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Series GSE73410 Query DataSets for GSE73410
Status Public on Nov 01, 2015
Title Diversity in Modulation of Interferon Stimulated Genes by Dobrava, Kurkino, and Sochi Genotypes of Dobrava-Belgrade Hantavirus in comparison to Tula Virus
Organism Homo sapiens
Experiment type Expression profiling by array
Summary We used an in vitro model to study the impact of hantavirus infection on the cellular gene expression profile. To do so, A549 cells were infected with pathogenic DOBV genotypes Dobrava, Kurkino, and Sochi and less-pathogenic TULV . A549 cells were chosen because of their high susceptibility towards hantavirus infection and because many fundamental studies on hantavirus biology and on host gene expression changes following infection have been performed with this cell line. Cells were infected at a high multiplicity of infection of 5 focus forming units (FFU) per cell to guarantee uniform infection of all cells. Total RNA from infected and mock-infected control cells was isolated at 12 h post infection. This point of time was chosen to allow enough time for establishment of infection and progression to early viral gene expression but to avoid the risk of missing gene expression changes associated with the onset of the cellular innate immune response towards infection. The distinct modulation of cellular transcription of A549 cells was analyzed by means of a whole genome cRNA microarray. All experiments were performed in duplicate using RNA samples from two independently infected cell cultures for each analysis. To compare the gene expression profiles, ratios were calculated by dividing the merged normalized signal intensities of infected samples by mock-control signal intensities. Genes that exhibited a ≥2-fold change (FC) in gene expression and signal intensities that were significantly above the background with p-values ≤ 0.01 were chosen for further analysis. The successful infection of A549 cells with all viruses and the uniform progression of infection were confirmed by immunofluorescence microscopy of cells infected in parallel. At 12 h post infection with each virus nearly all cells were infected without showing cytopathic effects. Since different clinical courses are caused by infection with distinct DOBV genotypes, genotype-specific regulation of cellular transcripts were investigated that may be crucial for pathogenesis in vitro. Selected infection regulated candidates were verified by qPCR at different time points after infection.
Overall design We analyzed the gene expression profile of A549 cells wich were either mock-infected or infected with Dobrava Virus (DOBV) Dobrava, Kurkino or Sochi, or with Tula Virus (TULV) at a multiplicity of infection of 5. Experiments were performed in duplicate. At 12 h post infection total RNA was isolated from infected cells and used for microarray analysis.
Contributor(s) Witkowski PT, Bourquain D, Bankov K, Auste B, Nitsche A, Dabrowski PW, Krüger DH, Schaade L
Citation(s) 27058765
Submission date Sep 24, 2015
Last update date Nov 27, 2018
Contact name Daniel Bourquain
Phone 0049 (0)30187543825
Organization name Robert Koch Institute
Department Centre for Biological Threats and Special Pathogens 1
Lab Highly Pathogenic Viruses
Street address Seestraße 10
City Berlin
State/province Berlin
ZIP/Postal code 13353
Country Germany
Platforms (1)
GPL13607 Agilent-028004 SurePrint G3 Human GE 8x60K Microarray (Feature Number version)
Samples (10)
GSM1893054 A549_DOBV_Kurkino_12h_1
GSM1893055 A549_DOBV_Kurkino_12h_2
GSM1893056 A549_DOBV_Dobrava_12h_1
BioProject PRJNA296902

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE73410_RAW.tar 127.7 Mb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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