GSM8565646: Single_species_Ef_Bio3; Enterococcus faecalis OG1RF; RNA-Seq
Biofilm samples were pelleted at 4,000 x rpm for 10 min, then suspended in RNAprotect solution (Qiagen, Hilden, Germany) for 5 mins. Then, samples were pelleted at 4,000 x rpm for 10 min again for downstream RNA extraction. Subsequent RNA extraction steps were performed according to the manufacturer's protocol using PureLink RNA mini kit (Thermofisher, Massachusetts, USA) with minor modifications. Briefly, samples were incubated with 30 mg ml-1 of lysozyme for 30 mins prior to extracting RNA. After extraction, RNA samples were further processed using Monarch RNA cleanup kit (New England Biolabs, Massachusetts, USA). Then, the extracted RNA was quality checked using the RNA ScreenTape on a TapeStation instrument (Agilent Technologies, USA). Every sample had a minimum RNA concentration of 25 ng/µL and a RINe value ≥8.0. Extracted RNA samples were sent to SeqCenter (Pennsylvania, USA) for library preparation, ribosomal RNA depletion, sequencing and downstream bioinformatic analysis. Library preparation was performed using Illumina's Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and 10bp unique dual indices (UDI).