Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: GEMS Typical EPEC Genome Sequencing

PROVIDER: PRJNA849823 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR19671034_1.fastq.gz	Fastqsanger.gz
	SRR19671034_2.fastq.gz	Fastqsanger.gz
	SRR19671035_1.fastq.gz	Fastqsanger.gz
	SRR19671035_2.fastq.gz	Fastqsanger.gz
	SRR19671036_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 130

Similar Datasets

Genomic Comparison of the O-antigen Biosynthesis Gene Clusters of E. coli O55 Strains Belonging to Three Lineages.

Project description:Typical enteropathogenic Escherichia coli (EPEC) O55:H7 is regarded as the closest relative of enterohemorrhagic E. coli (EHEC) O157:H7. Both serotypes usually express the γ1 intimin subclass and trigger actin polymerazation by the Tir-TccP pathway. However, atypical O55:H7 strains capable of triggering actin polymerization via the Tir-Nck pathway have recently been identified. In this study, we investigated the genotypic differences and phylogenetic relationships between typical and atypical O55:H7 strains. We show that the atypical O55:H7 strains, which express the θ intimin subclass and lack both tccP and tccP2, belong to an E. coli lineage distinct from the typical O55:H7 and from the EPEC O55:H6, which also uses the Tir-Nck actin polymerization pathway. We conducted genomic comparisons of the chromosomal regions covering the O-antigen gene cluster and its flanking regions between the three O55 lineages by restriction fragment length polymorphism analysis of PCR products and DNA sequencing analysis of about 65-kb chromosomal regions. This unexpectedly revealed that horizontal transfer of large fragments (≥ 40 kb) encoding the O55-antigen gene cluster and part of neighboring colanic acid gene cluster is involved in the emergence of the three O55 E. coli lineages. The data provide new insights into the mechanisms involved in the generation of a wide variety of O-serotypes in Gram-negative bacteria. Keywords: comparative genomic hybridization

2008-04-01 | GSE8889 | GEO

Genomic Comparison of the O-antigen Biosynthesis Gene Clusters of E. coli O55 Strains Belonging to Three Lineages.

Project description:Typical enteropathogenic Escherichia coli (EPEC) O55:H7 is regarded as the closest relative of enterohemorrhagic E. coli (EHEC) O157:H7. Both serotypes usually express the Î³1 intimin subclass and trigger actin polymerazation by the Tir-TccP pathway. However, atypical O55:H7 strains capable of triggering actin polymerization via the Tir-Nck pathway have recently been identified. In this study, we investigated the genotypic differences and phylogenetic relationships between typical and atypical O55:H7 strains. We show that the atypical O55:H7 strains, which express the Î¸ intimin subclass and lack both tccP and tccP2, belong to an E. coli lineage distinct from the typical O55:H7 and from the EPEC O55:H6, which also uses the Tir-Nck actin polymerization pathway. We conducted genomic comparisons of the chromosomal regions covering the O-antigen gene cluster and its flanking regions between the three O55 lineages by restriction fragment length polymorphism analysis of PCR products and DNA sequencing analysis of about 65-kb chromosomal regions. This unexpectedly revealed that horizontal transfer of large fragments (â¥ 40 kb) encoding the O55-antigen gene cluster and part of neighboring colanic acid gene cluster is involved in the emergence of the three O55 E. coli lineages. The data provide new insights into the mechanisms involved in the generation of a wide variety of O-serotypes in Gram-negative bacteria. Keywords: comparative genomic hybridization Total 8 test samples were analyzed. Genomic DNA from each test strain and a reference strain (O157 Sakai) were labeled with Cy3 and Cy5, respectively, and were cohybridized on a single array. Labeling and hybridization were performed twice independently.

2010-05-22 | E-GEOD-8889 | biostudies-arrayexpress

Transcriptional Response to Ciprofloxacin in Enteropathogenic Escherichia coli Deng

2015-12-15 | GSE75988 | GEO

Transcriptional Response to Ciprofloxacin in Enteropathogenic Escherichia coli Deng

Project description:We employed a genome-wide microarray approach to obtain a profile of the transcriptional events in ciprofloxacin-treated EPEC shedding light on how ciprofloxacin affects EPEC transcriptional events and growth, aside from resistance mechanisms, and how this bacterium tolerates antibiotic stress. Sample of each culture immediately after the addition of ciprofloxacin (t0), 45 min (t45), 90 min (t90), 135 min (t135), and 180 min (t180), ciprofloxacin induced gene expression in EPEC Deng strain were measure by microarray statistical analysis

2015-12-15 | E-GEOD-75988 | biostudies-arrayexpress

A multicenter translational biomarker phase II trial of regorafenib in patients with non-resectable pretreated colorectal cancer.

Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS). Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).

| 2533916 | ecrin-mdr-crc

Comparative transcriptomics of the virulence regulons of enteropathogenic Escherichia coli from diverse phylogenomic lineages

Project description:Global transcriptional analysis of eleven EPEC strains, including the most frequently studied strains used in laboratory studies investigating EPEC virulence mechanisms.

2017-05-10 | GSE73885 | GEO

Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic Escherichia coli 402290

Project description:Global transcriptional analysis of EPEC/ETEC hybrid isolates.

2017-08-15 | GSE86639 | GEO

Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic Escherichia coli 401140

Project description:Global transcriptional analysis of EPEC/ETEC hybrid isolates.

2017-08-15 | GSE86638 | GEO

Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic Escherichia coli 102712

Project description:Global transcriptional analysis of EPEC/ETEC hybrid isolates.

2017-08-15 | GSE86637 | GEO

Comparative genomics and transcriptomics of Escherichia coli isolates carrying virulence factors of both enteropathogenic and enterotoxigenic Escherichia coli 102651

Project description:Global transcriptional analysis of EPEC/ETEC hybrid isolates.