Transcriptome RNA Sequencing Data Set of Differential Gene Expression in <named-content content-type='genus-species'>Escherichia coli</named-content> BW25113 Wild-Type and <italic toggle='yes'>slyA</italic> Mutant Strains

Escherichia coli laboratory strains remain instrumental for the development of tools and techniques in molecular microbiology. The transcriptional regulator SlyA, associated with host-derived oxidative stress, antibiotic resistance, and virulence, is prominent in Enterobacteriaceae. Here, we announce a transcriptome data set detailing the global gene expression in E. coli BW25113 and its slyA mutant. Laboratory strains of Escherichia coli K-12 have been instrumental in the development of molecular tools and techniques in microbiology. Ecological evolutionary developmental biology has revealed remarkable diversity among E. coli strains, especially in the post-genomic era (1). The E. coli K-12-derived strain BW25113 became the parent strain for the Keio collection, a major resource consisting of about 4,000 singlegene deletion mutants (2, 3). However, the complete genome sequence for strain BW25113 remained unavailable until 2014 (4). The transcriptional regulator SlyA, a member of the multiple antibiotic resistance regulator (MarR) transcription factor family, is often associated with bacterial responses to host-derived oxidative stress, antibiotic resistance, and virulence (5). Previous work has shown that SlyA directly activates the expression of two genes in E. coli K-12 (hlyE and fimB) by antagonizing H-NS repression, a countersilencing mechanism also reported for other members of Enterobacteriaceae (6–8). Microarray-based gene expression profiling of chemostat cultures of an E. coli K-12 MG1655 slyAmutant showed no significant differences in transcript abundance compared to wild-type cells, likely because of very low slyA expression in wild-type cells, whereas overproduction of SlyA resulted in the identification of additional SlyA targets (6). Here, we present a transcriptome RNA sequencing data set for E. coli BW25113 and its slyAmutant. E. coli BW25113 (wild type) and the slyA mutant JW5267-1 were obtained from the Yale University E. coli Genetic Resources Coli Genetic Stock Center (9). The wild-type strain is designated F2, D(araD-araB)567, DlacZ4787(::rrnB-3), l-, rph-1; D(rhaD-rhaB)568, hsdR514, while the slyA mutant is designated F2, D(araD-araB)567, DlacZ4787(::rrnB-3), l2, DslyA720::kan, rph-1, D(rhaD-rhaB)568, hsdR514. Duplicate biological replicates of each variant were grown to mid-log phase in Luria-Bertani (LB) broth at 37°C with orbital shaking at 200 rpm. Total RNA was prepared using the RNeasy minikit and RNase-free DNase kit (Qiagen). RNA sequencing was performed by Applied Biological Materials (Richmond, BC, Canada). The RNA integrity was verified using an Agilent 2100 Bioanalyzer and the RNA 6000 Pico kit (Agilent). rRNA depletion was carried out using the NEBNext rRNA depletion kit (New England Biolabs). Libraries were generated using the TruSeq stranded mRNA low-throughput (LT) configuration (Illumina). Clustering of libraries was performed using the Illumina Citation Ojo O, Scott D, Iwalokun B, Odetoyin B, Grove A. 2021. Transcriptome RNA sequencing data set of differential gene expression in Escherichia coli BW25113 wildtype and slyAmutant strains. Microbiol Resour Announc 10:e00294-21. https://doi.org/10 . 1128/MRA.00294-21. Editor Frank J. Stewart, Georgia Institute of Technology Copyright © 2021 Ojo et al. This is an openaccess article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to Olabisi Ojo, olabisi.ojo@asurams.edu. Received 21 March 2021 Accepted 16 April 2021 Published 13 May 2021 Volume 10 Issue 19 e00294-21 mra.asm. org 1 OMICS DATA SETS