Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA sequencing of increasing virulence in Plasmodium chabaudi

ABSTRACT: We aim to identify the sequence of changes in gene expression associated with increasing virulence over successive blood passages. With the B cell-deficient mice we hope to establish how a reduction in immune pressure changes the response of the parasite. This work is in collaboration with Jean Langhorne at NIMR.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/

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Plasmodium chabaudi

SUBMITTER:

PROVIDER: E-ERAD-288 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Antigenic variation in recrudescent Plasmodium chabaudi infection

Project description:The aim of this study is to look at antigenic variation in recrudescent Plasmodium chabaudi infections and to identify the genes, if any, which allow the parasite to avoid the acquired immune response during recrudescence. This has been done in collaboration with Jean Langhorne at NIMR whose group performed the mouse work and extracted the RNA. 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/

2014-01-21 | E-ERAD-206 | biostudies-arrayexpress

RNA-seq of mosquito transmitted and blood transmitted Plasmodium chabaudi

Project description:This study is a collaboration with Phil Spence and Jean Langhorne at NIMR, Mill Hill where Phil is studying the differences in aetiology of rodent malaria when mice are infected by mosquito bite versus intraperitoneal injection of blood stage parasites. The aim is to determining transcriptomic differences using RNA-Seq between parasites transmitted by mosquito and those transmitted by injection. 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/Protocol: Mice were bled out at 6 days post-infection, and RNA was extracted from purified parasite populations using Trizol reagent and DNase treated. Poly A+ mRNA was purified from total RNA using oligo dT dyna bead selection and libraries were created using a modified RNA-seq protocol, where RNA was fragmented using Covaris AFA sonication instead of metal ions. The samples were sequenced on an Illumina HiSeq 2000.

2012-11-27 | E-ERAD-95 | biostudies-arrayexpress

Simultaneous host parasite RNA sequencing of rodent malaria infection time course

Project description:We have shown previously (Reid & Berriman, NAR, 2012) that by simultaneously examining host and parasite gene expression over the course of infection we can determine pairs of genes involved in host-parasite interaction. Here we are producing a high quality dataset which will specifically allow us to exploit this finding to identify genes involved in malaria host-parasite interaction. This has been done in collaboration with Jean Langhorne at NIMR. 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/

2013-05-13 | E-ERAD-136 | biostudies-arrayexpress

Simultaneous host parasite RNA sequencing of mosquito transmistted rodent malaria in two host backgrounds

Project description:The aim of this study is to explore the role of differences in host genetic background which will supplement our current analysis of a timecourse of P.chabaudi infection in C57BL/6 mice over the peak of parasitemia. We have also published a paper showing that infections using mosquito-transmitted parasites have a quite different effect on the host immune system (Spence et al, Nature, 2013) and using this study we can compare the effects in host and parasite of serially blood passaged parasites versus mosquito transmitted parasites. This is in collaboration with Jean Langhorne at NIMR.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/

2014-03-04 | E-ERAD-221 | biostudies-arrayexpress

XT mutant RNAseq

Project description:RNA was isolated from Xenopus tropicalis rax mutants and wild type siblings. We have identified by tilling a Xenopus tropicalis rax mutant in which the gene has a premature stop codon before the homeobox domain. The rax gene is essential for eye development and has been identified as a causative gene for human ocular malformations such as anophthalmia and microphthalmia. The phenotype of the X.tropicalis mutant replicates the human condition with complete loss or small eyes. By analysis of the full RNA complement of rax mutants compared to wild type siblings we hope to gain a better understanding of the role of rax during eye development and the genes that it regulates. This is part of an ongoing collaboration with Dr Robert Grainger, University of Virginia. 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 www.sanger.ac.uk/datasharing/

2011-01-19 | E-ERAD-0 | biostudies-arrayexpress

RNA sequencing of the intra erythrocytic lifecycle of Plasmodium chabaudi

Project description:The aim of this study is to characterise gene expression in the rodent malaria intra-erthrocytic development cycle. This will inform two further studies looking at host-parasite interactions in rodent malaria and in comparison to the same stage of human malaria will provide insight into variation in lifecycles between human and rodent malaria. 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/

2013-07-01 | E-ERAD-162 | biostudies-arrayexpress

RNA-Seq of Plasmodium chabaudi AS erythrocytic stages

Project description:Recent advances in high throughput sequencing methodologies allow the opportunity to probe in depth the transcriptomes of organisms including important human pathogens. In this project, we are using Illumina sequencing technology to analyze the transcriptome (RNA-Seq) of experimentally accessible stages of the mouse malaria parasite, P. chabaudi AS. The aim is to analyse cir gene expression during Plasmodium chabaudi infection and determine whether host genetic background can influence cir expression. 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/. Abstract: Transcriptome sequencing of blood stage P. chabaudi AS parasites grown under different host genetic backgrounds.

2011-11-03 | E-ERAD-25 | biostudies-arrayexpress

CLASH RNAseq of RNP bound RNAs

Project description:We are investigating the possible role of ribonucleoprotein-bound RNAs on the pathogenesis of AML. This study uses antibody-pulldown of specific ribonucleoproteins followed by RANSeq. We hope to describe this interaction in wild type cells befire studying the effects of specific mutations 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/

2014-03-25 | E-ERAD-226 | biostudies-arrayexpress

RNA sequencing of mosquito transmitted and blood transmitted Plasmodium chabaudi CB parasites and host spleens

Project description:We have published a paper showing that infections using mosquito-transmitted parasites have a quite different effect on the host immune system (Spence et al, Nature, 2013). Here we are repeating the experiment but using a more virulent strain of the parasite: P. chabaudi CB, to study further how mosquito transmission regulates parasite virulence. 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/

2014-08-27 | E-ERAD-289 | biostudies-arrayexpress

RNA Seq of the blood stage transcriptome of Plasmodium falciparum IT4 and HB3

Project description:New insights into the blood-stage transcriptome of Plasmodium falciparum using RNA-Seq was published in 2010 (Otto et al. Molecular Microbiology 2010, April;67 (1), pp. 12-24). Here in collaboration with Manuel Llinas (Princetown University) we are utilising advances in RNA-Seq to gain further understanding of Plasmodium falciparum blood-stage transcription. 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/

2013-03-05 | E-ERAD-86 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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