GSM6856790
ATAC–seq of HOTAIR-Ctrl, HOTAIR-OE, HOTAIR-Ctrl YTHDF3-KO and HOTAIR-OE YTHDF3-KO cells were performed as previously described (Corces et al., 2017). Briefly, 50000 cells were pelleted, resuspended in 50 μl of lysis buffer (10 mM Tris-HCl, pH 7.4, 3 mM MgCl2, 10 mM NaCl, 0.1% NP-40, and immediately centrifuged at 500g for 10 min at 4 °C. The nuclei pellets were resuspended in 50 μl of transposition buffer (25 μl of 2× TD buffer, 22.5 μl of distilled water, 2.5 μl of Illumina Tn5 transposase) and incubated at 37 °C for 30 min. Transposed DNA was purified with the DNA Clean & Concentrator-5 kit (Zymo Research), and eluted in 10 μl of EB buffer. Library fragments were amplified using NEBnext PCR master mix as previously described (Corces et al., 2017)