Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Differential RNA-Seq (dRNA-seq) of Escherichia coli O104:H4

ABSTRACT: We performed a high-throughput mapping of the 5’ end transcriptome of the pAA plasmid of the clinical Escherichia coli O104:H4 (E. coli O104:H4) isolate LB226692. We employed differential RNA-sequencing (dRNA-seq), a terminator exonuclease (TEX)-based RNA-seq approach allowing for the discrimination of primary and processed transcripts. This method has proven to be a powerful tool for the mapping of transcription start sites (TSS) and detection of non-coding RNAs (ncRNAs) in bacteria. We catalogued pAA-associated TSS and processing sites on a plasmid-wide scale and performed a detailed analysis of the primary transcriptome focusing on pAA virulence gene expression.

ORGANISM(S): Escherichia coli O104:H4

PROVIDER: GSE78041 | GEO | 2016/10/19

SECONDARY ACCESSION(S): PRJNA312402

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

RpoS acts as a global repressor of virulence gene expression in Escherichia coli O104:H4 and enteroaggregative E. coli

Project description:In 2011, in Germany, Escherichia coli O104:H4 caused the enterohemorrhagic E. coli (EHEC) outbreak with the highest incidence rate of hemolytic uremic syndrome. This pathogen carries an exceptionally potent combination of EHEC- and enteroaggregative E. coli (EAEC)-specific virulence factors. Here, we identified an E. coli O104:H4 isolate that carried a single nucleotide polymorphism (SNP) in the start codon (ATG>ATA) of rpoS, encoding the alternative sigma factor S. The rpoS ATG>ATA SNP was associated with enhanced EAEC-specific virulence gene expression. Deletion of rpoS in E. coli O104:H4 Dstx2 and typical EAEC resulted in a similar effect. Both rpoS ATG>ATA and DrpoS strains exhibited stronger virulence-related phenotypes in comparison to wild type. Using promoter-reporter gene fusions, we demonstrated that wild-type RpoS repressed aggR, encoding the main regulator of EAEC virulence. In summary, our work demonstrates that RpoS acts as a global repressor of E. coli O104:H4 virulence, primarily through an AggR-dependent mechanism.

2024-04-04 | GSE243699 | GEO

dRNA-seq of Shewanella oneidensis MR-1

Project description:We combined high-resolution tiling microarrays and 5'-end RNA sequencing to obtain a genome-wide map of transcription start sites (TSSs) for Shewanella oneidensis MR-1. To test the reliability of these TSSs, we compared our result to those from differential RNA sequencing (dRNA-seq), which discriminates primary and processed ends of transcripts. We found that our identified TSSs tend to have significantly more mapped reads in the TEX(+) sample than the TEX(-) sample. Overall, the dRNA-seq results support the validity of our predictions for TSS. S. oneidensis MR-1 was grown to mid-log phase in Luria-Bertani broth (LB) or defined lactate minimal medium, and total RNA was isolated and used for differential RNA-sequencing (dRNA-seq) by next-generation sequencing, which is used to verify genome-wide transcription start sites. For dRNA-seq, total RNA was partially treated with Terminator Exonuclease (TEX) to digest processed RNA and thereby enrich for primary transcript ends.

2014-06-12 | E-GEOD-58292 | biostudies-arrayexpress

dRNA-seq of Shewanella oneidensis MR-1

2014-06-12 | GSE58292 | GEO

Escherichia coli O104:H4

Project description:Differential RNA-Seq (dRNA-seq) of Escherichia coli O104:H4

| PRJNA312402 | ENA

RNA-seq of Escherichia coli K-12 MG1655 and Stx2 phage lysogens

Project description:Here, we investigated the impact of Stx2 phage carriage on Escherichia coli (E. coli) K-12 MG1655 host gene expression. Using quantitative RNA-seq analysis, we compared the transcriptome of naïve MG1655 and the lysogens carrying the Stx2 phage of the 2011 E. coli O104:H4 outbreak strain or of the E. coli O157:H7 strain PA8, which share high degree of sequence similarity.

2019-06-17 | GSE126710 | GEO

Differential RNA-Seq (dRNA-seq) data from Sphingopyxis granuli strain TFA grown in two different carbon sources and RNA-seq from Hfq-coIP experiment.

Project description:We performed differential RNA-sequencing (dRNA-seq) experiments in both minimal medium (MM) plus β-hydroxybutyrate (β-HB) and MM plus tetralin (THN) of Sphingopyxis granuli strain TFA. The objective was mapping the Transcription Start Site (TSS) of each gene in the genome in both conditions, detecting non-coding RNAs (ncRNAs) and comparing the gene expression profile in a preferential carbon source (β-HB) versus tetralin (an aromatic pollutant). The dRNA-seq technique consists of using a termination exonuclease (TEX) to allow the discrimination of primary and processed transcripts. Furthermore, to detect Hfq-bound RNAs we co-immunoprecipitated RNA from the wild type strain (negative control) and a TFA strain with an Hfq-3xFlag tagged version (MPO501 strain) using an anti-3xFlag antibody and performed RNA-sequencing from the precipitated RNA.

2018-08-14 | GSE111181 | GEO

Escherichia coli O104:H4

Project description:Escherichia coli O104:H4

| PRJEB49642 | ENA

Project description:E. coli O104:H4 strains

| PRJNA793757 | ENA

Escherichia coli O104:H4

Project description:Escherichia coli O104:H4 outbreak

| PRJNA68275 | ENA

Secreted Proteins of Escherichia coli Serotypes O157:H7 and O104:H4 Cultured in Minimal Medium

Project description:Escherichia coli is a diverse species of bacteria. Some isolates of E. coli can cause hemorrhagic uremic syndrome in humans through consumption of contaminated food. We hypothesize that secreted and surface-associated proteins in E. coli may contribute to bacterial persistence in food products and to pathogenicity in humans. Here we report the proteomic analyses of secretomes from two serotypes of E. coli, O157:H7 and O104:H4, that cause human foodborne illness. The secreted proteins were isolated from the liquid cultures and analyzed by liquid chromatography-tandem mass spectrometry. We report 57 secreted proteins for O157:H7 and 67 for O104:H4 with increased abundance in minimal medium. As signature proteins, O157:H7 expressed intimin and translocated intimin receptor. By contrast, O104:H4 expressed enteroaggregative fimbriae, serine protease autotransporters, Shiga toxin, and beta-lactamase. The E. coli O104:H4 released more cytosolic proteins into the culture media than the O157:H7 serotype, indicating that it might be a leaky strain. The differential abundance of two transpeptidases YbiS and YnhG, along with other lipoproteins in O157:H7 indicates that this serotype secretes several peptidol-lipoprotein components of biofilm. In addition, we observed differential abundance of several ABC transporters, proteases and lipoproteins, which give each strain a unique survival strategy and drug resistance. The identification of secreted proteins will enable us understand better how these bacteria persist in food products and cause human disease.

| MSV000079326 | MassIVE

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data