Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Transcript error studies on Escherichia coli, Bacillus subtilis, Agrobacterium tumefaciens, and Mesoplasma florum

PROVIDER: PRJNA592142 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR10541839.fastq.gz	Fastqsanger.gz
	SRR10541840.fastq.gz	Fastqsanger.gz
	SRR10541841.fastq.gz	Fastqsanger.gz
	SRR10541842.fastq.gz	Fastqsanger.gz
	SRR10541843.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Transcriptome profiling of Mesoplasma florum strain L1 using RNA sequencing (RNA-Seq) and genome-wide 5'-rapid amplification of cDNA ends (5'-RACE)

Project description:Mesoplasma florum is a near-minimal bacterium belonging to the Mollicutes class particularly characterized by its small genome, fast growth rate, and lack of pathogenic potential. Here, we report the first genome-wide transcriptomic analysis of this microorganism using directional RNA sequencing (RNA-Seq) and 5'-rapid amplification of cDNA ends (5'-RACE). 5'-RACE sequencing reads were used to identify 605 putative transcription start sites (TSSs), of which more than 400 could be associated to a conserved promoter sequence. Along with terminator predictions, these TSSs allowed the reconstruction of M. florum transcription units, covering more than 90% of annotated genes. We evaluated the expression level of all M. florum protein coding genes using paired-end RNA-Seq reads according to the number of fragments per kilobase per million of mapped reads (FPKM). FPKM values were converted to absolute transcript abundances using biomass quantification data. These efforts aim at reaching a deep understanding of global cellular mechanisms in M. florum and will guide future genome engineering projects in this simple organism.

2020-11-02 | GSE152985 | GEO

Agrobacterium tumefaciens C58 whole-genome tiling microarray design and validation

Project description:This research focuses on the design, manufacturing and validation of a new Agrobacterium tumefaciens C58 whole-genome tiling microarray platform for novel RNA transcript discovery. A whole-genome tiling microarray allows both annotated genes as well as previously unknown RNA transcripts to be detected and quantified at once. The Agrobacterium tumefaciens C58 genome is re-acquired with next-generation sequencing and then used to design the tilinlg microarray with the thermodynamic analysis program Picky. Validations are performed by subjecting Agrobacterium tumefaciens C58 under various growth conditions and then using the tling microarrays to verify expected gene expression patterns.

2014-09-25 | GSE61737 | GEO

Mesoplasma florum proteome analysis by 2D LC-MS/MS

Project description:The near-minimal bacterium Mesoplasma florum constitutes an interesting model for synthetic genomics and systems biology studies due to its small genome, fast growth rate, and lack of pathogenic potential. However, some fundamental aspects of its biology remain largely unexplored. Here, we report a broad yet remarkably detailed characterization of M. florum by combining a wide variety of experimental approaches. More specifically, we investigated several physical and physiological aspects of this bacterium, and performed the first genome-wide analysis of its transcriptome and proteome using RNA sequencing techniques and two-dimensional liquid chromatography-tandem mass spectrometry. These analyses notably revealed the M. florum consensus promoter, a first experimental cartography of transcription units, as well as the transcription and expression levels of all annotated genes. We also converted gene transcription and expression levels into absolute molecular abundances using biomass quantification results, generating an unprecedented view of the M. florum cellular composition and functions. These characterization efforts will provide an experimental foundation for the development of a genome-scale metabolic model for M. florum and will guide future genome engineering endeavours in this simple organism.

2020-11-16 | PXD019922 | Pride

Mesoplasma florum W37

Project description:Mesoplasma florum W37 Genome sequencing

| PRJNA222289 | ENA

The biotroph Agrobacterium tumefaciens thrives in tumors by exploiting a wide spectrum of plant host metabolites

Project description:Purpose: The goals of this study is to compare the reponse of Agrobacterium tumefaciens C58 in the presence of GHB and GABA to delineated the key-genes associated to the response of these metabolites in A. tumefaciens C58.

2019-04-29 | GSE121889 | GEO

Arabidopsis thaliana Col-0 leaf transcriptome response to Agrobacterium tumefaciens C58

Project description:As sessile organisms, plants require dynamic pathways in order to recognize pathogens and coordinate plant defenses by signalling. Agrobacterium tumefaciens C58 is able to avoid triggering plant defenses prior to entering the cell, and therefore is only detected once infection has begun making Agrobacterium a plant pathogen to numerous plant species. Understanding plant responses to Agrobacterium will be useful in improving plant defenses and potentially may also improve plant transformation efficiency. Microarrays were utilized for detailing the global gene expression pattern in A. thaliana Col-0 leafs in response to A. tumefaciens C58 for the identification of differentially expressed genes.

2014-10-28 | GSE62749 | GEO

Arabidopsis thaliana Col-0 root transcriptome response to Agrobacterium tumefaciens C58

Project description:As sessile organisms, plants require dynamic pathways in order to recognize pathogens and coordinate plant defenses by signalling. Agrobacterium tumefaciens C58 is able to avoid triggering plant defenses prior to entering the cell, and therefore is only detected once infection has begun making Agrobacterium a plant pathogen to numerous plant species. Understanding plant responses to Agrobacterium will be useful in improving plant defenses and potentially may also improve plant transformation efficiency. Microarrays were utilized for detailing the global gene expression pattern in A. thaliana Col-0 roots in response to A. tumefaciens C58 for the identification of differentially expressed genes.

2014-10-28 | GSE62750 | GEO

Arabidopsis thaliana

Project description:Transcript error studies on Arabidopsis thaliana

| PRJNA791609 | ENA

Trancriptome analysis of Agrobacterium tumefaciens C58 cells in the presence of abundant opines

Project description:Purpose: The goals of this study is to compare the reponse of Agrobacterium tumefaciens C58 in the presence and absence of the two opines nopaline and agrocinopine (more precisely agrocinopine A) to delineated the key-genes associated to opines-response in A. tumefaciens C58.

2018-09-01 | GSE106257 | GEO

Mesoplasma florum

Project description:Mesoplasma florum Genome sequencing and assembly

| PRJNA412852 | ENA