Nucleotide resolution of RNA polymerase II transcription in human cytomegalovirus

We performed paired-end PRO-Seq and/or PRO-Cap on human foreskin fibroblasts (HFF) infected with human cytomegalovirus (HCMV) for 4 h (strain TB40/E) or 96 h (strain Towne varS). Each sample has matched uninfected controls. Towne experiments were also performed with adapters containing 4 nt of random sequence flanking both sides (8 total bases of randomness) to enable deduplication. Reads were first mapped to the human genome (hg38) (files available on GEO). Unmapped reads were then mapped to HCMV (Genbank FJ616285.1) (track hub available at https://github.com/P-TEFb/trackHub_HCMV). TB40/E: PRO-Seq on uninfected HFF treated with 0.1% DMSO 1 h, or 4 h infected HFF treated with 0.1% DMSO 1 h or 1 µM flavopiridol 1 h. Towne: PRO-Seq and PRO-Cap on uninfected or 96 h infected HFF treated with 0.1% DMSO 1 h or 1 µM flavopiridol 1 h.