GSM8991873: EcN, CDCA, 15 min, rep1; Escherichia coli Nissle 1917; RNA-Seq
RNA was harvested using the Qiagen RNeasy Mini kit, following the manufacturer's protocol with the following modifications: The cells were treated with 215 µL of lysozyme (15 mg/mL) and proteinase K (Qiagen, 1.5 mg/mL) in TE buffer at 37C for 10 min prior to the addition of Buffer RLT. The manufacturer's recommended on-column DNase treatment step was performed. After extraction, the RNA was treated with the Turbo DNA-free kit (Invitrogen) following the manufacturer's "rigorous" protocol. Sequencing libraries were generated from 400 ng of total RNA using the TruSeq Stranded Total RNA Kit (Illumina, catalog no. 20020596) in combination with the Illumina Ribo-Zero Plus rRNA Depletion Kit (Illumina, catalog no. 20037135).