Transcriptional response of Acinetobacter baumannii to tigecycline

Acinetobacter baumannii 6772166 Muller-Hinton (Oxoid, United States) broth cultures at OD₆₀₀ 0.6 with and without 2.5 μg/ml tigecycline (Sigma-Aldrich, United States) treatment were grown for 30 min at 37°C with shaking. Three biological replicates were prepared. The total RNA of each sample was extracted using the miRNeasy Mini Kit (QIAGEN, Germany) following the manufacturer’s instructions. rRNA was depleted by using the Ribo-Zero Magnetic kit (bacteria) (Illumina, Inc., United States), and converted to cDNA which was sequenced via Illumina HiSeq2500 at Ramaciotti Center for Genomics. Nearly 75 million unique 101 bp reads were obtained from each RNA sample representing more than 310-fold genome coverage. The sequence reads from the 6 RNA-Seq samples (GEO accession no: GSE131451) were aligned against the A. baumannii AB0057 genome and transcriptional coverage for each gene was determined using EDGE-pro (Estimated Degree of Gene Expression in Prokaryotic Genomes) (Magoc et al., 2013 (link)). More than 99% of the RNA-Seq reads of each sample were mapped to AB0057 genome sequence. Genes with significantly different transcription between the control and experimental samples were identified using the DEseq R package (Supplementary Data). Gene differential expression was visualized by metabolic cellular view in Biocyc (Caspi et al., 2016 (link); Karp et al., 2019 (link)).