library_construction_protocol: Infected cells were harvested by scraping at the indicated time points, washed, lysed with mild lysis buffer according to the published OMNI-ATAC-seq protocol, incubated with Tn5 transposase (tagmentase) for 30 minutes, lysed in Qiagen's PB buffer, DNA purified according to the MinElute protocol. Libraries were prepared using Illumina-compatible primers (like Nextera primers but custom sets with dual-unique barcodes). Initially, quantitative PCR was performed to judge how many cycles are required for optimal library preparation. 35bp paired-end, NextSeq 500 (Illumina)