title: RNA-Seq of C. coli: time 6h aerobic condition
design: Sample was collected at Time 0 under microaerobic conditions, then broth cultures were transferred to aerobic conditions and samples collected at 0.25h, 0.5h, 0.75h, 1h, 3h, 6h, 9h, 12h, and 15. Samples were added to 100 L of pre-chilled 90% ethanol and 10% buffered phenol, then flash-frozen in an ethanol ice bath and stored at -80 degrees Celsius. RNA was isolated using the Directzol RNA miniprep kit from Zymo Research and samples were purified of DNA using the TURBO DNA-free kit from Invitrogen. The rRNA was depleted using the NEBNext rRNA Depletion kit from New England Biolabs. The cDNA library was prepared using NEBNext Ultra II Directional RNA Library Preparation Kit for Illumina from New England Biolabs, using approximately 100 ng of RNA per sample. Sequencing was outsourced to the OMRF Clinical Genomics Center and conducted using a NovaSeq 6000 platform.