Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ArcZ comparative RIL-seq

ABSTRACT: ArcZ comparative RIL-seq

PROVIDER: PRJEB33914 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR3473050_1.fastq.gz	Fastqsanger.gz
	ERR3473050_2.fastq.gz	Fastqsanger.gz
	ERR3473051_1.fastq.gz	Fastqsanger.gz
	ERR3473051_2.fastq.gz	Fastqsanger.gz
	ERR3473052_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

ArcZ comparative RIL-seq

Project description:E. coli ΔarcZ hfq-Flag strain was transformed with a WT arcZ, mut arcZC81G or a mut arcZC81T,T82G,G83A plasmids. Single colonies of the transformants were grown overnight in LB at 37 °C with shaking (200 r.p.m.). Cultures were diluted 100-fold in fresh LB re-grown with shaking at 37 °C to an optical density of OD600 = 1.0 and induced with IPTG (1mM, 20 min), RIL-seq experiments were preformed as described in Melamed et al 2018, each repeated three times.

2020-03-03 | E-MTAB-8224 | biostudies-arrayexpress

Hfq RIL-seq analysis

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

2022-11-15 | GSE198671 | GEO

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

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 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

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

PAO1 Hfq-V RIL-seq and RNA-seq

Project description:PAO1 Hfq-V RIL-seq and RNA-seq

| PRJNA892133 | ENA

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

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