Pol II density and pausing index

Promoter proximal was defined as ±250 bp around TSS, and gene body was defined as the remaining length of gene. Calculation of Pol II density as reads per million per kilobase (RPM/kb) was carried out in promoter proximal and gene body of each gene longer than 251 bp. The Pol II density ratio of promoter proximal and gene body was defined as pausing index or traveling ratio (54, 55).

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