Genomics

Dataset Information

346

DNA-seq of differentially induced promoter regions in E. coli UTI89 strain grown in either J82 bladder epithelial cells, urine, DMEM or LB medium.


ABSTRACT: The method DFI-seq was developed to enable identification of differentially expressed genes in uropathogenic E. coli strain UTI89 during growth in human urine and in bladder epithelial cells. By utilising this new method, the aim was to identify novel virulence genes in UTI89. DFI-seq is a combination of differential fluorescence induction (DFI) with next-generation sequencing. DFI-seq was compared to DFI by analysing gene expression of UPEC in human urine and thereby confirming that DFI-seq gives a better overview of gene expression. DFI-seq was hereafter used to look at gene expression in UTI89 while infecting bladder epithelial cells. We demonstrate the usefulness of DFI-seq for identification of genes required for optimal growth of UPEC in human urine, as well as potential virulence genes upregulated during infection of bladder epithelial cells. DFI-seq holds potential for the study of bacterial gene expression in live-animal infection systems.

INSTRUMENT(S): Illumina HiSeq 1500

ORGANISM(S): Escherichia coli UTI89  

SUBMITTER: Michelle Madelung   Thomas K Doktor  

PROVIDER: E-MTAB-5657 | ArrayExpress | 2017-05-01

SECONDARY ACCESSION(S): ERP022457

REPOSITORIES: ArrayExpress, ENA

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Publications

DFI-seq identification of environment-specific gene expression in uropathogenic Escherichia coli.

Madelung Michelle M   Kronborg Tina T   Doktor Thomas Koed TK   Struve Carsten C   Krogfelt Karen Angeliki KA   Møller-Jensen Jakob J  

BMC microbiology 20170424 1


During infection of the urinary tract, uropathogenic Escherichia coli (UPEC) are exposed to different environments, such as human urine and the intracellular environments of bladder epithelial cells. Each environment elicits a distinct bacterial environment-specific transcriptional response. We combined differential fluorescence induction (DFI) with next-generation sequencing, collectively termed DFI-seq, to identify differentially expressed genes in UPEC strain UTI89 during growth in human urin  ...[more]

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