Instrument: Illumina NovaSeq 6000
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Construction protocol: To analyze the influence of ambigols on the transcriptome of Serratia, six S39006 cultures were grown for 7 h in 6-well microtiter plates. Three cultures were incubated with 15.6 μM ambigol C in DMSO, whereas the other three were incubated with DMSO. 0.1 mL of each culture was mixed with two volumes of RNAprotect Bacteria Reagent (QIAGEN). The RNeasy Mini Kit (QIAGEN) was used for total RNA extraction, using the manufacturer's instructions (protocol 4 from the RNAprotect Bacteria Reagent Handbook), followed with two treatments of DNase (QIAGEN). RNA concentrations and quality were evaluated using an Agilent Bioanalyzer (Agilent Technologies). RNA sequencing was performed at the genomics service company GENEWIZ (Leipzig, Germany). RNA was depleted from rRNA using a NEBNext rRNA Depletion Kit (New England Biolabs GmbH), and a sequencing library was constructed using the NEBNext Ultra II RNA Library Prep Kit (New England Biolabs GmbH).