Enterococcus ratti
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA89347 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Whole genome sequencing of Enterococcus ratti, an opportunistic pathogen
| PRJDB2554 | ENA
Project description:Enterococcus ratti ATCC 700914 Genome sequencing
| PRJNA88847 | ENA
Project description:The genus Strongyloides spp. include important human parasites. There is also a well studied rodent model, S. ratti. Uniquely among parasitic nematodes, the Strongyloides life-cycle includes both a parasitic female stage and a genetically identical free-living female stage. Differences between these two female forms must be epigenetic, presumably controlled by altered transcription and translation. This is a project to compare the proteome and transcriptome of the parasitic and free-living females of S. ratti. From this we will define the genes and gene products of the parasitic female stage. This approach exploits the currently advanced S. ratti genome sequencing project. This work will give an understanding of the molecular basis of nematode parasitism, and so define new potential drug targets. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2013-06-11 | E-ERAD-151 | biostudies-arrayexpress
Project description:Strongyloides ratti is a common gastro-intestinal parasite of the rat. The adult parasites are female only, about 2mm long and live in the mucosa of the small intestine. These parasites produce eggs that pass out of the host in its faeces. In the environment infective larval stages develop either directly or after a facultative sexual free-living adult generation. Infective larvae infect hosts by skin penetration.S. ratti is the laboratory analogue of the parasite of humans, S. stercoralis. S. stercoralis is a wide-spread parasite of humans, occurring principally in the tropics and sub-tropics: some 100-200 million people are infected worldwide. Infection of immunosuppressed individuals can result in disseminated strongyloidiasis, in which worms occur throughout the body. This can be fatal unless anti-Strongyloides therapy is given. Other species of Strongyloides parasitise a wide range of vertebrates. As part of the Strongyloides ratti genome project we are profiling the transcriptome of the parasite across its life cycle using RNA-Seq.. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2013-01-28 | E-ERAD-92 | biostudies-arrayexpress
Project description:In previous studies we have shown that the two adult females morphs of S. ratti have very different lifespans. This experiment was designed to try to identify differentially expressed genes in these two adult morphs that may account for these differing lifespans. The genes expressed by S. ratti parasitic females at day 6 p.i. were compared to the genes expressed by S. ratti free living females at 3 days 19 degrees C. This comparison was done using a microarray chip that is spotted with PCR fragments from the libraries that were generated from parasitic females extracted at day 6 and day 15 p.i., and a microarray chip that is spotted with PCR fragments from the libraries that were generated from free-living larval stages L1, L2 and infective L3s and from free-living males and females.
2008-05-24 | E-TABM-236 | biostudies-arrayexpress
Project description:Strongyloides ratti is a parasitic nematode of rats and a laboratory model for nematode infection more generally. The response of two lines of S. ratti were compared in contrasting immunological environments: (i) day 5 post infection (p.i.) in naive rats; (ii) day 12 p.i. in naive rats; day 5 p.i. in rats previously immunised with 10 iL3s; and day 12 p.i. in rats previously immunised with 10 iL3s. The gene expression response of parasitic females were assayed using cDNA microarrays. Large numbers of responding genes were found (but with modest fold changes) and clusters of co-expressed genes identified with differences observed between worms taken from naive and previously exposed hosts and from the two time points.
2009-09-03 | E-MAXD-53 | biostudies-arrayexpress
Project description:Strongyloides ratti isolate:ED321 Raw sequence reads
| PRJNA342789 | ENA
Project description:We wished to determine the changes in gene expression that occurred in S. ratti parasitic females as an infection progressed and thus as these stages are exposed to an anti-S. ratti immune response. To do this we compared gene expression in parasitic females recovered 6 days p.i. (i.e. no or very low immune response) with those recovered at 15 days p.i. (i.e. high immune response); for convenience, we refer to these as parasitic females subject to "low immune pressure" and "high immune pressure", respectively. These days were chosen because previous analyses of S. ratti parasitic females have shown significant differences in the size, appearance etc. of worms at these time points. The experimental design used, was to have at least three biological replicates for each sample (i.e. three independent preparations of the relevant worm samples and their RNA) and to have at least three technical replicates (i.e. independent, separate cDNA synthesis, amplification and hybridization etc.) for each biological replicate. For each hybridisation (below) a dye-swap was used i.e. each sample to be used in a hybridisation was labelled, separately, with each of the two dyes (below).<br> <br> 21,085 ESTs were sequenced from various S. ratti stage-specific libraries, of which 14,761 resulted in sequence data above a quality threshold that were then submitted to public databases. 11,551 clones were derived from the S. ratti parasitic libraries of which 7,385 produced sequence data (above a quality threshold); all of these 7,385 clones were arrayed together with a random sample of 1,619 of clones for which no sequence data were available. These 7,385 ESTs are highly redundant since they represent 2,963 contigs and 2,125 clusters, both including 1,220 singletons (i.e. clusters or contigs containing only one EST). Notwithstanding this redundancy, they were used in the microarray construction for two reasons: (i) this approach was less error-prone than attempting to select a unique clone set and (ii) this in-built redundancy provides many replicates of individual contigs and clusters, which can be exploited in quality-control analyses. In addition to these 9,004 S. ratti clones, the following controls were included: 281 EST clones from the mixed iL3/free-living adult library (representing 173 contigs and 167 clusters, 67 of which are singletons) to ensure that gene expression in the parasitic and free-living stages could be differentiated; 230 commercially available controls (Amersham Biosciences UK, Ltd.). 12 poly-A and 457 spotting buffer-only controls. Thus, in total 9,984 spots were arrayed.
2007-04-07 | E-MEXP-1010 | biostudies-arrayexpress