• Blood transcriptome analysis of patients with uncomplicated bacterial infection and sepsis.

      Herwanto, Velma; Tang, Benjamin; Wang, Ya; Shojaei, Maryam; Nalos, Marek; Shetty, Amith; Lai, Kevin; McLean, Anthony S; Schughart, Klaus; HZI,Helmholtz-Zentrum für Infektionsforschung GmbH, Inhoffenstr. 7,38124 Braunschweig, Germany. (BioMedCentral, 2021-02-27)
      The data presented here consists of raw and processed transcriptome data obtained by next generation RNA sequencing from 105 peripheral blood samples from patients with uncomplicated infections, patients who developed sepsis, septic shock patients, and healthy controls. It is provided as raw sequenced reads and as normalized log2 transformed relative expression levels. This data will allow performing detailed analyses of gene expression changes between uncomplicated infections and sepsis patients, such as identification of differentially expressed genes, co-regulated modules as well as pathway activation studies.
    • Hematological parameters in the early phase of influenza A virus infection in differentially susceptible inbred mouse strains.

      Preusse, Matthias; Schughart, Klaus; Wilk, Esther; Klawonn, Frank; Pessler, Frank; Helmholz Centre for Infection Research (2015)
      Hematological parameters have not received much attention in small animal models of infection, particularly at very early time points. We therefore studied changes in leukocyte and thrombocyte numbers in a mouse model of influenza A virus (IAV) infection, including measurements within the first 24 h after infection, and also assessing effects, if any, of the infection/anesthesia procedure on these parameters.
    • Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics.

      Gruenberger, Michael; Alberts, Rudi; Smedley, Damian; Swertz, Morris; Schofield, Paul; Schughart, Klaus; Department of Infection Genetics, Helmholtz Centre for Infection Research & University of Veterinary Medicine Hannover, Inhoffenstr, 7, D-38124 Braunschweig, Germany. kls@helmholtz-hzi.de. (2010)
      ABSTRACT: BACKGROUND: The integration of information present in many disparate biological databases represents a major challenge in biomedical research. To define the problems and needs, and to explore strategies for database integration in mouse functional genomics, we consulted the biologist user community and implemented solutions to two user-defined use-cases. RESULTS: We organised workshops, meetings and used a questionnaire to identify the needs of biologist database users in mouse functional genomics. As a result, two use-cases were developed that can be used to drive future designs or extensions of mouse databases. Here, we present the use-cases and describe some initial computational solutions for them. The application for the gene-centric use-case, "MUSIG-Gen" starts from a list of gene names and collects a wide range of data types from several distributed databases in a "shopping cart"-like manner. The iterative user-driven approach is a response to strongly articulated requests from users, especially those without computational biology backgrounds. The application for the phenotype-centric use-case, "MUSIG-Phen", is based on a similar concept and starting from phenotype descriptions retrieves information for associated genes. CONCLUSION: The use-cases created, and their prototype software implementations should help to better define biologists' needs for database integration and may serve as a starting point for future bioinformatics solutions aimed at end-user biologists.