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Series GSE199248 Query DataSets for GSE199248
Status Public on Dec 31, 2022
Title Landscapes of collateral fitness effects of mutations in antibiotic resistance genes
Organism Escherichia coli
Experiment type Expression profiling by high throughput sequencing
Summary We performed RNA-seq experiments to compare the gene expression profiles of cells expressing single-codon substitutions in the antibiotic resistance genes NDM-1, CAT-I, or aadB in the absence of antibiotics. Mutations with deleterious fitness effects in the absense of antibiotics also caused significant changes in gene expression in a number of genes related to stress-response pathways including the regulator of colanic acid capsule synthesis (Rcs) response, the phage shock protein response (Psp), and the oxidative stress response. Fold differences in gene expression were mutation- and gene-dependent.
 
Overall design E. coli cells containing single-codon substitutions in either the NDM-1, CAT-I, or aadB antibiotic resistance genes were grown in monoculture growth assays. Controls consisted of cells with the wildtype allele that were not induced with IPTG as well as cells harboring a Δ antibiotic resistance gene deletion that were induced with IPTG. Growth was halted at about 330 minutes to ensure the cells were still in exponential growth phase based on OD measurements. Total RNA was extracted from pelleted cell cultures. mRNA was enriched and used to synthesize double-stranded cDNA. The double-stranded cDNA was end prepped and purified. Illumina adaptor sequences were ligated to the double stranded cDNA and PCR enriched before being purified and pooled for Illumina Tru-Seq (2 x 75 bp reads).
 
Contributor(s) Mehlhoff J, Ostermeier M
Citation(s) 36798991
Submission date Mar 23, 2022
Last update date Apr 03, 2023
Contact name Marc Ostermeier
E-mail(s) oster@jhu.edu
Phone 4105164146
Organization name Johns Hopkins University
Department Chemical & Department of Chemical & Biomolecular Engineering
Lab Ostermeier Lab
Street address 3400 N. Charles St.
City Baltimore
State/province MD
ZIP/Postal code 21218
Country USA
 
Platforms (1)
GPL21222 Illumina NextSeq 500 (Escherichia coli)
Samples (20)
GSM5968104 Uninduced WT CAT-I
GSM5968105 Induced WT CAT-I
GSM5968106 S27M CAT-I
Relations
BioProject PRJNA819053

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE199248_RNA-Seq_ProcessedData.xlsx 4.5 Mb (ftp)(http) XLSX
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Raw data are available in SRA
Processed data are available on Series record

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