Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Hfq RIL-seq analysis

ABSTRACT: In this study we used RIL-seq (RNA interaction by ligation and sequencing) to identify Hfq-mediated RNA-RNA interactions in V. cholerae.

ORGANISM(S): Vibrio cholerae

PROVIDER: GSE198671 | GEO | 2022/11/15

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptome wide mapping of Hfq mediated RNA-RNA interactions in E. coli (RIL-seq)

Project description:Most E. coli sRNAs interact with their mRNA targets through simultaneous binding to the Hfq chaperon. In this experiment we cross-linked RNA to proteins in-vivo then did Hfq IP followed by ligation of bound RNAs and sequencing to identify sRNA-mRNA interactions. We termed the method RIL-seq for RNA Interactions by Ligation - sequencing.

2016-07-30 | E-MTAB-3910 | biostudies-arrayexpress

Hfq RIL-seq in Salmonella

Project description:We have used the RIL-seq technique to map the global RNA-RNA interactome on the sRNA chaperone Hfq in Salmonella enterica.

2021-12-07 | GSE163336 | GEO

PAO1 Hfq-V RIL-seq

Project description:A key challenge for understanding the role(s) played by short, non-coding RNAs (sRNAs) in bacteria is identifying the mRNA targets regulated by the sRNAs. Because the Hfq protein mediates the interactions between many sRNAs and the corresponding target mRNAs, one apporach to identify the mRNA targets of sRNAs is to capture sRNA:mRNA interactions occuring on Hfq by exposing cells to UV-irradiation, which forms cross-links between nucleic acids and proteins. We subjected cells of P. aeruginosa strain PAO1 and a derivative of PAO1 harboring a C-terminal VSV-G epitope on Hfq to UV-irradiation, immune-precipitated the Hfq-RNA complexes, ligated neighboring RNA molecules together with RNA Ligase, and then purififed the resulting RNAs. These RNAs were converted into cDNA libraries and sequenced using the Illumina NextSeq platform and then subjected to RIL-seq analysis pipeline (version 0.78) to identify chimeric RNA molecules. We also performed RNA-seq for PAO1 ∆phrS cells harboring an empty vector (pEV) or a vector expressing PhrS (pPhrS).

2023-05-03 | GSE216133 | GEO

Hfq RIL-seq analysis

Project description:Hfq RIL-seq analysis

| PRJNA816425 | ENA

Hfq RIL-seq in Salmonella

Project description:Hfq RIL-seq in Salmonella

| PRJNA685767 | ENA

PAO1 Hfq-V RIL-seq

Project description:PAO1 Hfq-V RIL-seq

| PRJNA892138 | ENA

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

Project description: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.

2021-01-29 | E-MTAB-8806 | biostudies-arrayexpress

Hfq LiRIP-seq in Salmonella

Project description:We have developed a novel approach named LiRIP-seq to profile the global RNA-RNA interactome in Salmonella enterica. By pulse expressing T4 RNA ligase from an inducible pBAD promoter, LiRIP-seq enables in vivo proximity ligation of Hfq-bound RNAs to their interaction partners. This is followed by enrichment of ligation products (RNA chimeras) using Hfq-coIP and subsequent RNA-seq analysis.

2023-06-16 | GSE234792 | GEO

Transcriptome wide mapping of Hfq mediated RNA-RNA interactions in E. coli (RIL-seq)

Project description:Transcriptome wide mapping of Hfq mediated RNA-RNA interactions in E. coli (RIL-seq)

| PRJEB10931 | ENA

RIL-seq analysis of MG1655 Escherichia coli experiencing long-term nitrogen starvation in Gutnick minimal media

Project description:RNA interaction by ligation and sequencing (RIL-seq) was carried out to compare the Hfq-RNA-RNA interactome of MG1655 E coli bacteria that grown in Gutnick minimal media. Wild-type and hfq::3xFLAG tagged K12 E.coli were grown in Gutnick minimal media with 3mM NH4Cl as the sole nitrogen source, and cell samples were taken during exponential growth (N+), ~20min following N-runout and induction of growth arrest (N-), 24hr following N-runout and induction of growth arrest (N-24) and 2hr following addition of NH4Cl to N-24 cells (N-24+2). All sampling was performed in triplicate for each strain and condition

2023-12-01 | E-MTAB-13403 | biostudies-arrayexpress

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