Factor Principles  References ChIP-chip and ChIP-seq Antibodies against Pol II, Pol II S2P, and Pol II S5P as well as various modified histones are used. [8,14,51,52] GRO-seq                Nascent RNAs that have incorporated 5-bromouridine 5’-triphosphate  are isolated with anti-deoxybromouridine antibody and sequenced.            [9,10,14]                PRO-seq Nascent RNAs that have incorporated biotinylated NTP are isolated with streptavidin beads for sequencing             [11] Short-capped RNA analysis              Short mRNAs (<100 bases) with a 5’ cap are isolated with anti-cap antibody and sequenced.  [12] Pol II: RNA Polymerase II; Pol II S2P: RNA Polymerase II with phosphorylated serine at the 2nd position in the carboxy-terminal heptapeptide repeat domain; GRO-seq: Global Run-On sequencing; PRO-seq: Precision Run-On sequencing

Table 1: Genome-wide approaches commonly used to detect PPP.