library_construction_protocol: After 3 days transfection, cells were harvested by cross-linking with 0.3% formaldehyde for 10 min at room temperature and lysing with RIPA lysis buffer (50 mM Tris (pH 7.6), 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% NP-40, 0.5% sodium deoxycholate, protease inhibitor and RNase inhibitor) for 10 min on ice before sonication. The supernatant was collected and incubated with IgG and FLAG antibodies at 4 °C overnight. After washing with RIPA buffer (50 mM Tris (pH 7.6), 1 M NaCl, 1 mM EDTA, 0.1% SDS, 1% NP-40, 0.5% sodium deoxycholate), RNA was eluted from the beads with elution buffer (0.1 M NaHCO3 and 1% SDS, addition with proteinase K and RNase inhibitor) at room temperature for 10 min with gently vortex. The eluted material was then de-cross-linked at 65 °C for 45–60 min and treated with RNase inhibitor and proteinase K. Afterwards, RNA was purified using TRIzol LS reagent (Life Technologies) and treated with DNase I to remove any residual DNA. RIP RNA was used for library preparation.