Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Campylobacter

ABSTRACT: Asymptomatic carriage isolates and acute infection with Campylobacter from children in the Peruvian Amazon. Genome sequencing and assembly

PROVIDER: PRJNA350267 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8797150_1.fastq.gz	Fastqsanger.gz
	SRR8797150_2.fastq.gz	Fastqsanger.gz
	SRR8797160_1.fastq.gz	Fastqsanger.gz
	SRR8797160_2.fastq.gz	Fastqsanger.gz
	SRR8797170_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 124

Similar Datasets

Host transcriptional analysis to improve the diagnosis of group A streptococcal pharyngitis.

Project description:Current diagnostic methods used to evaluate patients with pharyngitis for the presence of group A Streptococcus (GAS) do not discriminate between acute infection and asymptomatic carriage, potentially resulting in overuse of antibiotics. Host response as measured by the transcriptomic profile of peripheral blood leukocytes could make this distinction, and could also distinguish between GAS and viral infection. We used RNA sequencing to generate transcriptomes from whole blood samples from 37 children, including 10 with acute GAS pharyngitis, 5 asymptomatic GAS carriers, 3 with adenoviral pharyngitis, 3 with pharyngitis of unknown etiology, and 16 asymptomatic children negative for GAS. Transcriptional profiles from each group were distinct . 1357 genes were upregulated in the children with symptomatic GAS compared to those with asymptomatic carriage. A panel of 13 genes distinguished between children with acute GAS and all others with 91% accuracy. The gene encoding CD177, a marker of neutrophil activation, was markedly overexpressed in children with acute GAS and has potential as a diagnostic biomarker. We conclude that measurement of host response is highly promising to improve the diagnosis of GAS pharyngitis and could help limit unnecessary antibiotic use.

2021-01-01 | GSE158163 | GEO

Genome-scanning of Amazonian Plasmodium falciparum shows subtelomeric instability and clindamycin resistant parasites

Project description:Here we fully characterize the genomes of 14 Plasmodium falciparum patient isolates taken recently from the Iquitos regions using genome-scanning, a microarray-based technique which delineates the majority of single-base changes, indels and copy number variants distinguishing the coding regions of two clones. We show that the parasite population in the Peruvian Amazon is highly structured with a limited number of genotypes and low recombination frequencies. Despite the essentially clonal nature of some isolates, we see high frequencies of mutations in subtelomeric highly variable genes and internal var genes indicating mutations arising during self-mating or mitotic replication. The data also reveal that 1 or 2 meioses separate different isolates showing that P. falciparum clones isolated from different individuals in defined geographical regions could be useful in linkage analyses or quantitative trait locus studies. Through pair-wise comparisons of different isolates we discovered point mutations in the apicoplast genome that are close to known mutations that confer clindamycin resistance in other species but which were hitherto unknown in malaria parasites. Subsequent drug sensitivity testing revealed over 100-fold increase clindamycin EC50 in strains harboring one of these mutations. This evidence of clindamycin resistant parasites in the Amazon suggests a shift should be made in health policy away from quinine+clindamycin therapy for malaria in pregnant women and infants and that the development of new lincosamide antibiotics for malaria should be reconsidered. Genome DNA from Peruvian Isolates vs. Reference 3D7

2010-08-04 | E-GEOD-22861 | biostudies-arrayexpress

Comparison of Campylobacter jejuni isolates implicated in Guillain-Barre syndrome and strains that cause enteritis

Project description:We asked whether Campylobacter jejuni isolated from patients with Guillain-Barri syndrome (GBS) differ from isolates isolated from patients with uncomplicated gastrointestinal infection using DNA microarray analysis. We found that specific GBS genes or regions were not identified, and microarray analysis confirmed significant genomic heterogeneity among the isolates. An all pairs experiment design type is where all labeled extracts are compared to every other labeled extract. Keywords: all_pairs

2006-01-04 | GSE3967 | GEO

Array-based comparative genomics of Campylobacter jejuni sheep abortion isolates (Part 2)

Project description:Campylobacter jejuni has become the predominant cause of sheep abortions in the U.S. However, little is know about the genetic diversity among the isolates collected from different time periods. In this study, the genetic diversity of sheep aborion isolates of C. jejuni was investigated by Array-based CGH

2014-02-11 | GSE54859 | GEO

Array-based comparative genomics of Campylobacter jejuni sheep abortion isolates (Part 1)

Project description:Campylobacter jejuni has become the predominant cause of sheep abortions in the U.S. However, little is know about the genetic diversity among the isolates collected from different time periods. In this study, the genetic diversity of sheep abortion isolates of C. jejuni was investigated by Array-based CGH

2014-02-11 | GSE54858 | GEO

Comparison of Campylobacter jejuni isolates implicated in Guillain-Barre syndrome and strains that cause enteritis

2006-01-03 | E-GEOD-3967 | biostudies-arrayexpress

Comparative genomic hybridization of Campylobacter jejuni isolated from patients with Guillain-Barri syndrome (GBS) vs isolates isolated from patients with uncomplicated gastrointestinal infection

2005-11-01 | E-SMDB-2661 | biostudies-arrayexpress

Genome-scanning of Amazonian Plasmodium falciparum shows subtelomeric instability and clindamycin resistant parasites

2010-08-05 | GSE22861 | GEO

Investigation of Campylobacter concisus gastric epithelial pathogenicity

Project description:The gastric epithelial gene responses to Campylobacter concisus infection were investigated by comparative differential expression analysis

2023-12-27 | GSE242316 | GEO

Exposure of microaerobic Campylobacter jejuni to diffusible molecules from chicken caecal contents

Project description:Campylobacter jejuni is the major cause of acute gastroenteritis in the developed world. It is usually acquired through contaminated poultry as C. jejuni causes a silent asymptomatic infection of the chicken. Pathogens face different sources of stress during its transit through the gut. In this study, we describe the ability of C. jejuni to survive nitrosative stress at very low oxygen levels that reflect those in hypoxic gut environments. Specifically, we here explore an innovative model of signal recognition during colonization. We use a diffusion capsule to feed small, diffusible molecules from chicken caecal matter into a microaerobic C. jejuni culture to study the transcriptomic changes mounted as response to chemical signals present in the chicken gut. We find that in early stages of exposure to the caecal contents (10 min) the dual component colonization regulator, dccR, plays an important yet not fully understood role. Although the caecal material contains cyanide derived from plant sources, we find no role for a truncated globin (encoded by ctb), which has previously been implicated in resistance to this haem ligand.

2012-08-07 | GSE39917 | 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