Nascent RNAs were purified from Pol II IP products of solublilized chromatin. DNA were purified from chromatin IP products. Libraries were prepared according to the protocols of NEBNext small RNA library preparation kit (NEB) for mNET-seq; NEBNext Ultra II Directional RNA Library preparation kit (NEB) for Chromatin, Nucleoplasmic, Cytoplasmic and Nuclear poly(A)+ RNA-seq and RDIP-seq; QuantSeq 3' mRNA-Seq library preparation kit REV for Illumina (Lexogen) for 3'RNA-seq; NEBNext Ultra II DNA Library preparation kit (NEB) for mNucD-seq and ChIP-seq