Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptome comparison between emergent and historical emm4 group A Streptococcus strains from North America

ABSTRACT: Transcriptome comparison between emergent and historical emm4 group A Streptococcus strains from North America

PROVIDER: PRJNA674322 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR12972100_1.fastq.gz	Fastqsanger.gz
	SRR12972100_2.fastq.gz	Fastqsanger.gz
	SRR12972101_1.fastq.gz	Fastqsanger.gz
	SRR12972101_2.fastq.gz	Fastqsanger.gz
	SRR12972078_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 48

Similar Datasets

Transcriptome comparison between emergent and historical emm4 group A Streptococcus strains from North America

Project description:Clonal emergence is a major driver for changes in bacterial disease epidemiology. Recently, it has been proposed that episodic emergence of novel, hypervirulent clones of group A Streptococcus (GAS) results from horizontal gene transfer (HGT) and recombination events leading to increased expression of the cytotoxins Nga (NADase) and SLO (streptolysin O). We previously described a gene fusion event involving the gene encoding the GAS M protein (emm) and an adjacent M-like protein (enn) in the emm4 GAS population, a GAS emm type that lacks the hyaluronic acid capsule. Using whole genome sequencing of a temporally and geographically diverse set of 1,127 isolates, we discovered that the North American emm4 GAS population has undergone clonal replacement with emergent GAS strains completely replacing historical isolates by 2017. Emergent emm4 GAS strains were defined by a handful of small genetic variations, including the emm-enn gene fusion, and showed a marked in vitro growth defect compared to historical strains. In contrast to other previously described GAS clonal emergence events, emergent emm4 GAS lacked significant HGT events and showed no significant increase in transcript levels of nga/slo toxin gene via RNA sequencing and quantitative real-time PCR analysis relative to historic strains. Despite the in vitro growth differences, emergent emm4 GAS strains demonstrated hypervirulence in mouse and ex vivo growth in human blood compared to historical strains. Thus, these data detail the emergence and dissemination of a hypervirulent acapsular GAS clone defined by small genetic variation thereby defining a novel model for GAS strain replacement.

2021-05-05 | GSE160737 | GEO

A Metagenomics Analysis of Pandemic 2009 H1N1 Infection in Patients in North America

Project description:The Virochip microarray (version 4.0) was used to detect viruses in patients from North America with unexplained influenza-like illness at the onset of the 2009 H1N1 pandemic.

2010-11-01 | GSE24034 | GEO

A Metagenomics Analysis of Pandemic 2009 H1N1 Infection in Patients in North America

Project description:The Virochip microarray (version 4.0) was used to detect viruses in patients from North America with unexplained influenza-like illness at the onset of the 2009 H1N1 pandemic. We used metagenomics-based technologies (the Virochip microarray) and deep sequencing to analyze nasal swab samples from individuals with 2009 H1N1 infection. This Series includes the Virochip microarray data only.

2010-11-01 | E-GEOD-24034 | biostudies-arrayexpress

Candidatus Symbiopectobacterium sp. 'North America'

Project description:Candidatus Symbiopectobacterium sp. 'North America' (SyHa):How1 (Howardula aoronymphium) Genome sequencing

| PRJNA415854 | ENA

Paleo-Eskimo genetic legacy across North America

Project description:Paleo-Eskimo genetic legacy across North America: sequence data

| PRJEB30575 | ENA

Early Ileostomy Closure for Rectal Cancer Patients in North America

Project description:Our preliminary work demonstrates that there is buy-in from both patients and surgeons with regards to early ileostomy closure (EIC) for select rectal cancer patients undergoing restorative proctectomy (RP) and diverting loop ileostomy (DLI). The feedback from leaders in Europe further supports the need for a large scale randomized-controlled trial (RCT) on this subject in North America. Should the results of such a study be favourable, we believe it could support a change in practice that would be beneficial to patients and the health care system alike. Furthermore, our work will help identify which patients and practices are suitable for EIC. The goal of our project is to determine whether EIC in rectal cancer patients undergoing RP with a DLI is safe, feasible and beneficial in a North American population. Specifically, our primary objective is to compare the severity of complications between patients undergoing EIC versus traditional (late) closure. Our secondary objectives include assessing the difference in quality of life (QoL), early and late bowel function, and cost of care between these two groups.

| 2388367 | ecrin-mdr-crc

Genomic evidence for the Pleistocene and Recent population history of Native Americans

Project description:How and when the Americas were populated remains contentious. Using ancient and modern genome-wide data, we find that the ancestors of all present-day Native Americans, including Athabascans and Amerindians, entered the Americas as a single migration wave from Siberia no earlier than 23 thousand years ago (KYA), and after no more than 8,000-year isolation period in Beringia. Native Americans diversified into two basal genetic branches around 13 KYA, one in North and South America and the other restricted to North America. Subsequent gene flow resulted in some Native Americans sharing ancestry with present-day East Asians and Australo-Melanesians, the latter possibly through the ancestors of Aleutian Islanders. Putative relict populations in South America, including the historical Pericúes and Fuego-Patagonians, are not directly related to modern Australo-Melanesians.

2015-07-20 | GSE70987 | GEO

Historical faunal exchange between the Pontocaspian Basin and North America.

Project description:Ecrobia is a genus of small brackish-water mud snails with an amphi-Atlantic distribution. Interestingly, the species occurring in the northwestern Atlantic, Ecrobia truncata, is more closely related to the Pontocaspian taxa, Ecrobia grimmi and Ecrobia maritima, than to the species occurring in the northeastern Atlantic and Mediterranean Sea. At least three colonization scenarios may account for this peculiar biogeographical pattern: (1) a recent human-mediated dispersal, (2) a historical transatlantic interchange, and (3) a historical transpolar interchange. To test these three scenarios, we used five operational criteria-time of species divergence, first appearance in the fossil record, dispersal limitation as well as environmental filtering and biotic interactions along the potential migration routes. Specifically, we inferred a time-calibrated molecular phylogeny for Ecrobia and reconstructed a paleogeographical map of the Arctic Ocean at 2.5 million years ago (Mya). Based on the five operational criteria, scenarios 1 and 2 can likely be rejected. In contrast, all criteria support scenario 3 (historical transpolar interchange). It is therefore suggested that a bird-mediated and/or ocean current-mediated faunal interchange via the Arctic Ocean occurred during the Late Pliocene or Early Pleistocene. This dispersal was likely facilitated by reduced distances between the Eurasian and North American/Greenland landmasses, marine introgressions, and/or a stepping-stone system of brackish-water habitats in northern Siberia, as well as a lack of competition along the migration route. As for the direction of dispersal, the scientific data presented are not conclusive. However, there is clearly more support for the scenario of dispersal from the Pontocaspian Basin to North America than vice versa. This is the first study providing evidence for a natural faunal exchange between the Pontocaspian Basin and North America via the Arctic Ocean.

| S-EPMC6787871 | biostudies-literature

Historical Manihot glaziovii

Project description:Small RNA sequencing of historical cassave specimen

| PRJNA698751 | ENA

Expression profiling of the three clonotypic lineages of Toxoplasma gondii

Project description:Expression profiling of the three clonotypic lineages dominating T. gondii populations in North America and Europe provides a first comprehensive view of the parasite transcriptome.

2010-02-02 | GSE20145 | 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