Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome of E. coli during Long-Term Stationary Phase

ABSTRACT: Transcriptome of E. coli during Long-Term Stationary Phase

PROVIDER: PRJNA639834 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12026234.fastq.gz	Fastqsanger.gz
	SRR12026235.fastq.gz	Fastqsanger.gz
	SRR12026236.fastq.gz	Fastqsanger.gz
	SRR12026237.fastq.gz	Fastqsanger.gz
	SRR12026238.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 18

Similar Datasets

Transcriptome of E. coli during Long-Term Stationary Phase

Project description:Microbes live in complex and constantly changing environments, but it is difficult to replicate this in the laboratory. Escherichia coli has been used as a model organism in experimental evolution studies for years; specifically, we and others have used it to study evolution in complex environments by incubating the cells into long-term stationary phase (LTSP) in rich media. In LTSP, cells experience a variety of stresses and changing conditions. While we have hypothesized that this experimental system is more similar to natural environments than some other lab conditions, we do not yet know how cells respond to this environment biochemically or physiologically. In this study, we begin to unravel the cells’ responses to this environment by characterizing the transcriptome of cells during LTSP. We found that cells in LTSP have a unique transcriptional program, and that several genes are uniquely upregulated or downregulated in this phase. Further, we identified two genes, cspB and cspI, which are most highly expressed in LTSP, even though these genes are primarily known to respond to cold-shock. By competing cells missing these genes with wild-type cells, we show that these genes are also important for survival during LTSP. These data can help identify gene products that may play a role in survival in this complex environment, and lead to identification of novel functions of proteins.

2020-07-24 | GSE152619 | GEO

Xbp1 binding during log phase and stationary phase.

Project description:Xbp1 binding during log phase and stationary phase.

| PRJNA868333 | ENA

Xbp1 binding during log phase and stationary phase.

Project description:To determine where Xbp1 binds to chromatin during log phase and stationary phase, we performed ChIP-seq.

2022-08-17 | GSE210933 | GEO

Acinetobacter oleivorans DR1 : WT stationary phase vs. aqsR mutant stationary phase

Project description:Transcriptional profiling of A. oleivorans DR1 cells comparing wild type stationary phase cells with aqsR mutant stationary phase cells.

2013-02-16 | GSE44347 | GEO

Tup1 binding during log phase, diauxic shift, and stationary phase.

Project description:To determine where Tup1 binds to chromatin during log phase, diauxic shift and stationary phase, we performed ChIP-seq.

2022-08-17 | GSE210932 | GEO

Tup1 binding during log phase, diauxic shift, and stationary phase.

Project description:Tup1 binding during log phase, diauxic shift, and stationary phase.

| PRJNA868336 | ENA

Transcriptome of a malO deletion mutant of Clostridium perfringens during stationary phase growth.

Project description:The MalNO is a putative two-component signal transduction system, previously known as the VirJI sytem. MalO is the putative cognate response regulator of the MalN sensor histidine kinase. Based on previous evidence that suggested the plc gene, encoding α-toxin, was upregulated during stationary phase in the malO mutant, microarrays were used to analyse the transcriptome of a malO mutant during stationary phase growth.

2014-12-22 | GSE28699 | GEO

Stationary phase stimulon and CspC regulon

Project description:The cold shock proteins belong to a family of RNA binding proteins presenting a highly conserved domain, called cold shock domain (CSD). They are involved in various cellular processes, including adaptation to low temperature, nutritional stress, cell growth and stationary phase. Here we investigate the role of CspC in C. crescentus stationary phase and the molecular mechanisms underlying gene regulation by this protein. A global transcriptional profiling experiment comparing cspC and the wild type strain both at exponential and stationary phases was carried out. The results showed that the absence of cspC affected the transcription of 20 genes at exponential phase and 65 genes at stationary phase. Genes encoding enzymes of the glyoxylate cycle were severely downregulated in the mutant at stationary phase. The stationary phase-induced RNA binding protein CspC has an important role in gene expression at this phase. It is required for the expression of the essential gene sciP, the ECF sigma factor sigU, as well as of the genes for the glyoxylate cycle enzymes and for oxidative stress response.

2015-08-24 | GSE61726 | GEO

E. coli MG1655 pJV300 stationary phase

Project description:E. coli MG1655 pJV300 stationary phase

| PRJEB41581 | ENA

Acinetobacter oleivorans DR1 : WT stationary phase vs. aqsR mutant stationary phase

Project description:Transcriptional profiling of A. oleivorans DR1 cells comparing wild type stationary phase cells with aqsR mutant stationary phase cells. To identify genes regulated QS system in A. oleivorans DR1, the cells were grown to stationary phase (OD600 >0=2.0).

2013-02-16 | E-GEOD-44347 | 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