title: Nanopore sequencing of uninfected T84 colon cells: 24h BrdU incorporation
design: T84 immortalized colonic epithelial cells were grown in transwells to allow for cell polarization, and then apically infected with Shigella flexneri strain 2457T (or left uninfected as control).  Infected monolayers were incubated in 100 ug/ml gentamycin in DMEM for 24h to eliminate any residual extracellular bacteria.  New media was then added containing 150 uM BrdU or no BrdU control, and cells were harvested at the following timepoints: 1h, 4h, 24h.  DNA was isolated using a DNeasy PowerSoil Pro Kit (Qiagen) and prepared for Nanopore sequencing using a Rapid Barcoding Kit (Oxford Nanopore).  Library was sequenced for 24h on an R9.4.1 flow cell on a minION mk1C device.