouse anti-HA (901501, WB: 1:2500; IF: 1:100) were from BioLegend.
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