Transcriptomic data of Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S treated with novobiocin

In enteric bacteria, DNA supercoiling is highly responsive to environmental conditions. Host specific features of environment serve as cues for the expression of genes required for colonization of host niches via changing supercoiling [1]. It has been shown that substitution at position 87 of GyrA of Salmonella enterica str. SL1344 influences global supercoiling and results in an altered transcriptome with increased expression of stress response pathways [2]. Aminocoumarin antibiotics, such as novobiocin, can be used to relax supercoiling and alter the expression of supercoiling-sensitive genes. Meanwhile, Salmonella enterica demonstrates a significant resistance to this antibiotic and relatively small variability of supercoiling in response to the growth phase, osmotic pressure, and novobiocin treatment. Here we present for the first time transcriptome data of Salmonella enterica subsp. Enterica serovar Typhimurium str. 14028S grown in the presence of novobiocin. These data will help identify genes involved in novobiocin resistance and adaptation processes associated with torsion perturbations in S. enterica. Cleaned FASTQ files for the RNA-seq libraries are deposited in the NCBI Sequence Read Archive (SRA, Identifier: SRP239815) and have been assigned BioProject accession PRJNA599397.


a b s t r a c t
In enteric bacteria, DNA supercoiling is highly responsive to environmental conditions. Host specific features of environment serve as cues for the expression of genes required for colonization of host niches via changing supercoiling [1]. It has been shown that substitution at position 87 of GyrA of Salmonella enterica str. SL1344 influences global supercoiling and results in an altered transcriptome with increased expression of stress response pathways [2]. Aminocoumarin antibiotics, such as novobiocin, can be used to relax supercoiling and alter the expression of supercoilingsensitive genes. Meanwhile, Salmonella enterica demonstrates a significant resistance to this antibiotic and relatively small variability of supercoiling in response to the growth phase, osmotic pressure, and novobiocin treatment. Here we present for the first time transcriptome data of Salmonella enterica subsp. Enterica serovar Typhimurium str. 14028S grown in the presence of novobiocin. These data will help identify genes involved in novobiocin resistance and adaptation processes associated with torsion perturbations in S. enterica. Cleaned FASTQ files for the RNA-seq libraries are deposited in the NCBI Sequence Read Archive (SRA, Identifier: SRP239815) and have been assigned BioProject accession PRJNA599397.
© 2020 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4.0/).

Data description
The dataset of this article provides information on raw RNA-seq reads obtained from samples of S.
enterica cultures treated with novobiocin at concentrations of 100 and 500 mg per mL, and untreated cultures. The data sets were named based on novobiocin concentration and growth time after addition of novobiocin. Information on the treatment (sampling) time and growth rate of the cultures is presented in Table 1. This table also provides the NCBI SRA accession numbers of the cleaned FASTQ files for all biological replicates. Coverage estimates and reads mapping statistics are summarized in Table 2. PCA plot of RNA-seq data presented in Fig. 1 demonstrates the variance between sample groups and sample replicates according to gene expression levels.

Bacterial strains and growth conditions
Strain used in this work was Salmonella enterica subsp. enterica serovar Typhimurium ATCC 14028S (NCBI:txid588858). This strain was cultured on a Luria-Bertani (LB) agar plate (Sigma Aldrich) and a single colony was used to inoculate 10 mL of fresh LB broth for aerobic incubation at 37 C. After 12 h, 1 Specifications Table   Subject Biochemistry

Value of the Data
Resistance of bacterial pathogens to current antibiotics is an increasingly urgent worldwide problem. Host specific environmental conditions cause increased DNA supercoiling in enteric bacteria [1]. Many promoters of genes required for colonization of host niches respond to changes in the supercoiling state and apparently are sensitive to the novobiocin treatment [2,3]. The transcriptome data set generated for control and novobiocin treated samples of S. enterica str. 14028S helps in identification of differentially expressed genes for a better understanding of the molecular mechanism of the bacterial signaling and antibiotic resistance.
mL of this preculture was added to 50 mL of LB broth and incubated aerobically at 37 C until the middle of the exponential growth phase (A600 ¼ 0.6), which was reached approximately 4 h after the initial inoculation. Novobiocin (Sigma Aldrich) was added at various concentrations directly to the flask and turbidity was monitored by measuring the optical density.

Experiment design
The bacteria were grown in LB medium until middle log-phase where 0, 100 and 500 mg of novobiocin per mL was added. This increase in the antibiotic concentration has led to a gradual inhibition of the Salmonella growth, but by the end of time sampling the growth of bacteria in both cases resumed. At time zero and after 60 min 10 mL aliquots were taken and bacteria were harvested and fixed. The control sample and the sample supplemented with 500 mg of novobiocin per mL were also fixed after 10 and 20 minutes. Total RNA was isolated and cDNA libraries were prepared for RNA-sequencing. Directional libraries were sequenced on Illumina Hiseq2500 in single reads. The RNA-seq raw reads were further analyzed to get the clean reads and stored in FASTQ files.

Library construction and sequencing
Bacterial cultures were fixed with an equal volume of cold RNA-stabilizing solution (19% ethanol, 1% acidic phenol, pH 5.5) on ice for 30 minutes. Cells were harvested by centrifugation and total RNA was extracted using RNA Extract Reagent (Evrogen, Russia) according to the manufacturer's protocol. DNA contaminants were removed using RNase-free DNase I kit (Ambion, USA). The integrity of the RNA was checked by Agilent 2100 bioanalyzer (USA). rRNA depletion performed using Ribo-Zero rRNA Removal Kit for Gram-Negative Bacteria (Illumina, USA). Barcoded RNA libraries were generated. NEBNext Ultra Directional RNA Library Prep Kit for Illumina was used to prepare RNA-seq libraries. The resulting average size of the cDNA libraries was approximately 300 bp. Libraries were sequenced using the Illumina HiSeq 2500 sequencing platform.

Sequence QC and filtering
266,853,687 reads were obtained in total with a length of 60 nucleotides. Raw Fastq files and clean reads were quality controlled using FastQC software (Version 0.11.5) [4]. Raw reads were filtered using accounted for 45% and the second principal component (component 2) for 18% of the total variance in the dataset. Legend description: "0_N_0min", "0_N_10min", "0_N_20min" and "0_N_60min" e samples of cultures non treated with novobiocin and grown 0, 10, 20, 60 min respectively; "500_N_10min", "500_N_20min" and "500_N_60min" e samples of cultures treated with novobiocin at a concentration of 500 mg per mL, and incubated 10, 20, 60 min respectively; "100_N_60min" e samples of cultures treated with novobiocin at a concentration of 100 mg per mL, followed by incubation for 60 minutes.
HISAT2 version 2.1.0 [5] was used to build index of reference genome and align clean reads to genome with the following parameters: hisat2 -p -dta -x -U eS. SAM files of alignments created by HISAT2 were converted to BAM files using SAM-tools view [6]. Coverage estimates and reads mapping statistics are presented in Table 2. Mapped reads were summarized at the transcript level into a count matrix using the assembler of RNA-Seq alignments StringTie [7]. DESeq2 [8] was used to assess variance between sample groups and sample replicates using principal component analysis (PCA). PCA plot shown in the Fig. 1 demonstrates the overall quality of our sample collection, library preparation, and sequencing.