Whole genome sequencing of EPEC microcolonies from anaerobic conditions
Bacteria from anaerobic Microcolony-seq condition that were kept at the -80C were regrown in liquid LB at 37C for 5 hours. DNA was extracted from 1 mL of bacteria using the DNeasy Blood & Tissue Kit (Qiagen). Library preparation and sequencing was carried out by the Genomics Applications Laboratory, Core Research Facility, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel. DNA libraries for sequencing were prepared using the kit (ILMN DNA LP (M) Tagmentation (24 Samples, IPB) 20060060) (Illumina, Inc., USA) according to manufacturing instructions. At least 100X sequencing depth for each nucleotide in each sample was targeted. Samples were deep-sequenced with the Nextseq500 machine using the 150-cycle mid output kit (Illumina, Inc., USA) from the forward read direction.