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3 protocols using anti u2af65

1

Co-immunoprecipitation of Protein Complexes

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Co-immunoprecipitation of ILF2, YB-1 or U2AF65 complexes was performed by lysing JJN3 cells with NP40 lysis buffer containing phosphatase and protease inhibitor cocktails (Roche) on ice for 1 hr. Lysates were sonicated gently and centrifuged for 10 min at 4°C. One milligram of the lysate was incubated overnight at 4°C with Protein A-agarose beads (Roche) and anti-ILF2 (Abcam, ab113205), anti–YB-1 (Abcam, ab12148), anti-U2AF65 (Santa Cruz, sc53942) -or unspecific (rabbit/mouse immunoglobulin G [IgG], Santa Cruz, sc-2027/2025) antibodies for immunoprecipitation. The immunoprecipitates were then re-suspended in sample buffer, boiled for 5 min, and analyzed by Western blotting or mass spectrometry.
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2

Antibodies for ChIP and Western Blotting

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The following antibodies were used for chromatin immunoprecipitation (ChIP) or western blotting (WB): anti-PFDN5 (Santa Cruz, sc-271150, WB); anti-GAPDH (Santa Cruz, sc-47724, WB); anti-PFDN2 (Bethyl, A304-807A, WB); anti-Rpb1 CTD Ser2 phosphorylated (Abcam, ab5095, ChIP and WB); anti-Rpb1 CTD Ser5 phosphorylated (Abcam, ab5131, ChIP and WB); anti-Rpb1 8WG16 (Thermo Fisher MA1-10882, ChIP); anti-FLAG (Sigma, F3165, ChIP); anti-U2AF65 (Santa Cruz, sc-53942, ChIP and WB); anti-PRPF19 (Lührmann Laboratory, ChIP and WB); anti-PRGL1 (Lührmann Laboratory, WB); anti-CDK9 (Santa Cruz, sc-13130, ChIP and WB); anti-vinculin (Santa Cruz, sc-25336, WB).
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3

Antibody-based Immunoblotting Analysis

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Antibodies used for immunoblotting were anti-SRSF1 (1:1000, Invitrogen, 32–4500), anti-Rbfox1 (1:100, N-14, Santa Cruz Biotechnology, sc-135476), anti-Rbfox2 (1:2000, Bethyl Laboratories, A300-864A), anti-hnRNP F/H (1:500, Santa Cruz Biotechnology, sc-32310), anti-U1-70K (1:1000, Synaptic Systems, 203011), anti-U1A (1:1000, Thermo Fisher Scientific, PA5-27474), anti-U1C (1:1000, Sigma-Aldrich, SAB4200188), anti-GAPDH (1:2500, Sigma-Aldrich, G9545), anti-6xHis-tag (1:2500, Medical & Biological Laboratories, D291-3), anti-Flag M2 (1:1000, Sigma-Aldrich, F3165), anti-U2AF65 (1:400, MC3, Santa Cruz Biotechnology, sc-53942), anti-GFPT1 (1:500, Abcam, ab125069), anti-RL2 (1:800, Santa Cruz Biotechnology, sc-59624), anti-O-GlcNAc (CTD110.6) (1:2000, Cell Signaling Technology, 9875), anti-β-actin (1:1000, Santa Cruz Biotechnology, sc-47778), and anti-synaptophysin antibodies (1:50, Innovative Research, 18–0130). The secondary antibodies were anti-mouse IgG (1:2000, Cell Signaling Technology, 7076) conjugated to horseradish peroxidase, goat anti-rabbit IgG (1:2000, Cell Signaling Technology, 7074) conjugated to horseradish peroxidase, and Alexa 488-conjugated goat anti-rabbit antibody (1:1000, Thermo Fisher Scientific, A-11034). AChRs were visualized by Alexa 594-conjugated ɑ-bungarotoxin (1:1000, Invitrogen, B-13423).
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