Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

TeposParaC

ABSTRACT: Salmonella enterica genomes from victims of a major 16th century epidemic in Mexico

PROVIDER: PRJEB23438 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR2204590_1.fastq.gz	Fastqsanger.gz
	ERR2204590_2.fastq.gz	Fastqsanger.gz
	ERR2204600_1.fastq.gz	Fastqsanger.gz
	ERR2204600_2.fastq.gz	Fastqsanger.gz
	ERR2204610_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 168

Similar Datasets

The role of a single non-coding nucleotide in the evolution of an epidemic African clade of Salmonella

Project description:Salmonella enterica serovar Typhimurium ST313 is a relatively newly emerged sequence type that is causing a devastating epidemic of bloodstream infections across sub-Saharan Africa. Analysis of hundreds of Salmonella genomes has revealed that ST313 is closely-related to the ST19 group of S. Typhimurium that cause gastroenteritis across the world. The core genomes of ST313 and ST19 vary by just 1000 single-nucleotide polymorphisms (SNPs). We hypothesised that the phenotypic differences that distinguish African Salmonella from ST19 are caused by certain SNPs that directly modulate the transcription of virulence genes. Here we identified 3,597 transcriptional start sites (TSS) of the ST313 strain D23580, and searched for a gene expression signature linked to pathogenesis of Salmonella. We identified a SNP in the promoter of the pgtE gene that caused high expression of the PgtE virulence factor in African S. Typhimurium, increased the degradation of the factor B component of human complement, contributed to serum resistance and modulated virulence in the chicken infection model. We propose that high levels of expression PgtE of by African S. Typhimurium ST313 promotes bacterial survival and bacterial dissemination during human infection. Our finding of a functional role for an extra-genic SNP shows that approaches used to deduce the evolution of virulence in bacterial pathogens should include a focus on non-coding regions of the genome.

2017-12-15 | GSE108104 | GEO

A chromatin immunoprecipitation database for prokarytic organisms [salmonella]

Project description:Bacterial transcription factors (TFs) regulate gene expression to adapt to changing environments; when combined, the TF’s regulatory actions comprise transcriptional regulatory networks (TRNs). The chromatin immunoprecipitation (ChIP) assay is the major contemporary method for mapping in vivo protein-DNA interactions in the genome. It enables the genome-wide study of transcription factor binding sites (TFBSs) and gene regulation. Although rapidly accumulating publicly-available ChIP data are a valuable resource for the study of gene regulation, there are no full datasets of key regulators in Salmonella enterica Typhimurium LT2. Here, we present the genome-wide binding for YdcI in the Salmonella enterica Typhimurium LT2.

2021-08-15 | GSE181791 | GEO

Salmonella enterica

Project description:Salmonella enterica genomes

| PRJNA766315 | ENA

Salmonella enterica subsp. enterica

Project description:Salmonella enterica subsp. enterica genomes

| PRJNA448475 | ENA

Comparative genomic hybridization of strains of Salmonella enterica serovar Enteritidis from Uruguay, other distant geographical regions and other serovars isolated in Uruguay

Project description:Microarray based CGH was conducted over a group of 29 strains of S. Enteritidis spanning different epidemiological periods in Uruguay, plus 6 other S. Enteritidis strains isolated from distant geographical regions. We also included 9 Salmonella enterica strains of other serovars isolated in Uruguay. A S. Enteritidis dispensable genome of 233 chromosomal genes and high extent of variation in virulence plasmid was found. Strains isolated before the epidemic show the highest genomic differences as compared with the PT4 reference strain. Comparison with the gene content of other serovars demonstrate extensive horizontal gene transfer between circulating strains beyond serovar definition. Our results show that the epidemic of S Enteritidis in Uruguay was produced by the introduction of strains closely related to PT4, and corroborate the extensive genetic homogeneity among S. Enteritidis isolates worldwide. Phage SE14 emerges as the only specific region for S. Enteritidis. Genetic differences detected in pre-epidemic strains, mainly associated with the absence of phage SE20, suggest that genetic features encoded in this phage may be related to particular epidemiological behavior.

2009-03-03 | E-TABM-603 | biostudies-arrayexpress

FabR ChIP-chip on Salmonella enterica subsp. enterica serovar Typhimurium SL1344

Project description:FabR ChIP-chip on Salmonella enterica subsp. enterica serovar Typhimurium SL1344 using anti-Myc antibody against strain with chromosomally 9Myc-tagged FabR (IP samples) and wildtype strain (mock IP samples)

2014-12-31 | GSE52877 | GEO

High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq1 (NonSPI2, InSPI2, InSPI2Mg, M9glucose)

Project description:Salmonella enterica is comprised of genetically distinct “serovars”, that together provide an intriguing model for exploring the genetic basis of pathogen evolution. While the genomes of numerous Salmonella isolates with broad variations in host range and human disease manifestations have been sequenced, the functional links between genetic and phenotypic differences among these serovars remain poorly understood. Here, we conduct high-throughput functional genomics on both generalist (Typhimurium) and human-restricted (Typhi & Paratyphi A) Salmonella at unprecedented scale in the study of this enteric pathogen. Using a comprehensive systems biology approach, we identify gene networks with serovar-specific fitness effects across 25 host-associated stresses encountered at key stages of human infection. By experimentally perturbing these networks, we characterize previously undescribed pseudogenes in human-adapted Salmonella. Overall, this work highlights specific vulnerabilities encoded within human-restricted Salmonella that are linked to the degradation of their genomes, shedding light into the evolution of this enteric pathogen.

2024-04-12 | GSE261214 | GEO

High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq9 (LB, gentamycin, cotrimoxazole, rifampicin, polymyxin B)

2024-04-12 | GSE262848 | GEO

High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq2 (Bile, iron restriction, osmotic pressure, heat)

2024-04-12 | GSE261749 | GEO

High-throughput Fitness Experiments Reveal Specific Vulnerabilities of Human-Adapted Salmonella During Stress and Infection- Barseq13 (Typhi and Paratyphi A infection of THP-1 human macrophages)

2024-04-12 | GSE262769 | GEO