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

PROVIDER: PRJNA807530 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR18048866_1.fastq.gz	Fastqsanger.gz
	SRR18048867_1.fastq.gz	Fastqsanger.gz
	SRR18048868_1.fastq.gz	Fastqsanger.gz
	SRR18048869_1.fastq.gz	Fastqsanger.gz
	SRR18048870_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

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

Project description: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.

2022-06-24 | GSE196845 | GEO

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

Development of ONT-cappable-seq to unravel the transcriptional landscape of <i>Pseudomonas</i> phages.

Project description:RNA sequencing has become the method of choice to study the transcriptional landscape of phage-infected bacteria. However, short-read RNA sequencing approaches generally fail to capture the primary 5' and 3' boundaries of transcripts, confounding the discovery of key transcription initiation and termination events as well as operon architectures. Yet, the elucidation of these elements is crucial for the understanding of the strategy of transcription regulation during the infection process, which is currently lacking beyond a handful of model phages. 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 transcription of Pseudomonas aeruginosa phage LUZ7, obtaining a comprehensive genome-wide map of viral transcription start sites, terminators, and complex operon structures that fine-regulate gene expression. Our work provides new insights in the RNA biology of a non-model phage, unveiling distinct promoter architectures, putative small non-coding viral RNAs, and the prominent regulatory role of terminators during infection. The robust workflow presented here offers a framework to obtain a global, yet fine-grained view of phage transcription and paves the way for standardized, in-depth transcription studies for microbial viruses or bacteria in general.

| S-EPMC9163698 | biostudies-literature

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

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

| PRJNA967321 | ENA

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

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

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

| PRJNA890649 | ENA

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

Pseudomonas aeruginosa strain:US449

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

| PRJNA802725 | 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

Sourcing Phage-Encoded Terminators Using ONT-cappable-seq for SynBio Applications in <i>Pseudomonas</i>.

Project description:Efficient transcriptional terminators are essential for the performance of genetic circuitry in microbial SynBio hosts. In recent years, several libraries of characterized strong terminators have become available for model organisms such as Escherichia coli. Conversely, terminator libraries for nonmodel species remain scarce, and individual terminators are often ported over from model systems, leading to unpredictable performance in their new hosts. In this work, we mined the genomes of Pseudomonas infecting phages LUZ7 and LUZ100 for transcriptional terminators utilizing the full-length RNA sequencing technique "ONT-cappable-seq" and validated these terminators in three Gram-negative hosts using a terminator trap assay. Based on these results, we present nine terminators for E. coli, Pseudomonas putida, and Pseudomonas aeruginosa, which outperform current reference terminators. Among these, terminator LUZ7 T50 displays potent bidirectional activity. These data further support that bacteriophages, as evolutionary-adapted natural predators of the targeted bacteria, provide a valuable source of microbial SynBio parts.

| S-EPMC10204088 | biostudies-literature

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