Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RIL-seq of EPEC E2348/69 hfq-flag, in virulence activating and non-activating conditions.

ABSTRACT: RIL-seq experiment of EPEC hfq-flag mutant, in activating- conditions:growth on DMEM at 37°C to mid exponential growth phase (e.g., OD600=0.3). In these conditions EPEC strongly expresses its major virulence components, T3SS and BFP, mimicking infection. Non-activating conditions: overnight growth of static culture on LB medium at 37°C where virulence factors are not expressed. RIL-seq experiments are designed to reveal the interactions of sRNA and their targets.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Escherichia coli

SUBMITTER: Sivan Pearl

PROVIDER: E-MTAB-8806 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

RNA-seq of EPEC E2348/69 in virulence activating and non-activating conditions. Comparison of wt and dhfq strains.

Project description:Compared the transcriptome of wild type EPEC with that of an isogenic Δhfq mutant. Comparing activating- conditions:growth on DMEM at 37°C to mid exponential growth phase (e.g., OD600=0.3). In these conditions EPEC strongly expresses its major virulence components, T3SS and BFP, mimicking infection. Non-activating conditions: overnight growth of static culture on LB medium at 37°C where virulence factors are not expressed.

2021-01-29 | E-MTAB-8804 | biostudies-arrayexpress

RIL-seq of EPEC E2348/69 hfq-flag, in virulence activating and non-activating conditions.

Project description:RIL-seq of EPEC E2348/69 hfq-flag, in virulence activating and non-activating conditions.

| PRJEB36843 | ENA

RNA-seq of EPEC E2348/69 in virulence activating and non-activating conditions. Comparison of wt and dhfq strains.

Project description:RNA-seq of EPEC E2348/69 in virulence activating and non-activating conditions. Comparison of wt and dhfq strains.

| PRJEB36845 | ENA

CLIP-seq of CsrA foci in Enteropathogenic E. coli

Project description:The RNA content of the CsrA foci. EPEC (E2348/69 (strain O127:H6)) expressing CsrA-FLAGx3-GFP or wild-type EPEC expressing untagged CsrA (negative control) were grown to OD 0.6 in DMEM and subjected to the foci-enrichment protocol, followed by RNA extraction and library preparation. Six libraries were prepared, containing three biological repeats of csrA-3 x flag-gfp and three repeats of wt.

2025-04-14 | E-MTAB-14951 | biostudies-arrayexpress

Comparative transcriptomics of the virulence regulons of enteropathogenic Escherichia coli from diverse phylogenomic lineages

Project description:Global transcriptional analysis of eleven EPEC strains, including the most frequently studied strains used in laboratory studies investigating EPEC virulence mechanisms.

2017-05-10 | GSE73885 | GEO

Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic Escherichia coli E2348/69

Project description:Global transcriptional analysis of EPEC/ETEC hybrid isolates.

2017-08-15 | GSE86633 | GEO

RIL-seq of Klebsiella pneumoniae SGH10 grown in LB or DMEM medium

Project description:RIL-seq experiment allows identification of pairs of interacting RNA molecules while bound to the Hfq protein. SGH10 bacteria were grown under DMEM (Dulbecco's Modified Eagle Medium) and LB (Lysogeny broth) conditions. RIL-seq was performed as previously described in Melamed et al. 2018 with adaptation of the computational analysis to the SGH10. It was applied to three biological replicates, for each growth condition. Libraries were sequenced by paired-end sequencing using Nextseq 500 Sequencer (Illumina). sequence fragments were mapped to SGH10 which contains a chromosome NZ_CP025080.1 and a plasmid NZ_CP025081.1. RIL-seq derived sequence fragments that mapped to the same locus or to two different loci were defined as single and chimeric fragments respectively. Chimeric fragments that appeared statistically significantly more than expected at random (S-chimeras) were considered as representing putative interacting RNAs.

2023-12-01 | E-MTAB-13342 | biostudies-arrayexpress

EPEC-E2348/69-V2

Project description:EPEC E2348/69 variety 2. Wild-type strain.

| PRJEB18716 | ENA

E. coli MG1655 pJV300 stationary phase

Project description:Over-night cultures grown from three single colonies were diluted 1:100 in LB and grown with shaking at 37 °C for 6h. Bacteria were pelleted by centrifugation and fast-freezed in the presence of 0.9 mg/ml lysosyme in TE. Frozen cells were thawed and re-frozen twice in 37 °C and liquid nitrogen, respectively. Total RNA was extracted using TRI-reagent and used for construction of RNA-seq libraries according to the RNAtag-seq method. Libraries were paired-end sequenced using Illumina NextSeq 500 platform.

2020-12-07 | E-MTAB-9834 | biostudies-arrayexpress

Highly-conserved regulatory activity of the ANR family in the virulence of diarrheagenic bacteria through interaction with Master and Global regulators

Project description:To gain mechanistic insights into this phenomenon, we characterized the regulatory role of Rnr in the virulence of prototype EPEC strain E2348-69 by genetic, biochemical, and human organoid-based approaches. Accordingly, RNA-seq analysis revealed more than 500 genes differentially regulated by Rnr, including the type-3 secretion system (T3SS).

2023-05-03 | GSE225626 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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