Determination of human DNA replication origin position and efficiency reveals principles of initiation zone organisation

We describe a modification of initiation site sequencing (ini-seq, Langley et al., NAR 2016) in which density gradient centrifugation separates 'heavy' replicated DNA containing BrdU from DNA containing only 'light' dTTP before sequencing. This approach allows us to assign a replication initiation efficiency score to each of the 23905 origins identified. We also performed Short Nascent Strand sequencing (SNS-seq), an established method to map replication origins, in the same cell line as in Ini-seq2 for comparison. Overall design: Massive sequecing of human replication origin isolated from EJ30 cell line by either Ini-seq2 or SNS-seq method