Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Sequencing of 10 aEPEC strain genomes

PROVIDER: PRJEB27596 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR2681680_1.fastq.gz	Fastqsanger.gz
	ERR2681680_2.fastq.gz	Fastqsanger.gz
	ERR2681681_1.fastq.gz	Fastqsanger.gz
	ERR2681681_2.fastq.gz	Fastqsanger.gz
	ERR2681682_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 20

Similar Datasets

Transcriptomic profiles of host epithelial cells in response to actin rearrangement induced by atypical enteropathogenic Escherichia coli

Project description:Atypical enteropathogenic Escherichia coli (aEPEC) is amongst the leading causes of diarrheal disease worldwide. The colonization of the gut mucosa by aEPEC results in actin pedestal formation at the site of bacterial attachment. This cytoskeletal rearrangement is triggered by the interaction between the bacterial adhesin intimin and its receptor Tir, which is translocated through the type three secretion system, to the host cell. While some aEPEC require tyrosine phosphorylation of Tir and recruitment of the host Nck to trigger actin polymerization, certain aEPEC strains, whose Tir is not phosphorylated, rely on the effector EspFu for efficient actin remodeling. To understand how the host responds to these different actin polymerization signaling pathways, we analyzed gene expression changes in epithelial cells infected with pedestal-forming aEPEC strains using high-throughput RNA sequencing (RNA-seq).

2020-04-01 | GSE141446 | GEO

Escherichia coli

Project description:Genomes of aEPEC strains isolated in Brazil

| PRJNA490882 | ENA

Project description:10+ Genomes

| PRJNA544491 | ENA

Project description:3991-1 atypical enteropathogenic Escherichia coli (aEPEC) strain

| PRJEB30478 | ENA

Comprehensive Long Span Paired-End-Tag Mapping Reveals Characteristic Patterns of Structural Variations in Epithelial Cancer Genomes

Project description:Somatic genome rearrangements are thought to play important roles in cancer development. We optimized a long span paired-end-tag (PET) sequencing approach using 10 Kb genomic DNA inserts to study human genome structural variations (SVs). The use of 10 Kb insert size allows the identification of breakpoints within repetitive or homology containing regions of a few Kb in size and results in a higher physical coverage compared to small insert libraries with the same sequencing effort. We have applied this approach to comprehensively characterize the SVs of 15 cancer and 2 non-cancer genomes and used a filtering approach to strongly enrich for somatic SVs in the cancer genomes. Our analyses revealed that most inversions, deletions, and insertions are germline SVs, whereas tandem duplications, unpaired inversions, inter-chromosomal translocations, and complex rearrangements are overrepresented among somatic rearrangements in cancer genomes. We demonstrate that the quantitative and connective nature of DNA-PET data is precise in delineating the genealogy of complex rearrangement events, we observe signatures which are compatible with breakage-fusion-bridge cycles, and discover that large duplications are among the initial rearrangements that trigger genome instability for extensive amplification in epithelial cancers. Structural variations of 15 human cancer samples and 2 human normal samples were identified by long span paired-end sequencing

2011-04-06 | E-GEOD-26954 | biostudies-arrayexpress

Atypical Enteropathogenic Escherichia coli Virulence Regulation by QseC Quorum Sensing Adrenergic Sensor

Project description:Atypical EPEC (aEPEC) strains are part of group of pathogens capable of forming the Attaching and Effacing (A/E) lesion. This lesion is characterized by intimate adherence of bacteria to enterocytes, and microvilli destruction. The genes responsible to cause that lesion are located in a pathogenicity island called Locus of Enterocyte Effacement (LEE). Transcription of LEE genes is subjected to various levels of regulation, including quorum sensing through autoinducer 3 (AI-3) system. AI-3 is an aromatic compound with similar characteristics to the epinephrine and norepinephrine hormones. This similarity allows bacteria to use these hormones and AI-3 to perform cell – to – cell signaling processes and bacteria - host communication processes in order to modulate its virulence. AI-3, epinephrine and norepinephrine are detected by a sensor kinase named quorum sensing E.coli regulator (QseC). In order to investigate the role of QseC and epinephrine in atypical EPEC O55:H7 virulence, we constructed a QseC mutant of this strain and performed transcription and phenotypic analyses in the presence or absence of epinephrine. We have reported here, for the first time, the quorum sensing QseC regulation of virulence genes in atypical EPEC. Our results shown that QseC is a global regulator of gene expression in aEPEC and positively regulates flagellar genes, LEE and non-LEE encoded factors. We also have shown that the presence of epinephrine could be sensed by other receptor that acts as negative regulator of LEE4 and LEE5 genes.

2013-01-08 | GSE43325 | GEO

Escherichia coli

Project description:Hybrid atypical Enteropathogenic Escherichia coli: aEPEC/ExPEC and aEPEC/UPEC isolated from diarrhea

| PRJNA871776 | ENA

Mycobacterium tuberculosis variant bovis

Project description:Mycobacterium tuberculosis biovar. bovis strain Ravenel and strain 10-7428 genomes

| PRJNA713797 | ENA

Proteomic sequencing of mycelium collected after 4 and 10 days of culture of the WT strain and 10 days of culture of the Chatg8Δ mutant following knockout of the ChATG8 gene in Colletotrichum higginsianum IMI349063

Project description:We knocked out the ChATG8 gene of Colletotrichum higginsianum IMI349063 using Agrobacterium-mediated transformation technology and obtained the Chatg8Δ mutant, and subsequently collected mycelium from the WT strain after 4 days of incubation, the WT strain after 10 days of incubation, and the Chatg8Δ mutant after 10 days of incubation, respectively, for proteome sequencing.

2023-07-26 | PXD044122 |

Comparative Genome Hybridization of Porphyromonas gingivalis strains

Project description:CGH was used to compare the genomes of a non-invading P. gingivalis strain to the database W83 strain (invader). For hybridization and scanning, TIGR microarrays and protocols were used. The results were independently processed using two different software packages.

2011-07-28 | GSE18169 | GEO

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