Reference genome for Global Pneumococcal Sequence (GPS ) project
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB31141 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Clostridium difficile Ribotype Reference Genome Project
| PRJEB2101 | ENA
Project description:A monoploid reference sequence for the highly complex genome of sugarcane
| PRJEB26913 | ENA
Project description:Influenza A virus (IAV) predisposes individuals to secondary infections with the bacterium Streptococcus pneumoniae (the pneumococcus). Infections may manifest as pneumonia, sepsis, meningitis or otitis media (OM). It remains controversial as to whether secondary pneumococcal disease is due to the induction of an aberrant immune response or IAV induced immunosuppression. Moreover, as the majority of studies have been performed in the context of pneumococcal pneumonia, it remains unclear how far these findings can be extrapolated to other pneumococcal disease phenotypes. Here, we demonstrate that the viral hemagglutinin (HA) mediates bacterial OM by inducing a pro-inflammatory response in the middle ear cavity in a replication-dependent manner. Importantly, our findings show that it is the inflammatory response that mediates pneumococcal replication; not viral suppression of the immune system or epithelial damage. This study provide the first evidence that HA induced inflammation drives pneumococcal replication in the middle ear cavity, which has important consequences to the treatment of pneumococcal OM.
2013-01-01 | GSE41098 | GEO
Project description:Reference genome assemblies for umbrella project PRJEB43248
| PRJEB43239 | ENA
Project description:<p>Stanford contributed samples to the PAGE study that can act as a population reference dataset across the globe. Therefore this dataset includes reference individuals, without phenotypes, chosen to help infer ancestry that will help us understand the diverse samples available in PAGE. The complete dataset comprises individuals of European, African, Asian, Oceanian, and Native American descent, from a total of over 50 populations. A subset of these individuals from Puno, Peru and Easter Island (Rapa Nui), Chile, are included in the PAGE samples that were whole genome sequenced in 2015. Additional details are available in the Study Acknowledgments.</p> <p>The Global Reference Panel comprises 6 sample sets: <ul><li>A population sample of Andean individuals primarily of Quechuan/Aymaran ancestry from Puno, Peru</li> <li>A population sample of Easter Island (Rapa Nui), Chile</li> <li>Individuals of indigenous origin from Oaxaca, Mexico</li> <li>Individuals of indigenous origin from Honduras</li> <li>Individuals of indigenous origin from Colombia</li> <li>Individuals of indigenous origin from the Nama and Khomani KhoeSan populations of the Northern Cape, South Africa</li></ul> </p> <p>In addition, we genotyped publicly available samples that will be hosted on the Bustamante lab website (<a href="https://bustamantelab.stanford.edu/">https://bustamantelab.stanford.edu/</a>). These comprise large public datasets to provide an open reference dataset for the world:</p> <p> <ul><li>The additional related individuals from the Americas in the Human Genome Diversity Panel (H952) plus all additional samples from the Americas</li> <li>A subset of the unrelated individuals from the Maasai in Kinyawa, Kenya (MKK) dataset from the International Hapmap Project hosted at Coriell</li></ul> </p> <p>Additional samples will be available for restricted use with a data access agreement with the Bustamante Lab.</p> <p>This study is part of the Population Architecture using Genomics and Epidemiology (PAGE) study (<a href="./study.cgi?study_id=phs000356">phs000356</a>). </p>
| phs001033 | dbGaP
Project description:The NIH Roadmap Epigenomics Mapping Consortium aims to produce a public resource of epigenomic maps for stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease. Characterization of the reference epigenome in humans by use of ChIP-Seq in a diverse panel of ES cells, tissue stem cells, reprogrammed stem cells, primary cells and tissues **************** For data usage terms and conditions, please refer to: http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies ****************
2009-08-05 | GSE17312 | GEO
Project description:Patients with inflammatory bowel disease (IBD) will be assessed for immunologic response to pneumococcal vaccination. Patients with IBD meet criteria as outlined by the Centers for Disease Control (CDC) for pneumococcal vaccination, yet the investigators have found that pneumococcal vaccination in this population is under-utilized. It is unknown whether or not IBD or IBD-related medications impact the immune response to this recommended vaccine.
Three groups of 25 patients each will be recruited. The first group will consist of outpatients with IBD who are receiving infliximab (Remicade TM) while on concommitant immunosuppressive therapy (with either 6MP, azathioprine, or methotrexate). This group is intended to represent a common ‘heavily immunosuppressed’ patient group with IBD.
The second group will consist of patients with IBD seen in our outpatient clinic who are not on any immune-suppressive medications. These patients meet CDC criteria for vaccination by virtue of having a chronic medical illness. The third group will consist of healthy age-matched (to the first group) controls.
After obtaining informed consent, patients will be screened with baseline lab tests including testing for antibodies against pneumococcus. At the baseline visit, patients will also undergo a brief medical history, physical examination, and assessment of their IBD disease activity.
Included patients will then undergo a one-time intramuscular vaccination with 23-valent polysaccharide pneumococcal vaccine (Pneumovax TM). One month later, subjects will return for a blood draw to assess for response to pneumococcal vaccination.
| 2066877 | ecrin-mdr-crc
Project description:Anopheles Reference Genomes Project: Data and assemblies
| PRJEB51690 | ENA