Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

WGS of Salmonella isolates from coastal birds in Chile

ABSTRACT: Genomic study of Salmonella isolates from coastal birds in Chile

PROVIDER: PRJEB70652 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR12341384_1.fastq.gz	Fastqsanger.gz
	ERR12341384_2.fastq.gz	Fastqsanger.gz
	ERR12341385_1.fastq.gz	Fastqsanger.gz
	ERR12341385_2.fastq.gz	Fastqsanger.gz
	ERR12341386_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 16

Similar Datasets

Whole genome sequencing of Chlamydia isolates from birds

Project description:Illumina Miseq genome sequencing of Chlamydia isolates from birds

| PRJEB25740 | ENA

Comparative genomic hybridization of Vibrio cholerae from California coastal water compared to reference strain N16961

Project description:Environmental isolates of Vibrio cholerae from California coastal water compared to reference strain N16961.

2007-05-23 | E-SMDB-4063 | biostudies-arrayexpress

Comparison of gene expression profiles for heat-shocked and non-heat shocked stationary phase samples from heat tolerant isolates R1-0006 and R1-0007 and reference strain SL476

Project description:Salmonella Heidelberg is currently the 9th common serovar and has more than twice the average incidence of blood infections in Salmonella. A recent Salmonella Heidelberg outbreak in chicken infected 634 people during 2013-2014, with a hospitalization rate of 38% and an invasive illness rate of 15%. While the company’s history suggested longstanding sanitation issues, the strains’ characteristics which may have contributed to the outbreak are unknown. We hypothesized that the outbreak strains of S. Heidelberg might possess enhanced stress tolerance or virulence capabilities. Consequently, we obtained nine food isolates collected during the outbreak investigation and several reference isolates and tested their tolerance to processing stresses, their ability to form biofilms, and their invasiveness in vitro. We further performed RNA-sequencing on three isolates with varying heat tolerance to determine the mechanism behind our isolates’ enhanced heat tolerance. Ultimately, we determined that (i) many Salmonella Heidelberg isolates associated with a foodborne outbreak have enhanced heat resistance (ii) Salmonella Heidelberg outbreak isolates have enhanced biofilm-forming ability under stressful conditions, compared to the reference strain (iii) exposure to heat stress may also increase Salmonella Heidelberg isolates’ antibiotic resistance and virulence capabilities and (iv) Salmonella Heidelberg outbreak-associated isolates are primed to better survive stress and cause illness. This data helps explain the severity and scope of the outbreak these isolates are associated with and can be used to inform regulatory decisions on Salmonella in poultry and to develop assays to screen isolates for stress tolerance and likelihood of causing severe illness.

2018-09-01 | GSE103418 | GEO

Transcription profiling of Salmonella enterica serovar Typhimurium definitive phage type 104 (DT104) isolates

Project description:Salmonella enterica serovar Typhimurium (S. Typhimurium) definitive phage type 104 (DT104) has caused significant morbidity and mortality in humans and animals for almost three decades. We have completed the full DNA sequence of one DT104 strain, NCTC13348 and show that the main differences between the genome of this isolate and the previously sequenced S. Typhimurium LT2 lie in integrated prophage elements and the Salmonella Genomic Island 1 encoding antibiotic resistance genes. Thirteen isolates of S. Typhimurium DT104 with different pulsed field gel electrophoresis (PFGE) profiles were analyzed by multi locus sequence typing (MLST), plasmid profiling, hybridization to a Pan-Salmonella DNA microarray and prophage-based multiplex PCR. All the isolates belonged to a single MLST type ST19. Microarray data demonstrated that the 13 DT104 isolates were remarkably conserved in gene content. The PFGE band-size differences in these isolates could be explained to a great extent by changes in prophage and plasmid content. Thus, here the nature of variation in different S. Typhimurium DT104 isolates is further defined at the genome level illustrating how this phage type is evolving over time.

2008-09-05 | E-MTAB-20 | biostudies-arrayexpress

Passeriformes (song birds)

Project description:Birds Island Genomic

| PRJNA661201 | ENA

Birds of Borneo

Project description:Birds of Borneo

| PRJNA492327 | ENA

Monophasic Salmonella isolates

Project description:Monophasic Salmonella isolates

| PRJEB2132 | ENA

Paleoproteomics of birds - proteome data analysis

Project description:The project aims at taxonomy of extinct and extant birds using proteomics.

2019-05-20 | PXD009204 | Pride

Birds

Project description:Metagenomic of poultry and wild birds captured in Brazil

| PRJNA486322 | ENA

Open Ocean and Coastal Strains of Marine Synechococcus display distinctly different Global Responses to DNA Damaging Agents

Project description:We have looked at the transcriptional response of well characterised Synechococcus open ocean (WH8102) and coastal (CC9311) isolates to two DNA damaging agents, mitomycin C and ethidium bromide, using whole genome expression microarrays. The coastal strain, which was able to grow on higher concentrations of both chemicals, showed differential regulation of a larger proportion of its genome following ‘toxic shock’ treatment with each agent. Many of the orthologous genes in these strains, including those encoding sensor kinases, showed different transcriptional responses, with the CC9311 genes more likely to show significant changes for each tested treatment. While the overall response of each strain was considerably different, there were distinct transcriptional responses common to both strains observed for each DNA damaging agent, linked to the mode of action of each chemical. In both CC9311 and WH8102 there was evidence of SOS response induction under mitomycin C treatment, with genes encoding recA, the lexA repressor and umuC significantly upregulated in this experiment but not under ethidium bromide treatment. Conversely, ethidium bromide treatment tended to result in upregulation of the DNA-directed RNA polymerase genes, not observed following mitomycin C treatment. Interestingly, a large number of genes residing on putative genomic island regions of each genome also showed significant upregulation under one or both chemical treatments.

2013-08-01 | GSE39818 | 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