title: PRO-seq of A549 cells, rep B
design: PRO-seq was performed as described previously (Watts et al., 2019) with the following modifications. The 3 ligation adapter used oligo 5'p-NNNNNNGAUCGUCGGACUGUAGAACUCUGAAC-/3InvdT/, which contains a unique molecular index (UMI). PRO-seq was sequenced on an Illumina HiSeq 2500 instrument to a depth of >150 million reads per sample. Sequence reads were trimmed and aligned to hg19.  Identical reads sharing a UMI were considered duplicates and removed. The 3' ends of reads mapping to the mitochondrial genome were determined and normalized to the total number of reads mapping to the nuclear genome, and then lifted over to hg38 for downstream analysis