title: RNA-Seq of C. rodentium: bacterial culture of the croI deletion mutant strain of C. rodentium DBS100 grown in DMEM medium
design: RNA was isolated using the Qiagen RNeasy Mini Kit, and genomic DNA was digested on column by using the RNase-Free DNase Set (Qiagen). rRNA was depleted by using the bacterial NEBNext rRNA Depletion Kit (New England BioLabs, E7850). cDNA was generated using the Maxima H minus First Strand cDNA Synthesis Kit (Thermo Scientific, K1652) and the SuperScript Choice System for cDNA Synthesis (Life Technologies, 18090-019). Double stranded cDNA was purified using a 20% PEG, 1M NaCl Sera-Mag bead solution at a 1.8X ratio. The purified cDNA was then fragmented and sequencing libraries were created via end repair and phosphorylation, followed by 3 A-addition and adapter ligation using a custom reagent formulation (New England BioLabs, E6000B-10). Libraries were then indexed and pooled in equal molar amounts. RNA sequencing was performed using an Illumina HiSeqX platform (Ilumina) using paired-end (PE) reads.