Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages

ABSTRACT: We developed ONT-cappable-seq, a specialized long-read RNA sequencing technique that allows end-to-end sequencing of primary prokaryotic transcripts using the Nanopore sequencing platform. We applied ONT-cappable-seq to study the transcriptional landscape of Pseudomonas aeruginosa phage LUZ7, leading to a comprehensive genome-wide map of viral transcription start sites, terminators and complex operon structures that fine-regulate gene expression. At the same time, it provides new insights in the RNA biology of LUZ7 and paves the way for more in depth transcription studies that can help unveil the complex layers of phage-host interactions.

ORGANISM(S): Pseudomonas aeruginosa

PROVIDER: GSE196845 | GEO | 2022/06/24

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Refining the transcriptional maps of Pseudomonas aeruginosa phages using ONT-cappable-seq

Project description:The global transcriptional profiles of Pseudomonas aeruginosa phages LUZ19, LUZ24, YuA, PAK_P3, 14-1 and phiKZ was obtained using the long read RNA sequencing technique ONT-cappable-seq. Using this approach we obtained a comprehensive genome-wide map of viral transcription start sites, terminators and transcription units.

2024-03-13 | GSE231702 | GEO

ONT-cappable-seq for P23-45 bacteriophage 5 min post-infection

Project description:We performed the long-read RNA sequencing technique ONT-cappable-seq on RNA samples of T. thermophilus infected with phage P23-45 5 minutes post-infection. Using this approach, we obtained the primary transcriptome at the early infection stage and sequenced it in full-length. Based on this data, we were able to identify viral transcription start sites and termination sites and uncover distinct promoter motifs.

2023-12-12 | GSE215811 | GEO

Transcriptomics-driven characterization of novel T7-like temperate Pseudomonas phage LUZ100

Project description:The global transcriptional profile of novel T7-like Pseudomonas aeruginosa phage LUZ100 was obtained using the long read RNA sequencing technique ONT-cappable-seq. Using this approach we obtained a comprehensive genome-wide map of viral transcription start sites, terminators and transcription units and gained new insights in the molecular mechanisms of transcriptional regulation of T7-like temperate phages.

2023-02-08 | GSE211961 | GEO

Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages

Project description:Development of ONT-cappable-seq to unravel the transcriptional landscape of Pseudomonas phages

| PRJNA807530 | ENA

Assessing the transcriptional landscape of Pseudomonas chlororaphis phage 201f2-1: uncovering the small regulatory details of a giant phage

Project description:The global transcriptional profile of Pseudomonas chlororaphis infecting phage 201f2-1 was obtained using the long-read RNA sequencing technique ONT-cappable-seq. this resulted in a comprehensive genome-wide map of viral transcription start and termination sites. In addition, we were able to identify different transcription units and gained new insights in the molecular mechanisms of of transcriptional regulation of members of the Phikzvirus.

2024-10-17 | GSE245572 | GEO

Cappable-seq data for discovering condition-specific primary transcriptome in Campylobacter jejuni

Project description:The transcription start sites of the Campylobacter jejuni genome was identified by Cappable-seq, which captures primary transcripts by capping the 5´ triphosphorylated end

2022-05-27 | E-MTAB-11308 | biostudies-arrayexpress

Cappable RNA Sequencing of Streptomyces formicae to annotate transcription start sites under formicamycin producing conditions

Project description:Total RNA was extracted from Streptomyces formicae grown on SFM (soy flour, mannitol agar) on day 2, 3 and 4 and subjected to cappable RNA sequencing by Vertis Biotechnologie for annotation of TSSs across the genome.

2019-05-18 | E-MTAB-7975 | biostudies-arrayexpress

Enrichment of Wolbachia Endosymbiont Transcripts from Host Nematode RNA by Cappable-seq

Project description:We report the application of Cappable-seq to selectively enrich prokaryotic endosymbiont transcripts from mixed host-symbiont total RNA.

2017-01-05 | GSE93139 | GEO

SMRT-Cappable-seq reveals complex operon variants in bacteria

Project description:We develop a method SMRT-Cappable-seq that combines the isolation of unfragmented bacterial primary transcripts with the longread sequencing using PacBio. This method allows the identification and phasing of the transcrription start sites and the termination sites, thereby revealing the operon structure and the regulation of gene experession in bacteria. Applied to E.coli, our method results in an unprecedented definition of the transcriptome with 34% of the known operons from RegulonDB database being extended by at least one gene, and identifies a total of 2300 operons from which around 900 are novel.

2018-07-22 | GSE117273 | GEO

Cappable-seq analysis of Myxococcus xanthus at various developmental time points

Project description:Myxococcus xanthus is a model organism for studying social behaviors and cell differentiation in bacteria. Upon nutrient depletion, M. xanthus cells initiate a developmental program that culminates in formation of spore-filled fruiting bodies and peripheral rods outside of fruiting bodies. Completion of this developmental program depends on fine-tuned spatial and temporal regulation of gene expression, intercellular communication, signaling by nucleotide-based second messengers, and motility. In order to understand regulation of gene expression during growth and development, transcription start sites were identified using Cappable-seq. To this end, we extracted total RNA from vegetative cells (referred as 0 h of development) and from cells developed for 6, 12, 18 and 24 h under submerged conditions in two replicates.

2021-10-20 | E-MTAB-11042 | 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