Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Systematic Study on the Three-Dimensional Genome of Escherichia Coli and Its Thermal Adaptation Mechanism (RNA-Seq)

ABSTRACT: Total RNA was extracted and sequenced from Escherichia coli cultured to log phase and stable phase at 37 ° C and 45 ° C, respectively. The transcriptome data of Escherichia coli under four different growth conditions were obtained.

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

PROVIDER: GSE211824 | GEO | 2024/06/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Systematic Study on the Three-Dimensional Genome of Escherichia Coli and Its Thermal Adaptation Mechanism (3C-Seq)

Project description:Chromosome conformation capture and sequencing experiments were carried out at 37℃ and 45℃ for E. coli in logarithmic phase and stable phase, respectively. Three-dimensional DNA interaction data of E. coli under four different growth conditions and control group were obtained

2024-06-21 | GSE211823 | GEO

Differential gene expression of Escherichia coli ATCC 8739 in strawberry nectar after thermal and non-thermal treatments

Project description:Red fruits are valued for their vitamin C and polyphenol content, but traditional heat preservation methods used in juice and nectar production can significantly reduce these components. Therefore, alternative non-thermal methods are explored to inactivate foodborne pathogens like Escherichia coli while maintaining the nutritional value. However, knowledge about the effects of these technologies on bacterial cells is limited. This study analyzed differentially expressed genes of E. coli ATCC 8739 inoculated in strawberry nectar after exposure to three treatments with two sets of parameters each, namely thermal treatment, high-pressure processing (HPP), and moderate-intensity pulsed electric field (MIPEF). The highest inactivation efficiency was achieved with HPP at 400 MPa, 1 min, reducing microbial counts by 5.0±0.3 log cfu/mL, and thermal treatment at 60°C, 200 s, achieving a reduction of 4.4±0.2 log cfu/mL, while no inactivation was observed with MIPEF at 6 kV/cm. Transcriptomic analysis showed that thermal and HPP treatments caused similar molecular stress responses in E. coli. In both cases, the most overexpressed genes encoded outer membrane proteins, which may lead to the activation of the envelope stress response. Despite no microbial inactivation was revealed after MIPEF treatment, strong transcriptomic responses were observed, particularly in genes related to membrane integrity and metabolic activity. Numerous overexpressed genes associated with ABC transporters, outer membrane proteins, and lipoproteins were identified, which could increase the strain’s virulence. This study provides insights into the stress response mechanisms induced by conventional and novel treatments. Nevertheless, further research is needed to investigate the long-term effects on bacterial populations.

2024-12-03 | GSE283248 | GEO

Systematic Study on the Three-Dimensional Genome of Escherichia Coli and Its Thermal Adaptation Mechanism (RNA-Seq)

Project description:Systematic Study on the Three-Dimensional Genome of Escherichia Coli and Its Thermal Adaptation Mechanism (RNA-Seq)

| PRJNA872175 | ENA

Systematic Study on the Three-Dimensional Genome of Escherichia Coli and Its Thermal Adaptation Mechanism (3C-Seq)

Project description:Systematic Study on the Three-Dimensional Genome of Escherichia Coli and Its Thermal Adaptation Mechanism (3C-Seq)

| PRJNA872174 | ENA

High temperature adapted coli expression

Project description:Analysis of gene expression of mid log phase cultures of Escherichia coli Ancestor strain, and high temperature evolved lines 42-1, 42-2 and 42-3. Keywords: other

2003-07-14 | GSE533 | GEO

UV treated Escherichia coli reveals a high number of differentially expressed regions and many novel transcripts

Project description:The transcriptional changes in Escherichia coli upon induction of the SOS response are investigated by utilizing custom designed oligonucleotide microarrays. Keywords: Gene expression during the SOS response in Escherichia coli Escherichia coli K-12 MG1655 single colony in five parallells was grown to mid-log phase and exposed to UV to induce the SOS response. Total RNA was extracted from induced and uninduced cells and cDNA was prepared, fragmented and labelled prior to hybridizing to arrays. The arrays was designed to maximize the genomic coverage whilst simultaneous including only probes estimated to give an approximately uniform binding affinity. Regions coding for non-hypothetical proteins or RNAs where covered less densely than the intergenic parts.

2010-05-06 | E-GEOD-13829 | biostudies-arrayexpress

Psychological Evaluation According Colonic Colonization by Escherichia Coli of Patients After Colorectal Surgery

Project description:The purpose of this study is to determine whether the presence of pathogenic Escherichia coli in colon is associated with psychiatric disorders.

| 2230352 | ecrin-mdr-crc

Escherichia coli

Project description:Expression Data from Escherichia coli grown to mid-log growth phase.

| PRJNA126219 | ENA

Transcription profiling of two ancestral and evolved E. coli strains in three evolutionary conditions excess-nutrient adaptation, prolonged stationary phase adaptation and adaptation due to environmental shift

Project description:The mechanism of evolution in different conditions can be examined from various molecular aspects that constitute a cell, namely, transcript, protein or metabolite abundance. We have analyzed transcript and metabolite abundance changes in evolved and ancestor strains in three different evolutionary conditions, namely, excess-nutrient adaptation, prolonged stationary phase adaptation and adaptation due to environmental shift, in two different strains of Escherichia coli K-12 (MG1655 and DH10B).

2007-10-02 | E-MEXP-1166 | biostudies-arrayexpress

Enteropathogenic Escherichia Coli (EPEC): Does it Have a Role in Colorectal Tumourigenesis?

Project description:Despite the characterization of many aetiologic genetic changes. The specific causative factors in the development of sporadic colorectal cancer remain unclear. This study was performed to detect the possible role of Enteropathogenic Escherichia coli (EPEC) in developing colorectal carcinoma.

| 2184564 | ecrin-mdr-crc

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