EGAS00001001260-sc-2019-08-28T10:45:05Z - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001005298 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:This project aims to evaluate the transcriptional response to disease measured in whole blood of participants who developed enteric fever after challenge and, importantly, those who were challenged but stayed well throughout the challenge period. This data will provide unique coverage of the transcriptome and will yield invaluable insight after integration with a wealth of clinical data collected during this trial.
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/
| EGAS00001001260 | EGA
Project description:This studies describes the transcriptional response in whole blood derived from healthy adult volunteers experimentally infected with S. Paratyphi A. Samples were collected at pre-challenge baseline (Group: CTRL), at day 7 after challenge in those participants who stayed well over 14 days following challenge (Group: suspected Enteric Fever - sEF). Participants who developed signs of enteric fever were sampled at the time of inititiation of antibiotics (Group: EF).In this group diagnosis was confirmed by blood culture positive for S. Paratyphi (SPT). Antibiotic therapy commenced at time of diagnosis or at day 14 after challenge in those who did not develop symptoms. The clinical results of this study have been published in: Dobinson et al. Evaluation of the Clinical and Microbiological Response to Salmonella Paratyphi A Infection in the First Paratyphoid Human Challenge Model. Clin Infect Dis. 2017 Apr 15;64(8):1066-1073.
2019-09-02 | GSE114033 | GEO
Project description:In this study participants were experimentally challenged with an infective dose of S. Typhi (1-5x10^3-4 cfu) and followed over at least 14 days. Every study participant was treated with antibiotics (ciprofloxacin, 500 mg twice daily, 14 days) on day 14 after challenge unless diagnosed with typhoid fever at which time treatment commenced immediately (ciprofloxacin, 500 mg twice daily, 14 days). For details about the study design please refer to Waddington et al. CID 2014 May;58(9):1230-40. Criteria for typhoid diagnosis were either microbiological (≥1 positive blood culture collected after day 5) and/or clinical (fever ≥38°C sustained for ≥12hrs). 3mL of venous blood was obtained at pre-challenge baselines, 24hrs prior typhoid diagnosis, day of diagnosis, 24hrs post-diagnosis and day 14 after challenge in those diagnosed with acute typhoid fever. In those who did not develop typhoid despite oral challenge samples were obtained at pre-challenge, day 7 and day 14 after challenge. The samples are labelled with one of the following accronyms: V1: Day 0, i.e. pre-challenge control. D7: day 7 after challenge. TD-24: 24hrs prior to typhoid diagnosis. TD: day of typhoid diagnosis. TD+24: 24hrs after typhoid diagnosis. D14: day 14 after challenge.
2015-10-01 | E-MTAB-3423 | biostudies-arrayexpress
Project description:In this study, whole blood samples were used to determine the gene expression of febrile culture confirmed enteric fever cases (ST = S. Typhi; SPT = S. Paratyphi), febrile culture negative individuals presenting to hospital in Kathamandu (sEF = suspected enteric fever), and healthy community controls (CTRL).
2019-09-02 | GSE113866 | GEO
Project description:Background: Salmonella Typhi and Salmonella Paratyphi A are the agents of enteric (typhoid) fever; both can establish chronic carriage in the gallbladder. Chronic Salmonella carriers are typically asymptomatic, intermittently shedding bacteria in the feces, and contributing to disease transmission. Detecting chronic carriers is of public health relevance in areas where enteric fever is endemic, but there are no routinely used methods for prospectively identifying those carrying Salmonella in their gallbladder. Methodology/Principal Findings: Here we aimed to identify biomarkers of Salmonella carriage using metabolite profiling. We performed metabolite profiling on plasma from Nepali patients undergoing cholecystectomy with confirmed S. Typhi or S. Paratyphi A gallbladder carriage (and non-carriage controls) using two-dimensional gas chromatography coupled with time-of-flight mass spectrometry (GCxGC-TOFMS) and supervised pattern recognition modeling. We were able to significantly discriminate Salmonella carriage samples from non-carriage control samples. We were also able to detect differential signatures between S. Typhi and S. Paratyphi A carriers. We additionally compared carriage metabolite profiles with profiles generated during acute infection; these data revealed substantial heterogeneity between metabolites associated with acute enteric fever and chronic carriage. Lastly, we found that Salmonella carriers could be significantly distinguished from non-carriage controls using only five metabolites, indicating the potential of these metabolites as diagnostic markers for detecting chronic Salmonella carriers. Conclusions/Significance: Our novel approach has highlighted the potential of using metabolomics to search for diagnostic markers of chronic Salmonella carriage. We suggest further epidemiological investigations of these potential biomarkers in alternative endemic enteric fever settings.
2018-01-17 | MTBLS579 | MetaboLights
Project description:Study to stimulate WT and IL-10RB mutant macrophages with LPS in presence or absence of recombinant IL-10 and compare their gene expression profiles by RNASeq
These data are 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/ .
This dataset contains all the data available for this study on 2019-08-28.
| EGAD00001005300 | EGA
Project description:The goal of this project is to understand the etiology and pathology of host-pathogen interaction using high-throughput cellular phenotyping. By combining the expertise in pathogen biology, informatics and stem cell biology across the institute, this project will use targeted genetic modification in mouse embryonic stem cells to identify functions of host genes in innate immunity. We will also explore the biology of mouse embryonic stem cells and their differentiation into immune competent cells. To this end we will generate homozygous and inducible knockout lines in mouse embryonic stem cells, which will be differentiated into immune competent cells, such as macrophages or dendritic cells. These will be subjected to a panel of immune challenge and stimulation assays to characterise the functions of the disrupted genes. To identify new functions for mammalian genes in innate immunity we will:\Generate a panel of homozygous inducible gene knockout mouse ES cell lines working from a list of ca. 80 candidate genes (MGP phenotyping and GWAS hits). \Scale up differentiation protocols for immune challenge and stimulation assays.\Benchmark in vitro differentiated ES cell models against primary immune cells from selected MGP mouse lines and eventually against human iPS cells.\Screen a panel of 30 genetically modified cell lines in immunological challenge and stimulation assays, defining phenotypes at the cellular level by high content imaging, biochemically by assaying cytokine production, and at the molecular level by transcriptome analysis.\Define novel gene functions in innate immunity through network analysis of gene expression data from all challenged cell lines.\In the longer term scale up the production and phenotyping of genetically modified cell lines (mouse or human as appropriate).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-234 | biostudies-arrayexpress
Project description:Total RNA was extracted from adult male and female zebrafish. Illumina cDNA libraries were prepared from polyA+ RNA and sequenced using Illumina HiSeq paired-end sequencing. 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: Total RNA was extracted from zebrafish embryos using Trizol and DNase treated. Libraries were made using the Illumina cDNA protocol from polyA+ 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/
2013-01-07 | E-ERAD-54 | biostudies-arrayexpress
Project description: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/
2013-03-11 | E-ERAD-111 | biostudies-arrayexpress
Project description: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/
2014-01-28 | E-ERAD-187 | biostudies-arrayexpress