RNA-seq Analysis of E. faecalis Variants

RNA-seq analysis in E. faecalis H25 variants was carried out as described previously (23 (link)). Bacteria were grown to mid-log phase in BHI broth, harvested by centrifugation and lysed with 10 μg/ml lysozyme (Sigma, UK) and 10 U/ml Mutanolysin (Sigma, UK). RNA was extracted using the Maxwell^® 16 LEV SimplyRNA Cells Kit (Promega, USA) following the manufacturer's instructions. After depletion of rRNAs with Ribo-Zero from Illumina, the RNA samples were sequenced as 75-bp paired-end reads on an Illumina HiSeq 4000 and trimmed with trimmomatic/0.32 (44 (link)). Trimmed FASTq reads were aligned to the E. faecalis H25 genome generated by SMRT sequencing (accession GCA_002289045.2). RNA-seq was performed in triplicates on one clone for each variant and then a single RNA-seq for the second clone of each variant. The FASTq reads have been deposited in the SRA (accession PRJNA400682).