RNA-seq of WT E. coli strain MG1655-EcM2.1 at mid-log, replicate 3
Bacteria were grown in LB medium (10g tryptone, 10g sodium chloride, and 5g yeast extract per Liter) supplemented with 100 g/ml ampicillin. The MG1655-EcM2.1 strains (WT and EndoVm) grew at 34C, and the DH10B (mCherryOE and EndoVOE) at 37C. For the mCherryOE and EndoVOE strains, arabinose was added at the beginning of the experiment at a final concentration of 0.2%. At mid-log (OD600 of 0.5-0.68), 1 ml was collected for RNA extraction. RNA was extracted using the GeneJET RNA Purification Kit (Thermo Scientific #K0731). RNA samples were treated with 4 units of DNase I (NEB # M0303L) for 20 minutes at 37 C. We used RNA-seq to sequence three biological replicates collected on different days for the WT, EndoVm, mCherryOE, and EndoVOE strains. Ribosomal RNA was depleted using NEBNext rRNA Depletion Kit (Bacteria) (New England Biolabs, #E7850). RNA-seq libraries were constructed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, #E7760). DNA-seq libraries were prepared using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs, #E7805L). Finally, RNA-seq libraries were sequenced on the NovaSeq X platform (Illumina).
SUB16123164
WT-log3