Clear cell lysate was obtained by centrifugation at 10,000 rpm and 4 °C for 10 min. RQ I (Promega, 1U/μL) was added to a final concentration of 1 U/μL, and the sample was incubated in a water bath for 30 min at 37 °C. A stop solution was immediately added to the lysates to quench DNase. The mixture was then vibrated vigorously and centrifuged at 13,000 x g and 4 °C for 20 min to remove cell debris. The RNA was then digested using MNase (Thermo Scientific) cDNA libraries were prepared with the KAPA RNA Hyper Prep Kit (KAPA, KK8541) in accordance with the manufacturer's procedure. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina NovaSeq system for 150 nt paired-end sequencing.