Data Management, Analysis and Resources Dissemination Core

Sadzewicz, Lisa Deshong; Rasko, David A.

Abstract

The specific objective of the Data Management, Analysis, and Resources Dissemination Core is to provide systems and bioinformatics computing infrastructure necessary for tracking, storing, integrating, and disseminating the data and biological resources generated in Research Projects 1-4 and the Technology and Immunology Cores, Cores B and D, respectively. Data and resources from the Projects will be made available to the wider scientific community through submissions to public archives, where applicable, or a project portal when such archives do not exist. Using our customized Laboratory Information Management System (LIMS), project tracking systems, and integrated web tools, we will track all samples, data, IRB documentation, and their respective metadata throughout each of the Research Projects. We expect the Research Projects and Cores to generate significant amounts of data, and we will continue to scale our high-capacity data storage infrastructure to store, manage, and share these data with the scientific community. We will deploy the Open Science Data Framework (OSDF), a scalable file system platform developed at IGS for the storage of different data types along with their metadata. Finally, we will work with the Research Project PIs to ensure that all the primary data and derived analyses results will be made available to the wider scientific community. This will be accomplished by depositing the primary data in public archives such as the NCBI Short Read Archive (SRA), and the derived results such as genome assemblies, sequence variants, and expression data in NCBI Genbank, dbSNP, and the Gene Expression Omnibus (GEO). In addition to deposition of data to public archives, we will build a website for the scientific community to access all raw and custom data sets, analysis tools and standard operating procedure (SOP) documents.

Public Health Relevance

The proposed research in this U19 award will use state-of-the-art genomics approaches to study a variety of high-priority pathogens to better understand how they cause disease in infected individuals. This Data Management, Analysis and Resources Dissemination Core will ensure data and resources from the Projects will be made available to the wider scientific community through submissions to public archives.

Funding Agency

• Agency: National Institute of Health (NIH)
• Institute: National Institute of Allergy and Infectious Diseases (NIAID)
• Type: Research Program--Cooperative Agreements (U19)
• Project #: 1U19AI110820-01
• Application #: 8711766
• Study Section: Special Emphasis Panel (ZAI1)
• Project Start: 2014-04-15
• Project End: 2019-03-31
• Budget Start: 2014-04-15
• Budget End: 2015-03-31
• Support Year: 1
• Fiscal Year: 2014

Institution

• Name: University of Maryland Baltimore
• City: Baltimore
• State: MD
• Country: United States
• Zip Code: 21201

Publications

Ndungo, Esther; Randall, Arlo; Hazen, Tracy H et al. (2018) A Novel Shigella Proteome Microarray Discriminates Targets of Human Antibody Reactivity following Oral Vaccination and Experimental Challenge. mSphere 3:

Hazen, Tracy H; Mettus, Roberta; McElheny, Christi L et al. (2018) Diversity among blaKPC-containing plasmids in Escherichia coli and other bacterial species isolated from the same patients. Sci Rep 8:10291

Chung, Matthew; Teigen, Laura; Liu, Hong et al. (2018) Targeted enrichment outperforms other enrichment techniques and enables more multi-species RNA-Seq analyses. Sci Rep 8:13377

Watkins, Tonya N; Gebremariam, Teclegiorgis; Swidergall, Marc et al. (2018) Inhibition of EGFR Signaling Protects from Mucormycosis. MBio 9:

Andrianaki, Angeliki M; Kyrmizi, Irene; Thanopoulou, Kalliopi et al. (2018) Iron restriction inside macrophages regulates pulmonary host defense against Rhizopus species. Nat Commun 9:3333

Hazen, Tracy H; Mettus, Roberta T; McElheny, Christi L et al. (2018) Draft Genome Sequences of blaKPC-Containing Enterobacter aerogenes, Citrobacter freundii, and Citrobacter koseri Strains. Genome Announc 6:

Broxton, Chynna N; He, Bixi; Bruno, Vincent M et al. (2018) A role for Candida albicans superoxide dismutase enzymes in glucose signaling. Biochem Biophys Res Commun 495:814-820

Higginson, Ellen E; Ramachandran, Girish; Hazen, Tracy H et al. (2018) Improving Our Understanding of Salmonella enterica Serovar Paratyphi B through the Engineering and Testing of a Live Attenuated Vaccine Strain. mSphere 3:

Richter, Taylor K S; Hazen, Tracy H; Lam, Diana et al. (2018) Temporal Variability of Escherichia coli Diversity in the Gastrointestinal Tracts of Tanzanian Children with and without Exposure to Antibiotics. mSphere 3:

Baldin, Clara; Soliman, Sameh S M; Jeon, Heewon H et al. (2018) PCR-Based Approach Targeting Mucorales-Specific Gene Family for Diagnosis of Mucormycosis. J Clin Microbiol 56: