For RNA-seq and PRO-seq, RNA was isolated with TRIzol. For SLAM-seq, the 4sU-labeled RNA was isolated using a 1:1 volume of RNA XP magnetic beads. After 10 mins incubation at room temperature, the beads were washed twice with 200 μL 80% freshly prepared ethanol on the magnetic stand and the dried beads pellets were resuspended in 7 μL RNase-free water. For ATAC-seq and CUT&Tag, DNA was purified using the SPRI beads. For RNA-seq, libraries were prepared according to the Fast RNA-seq Lib Prep Kit V2 with 0.2 μg RNA following the manufacturer's protocols. For SLAM-seq, alkylated RNA was used for 3'-end polyA RNA sequencing library preparation with Smart-seq2 according to the manufacturer's protocol. For ATAC-seq, mESCs cells were digested with adapter-loaded Tn5 in the tagmentation buffer (33 mM Tris-Acetate, 66 mM K-Acetate, 10 mM Mg-Acetate,16% DMF, 0.02% Digitonin) for 30 mins at 37 °C, and the reaction was stopped by stop buffer (100 mM Tris pH 8.0, 100 mM NaCl, 0.4% SDS and 40 μg/mL Proteinase K) and incubated overnight at 55 °C. 25% Tween-20 was added to quench SDS. Sequencing libraries were prepared with NEBNext High-Fidelity 2x PCR Master Mix. The PCR product was purified using a 1:1.6 volume ratio of SPRI beads. For CUT&Tag, libraries were performed using the Hyperactive Universal CUT&Tag Assay Kit following the manufacturer's protocols. For PRO-seq, enriched RNA was ligated with RNA adapters. Reverse transcription was performed using the Superscript III enzyme. The reverse transcription products were proceeded to library amplification by using the Q5 enzyme mix.