Anti tfdp1

Whole cell lysates were obtained by re-suspending cell pellets in RIPA buffer (50 mM Tris pH7.4, 150 mM NaCl, 1% Triton X-100) with freshly added protease inhibitor (Roche) as previously described (Yang et al., 2021 (link)). Western blot analyses were performed with anti-MYCN (Proteintech, 10159-2), anti-BRG1 (Abcam, Ab110641), anti-E2F5 (Thermo Fisher, PA5-81166), anti-TFDP1 (Thermo Fisher, PA5-86135), anti-FOXP1 (Abcam, ab227649), anti-FOXP2 (Abcam, ab16046), anti-TWIST2 (Abcam, ab66031), and anti-β-actin (Sigma, A1978). For densitometrical quantification, densities of target proteins were normalized to those of β-actin as previously described (Liu et al., 2021b (link)). Data are expressed as relative protein levels compared to the control group which is arbitrarily set as 1.

Chromatin Immunoprecipitation (ChIP) assays were performed essentially as described before (Wu et al., 2020 (link)). In brief, chromatin in control and treated cells were cross-linked with 1% formaldehyde. Cells were incubated in lysis buffer (150 mM NaCl, 25 mM Tris pH 7.5, 1% Triton X-100, 0.1% SDS, 0.5% deoxycholate) supplemented with protease inhibitor tablet and phenylmethylsulfonyl fluoride (PMSF). DNA was fragmented into ∼200 bp pieces using a Branson 250 sonicator. Aliquots of lysates containing 200 μg of protein were used for each immunoprecipitation reaction with anti-BRG1 (Abcam, ab110641), anti-E2F5 (Thermo Fisher, PA5-81166), anti-TFDP1 (Thermo Fisher, PA5-86135), anti-acetyl H3 (Millipore, 06–599), anti-trimethyl H3K4 (Millipore, 17–614), anti-RNA polymerase II (Abcam, ab264350), anti-p300 (Abcam, ab275378), anti-KMT2A (Bethyl laboratories, A300-087A), or pre-immune IgG. Precipitated DNA was amplified with the following primers: 5′-AGGCTTTTCCCCGCCCTC-3′ and 5′-AGAGAGAGAGAGTCGGAAAAAAG-3′.