Dataset features

Specifications


Application: Gene expression microarray analysis
Number of samples: 12
Release date: Feb 1 2011
Last update date: Sep 20 2012
Access: Public
Diseases: Infection, Necrosis
Chemicals: Cholesterol, Nucleosides
Dataset link Stage-specific expression of TNFα regulates bad/bid-mediated apoptosis and RIP1/ROS-mediated secondary necrosis in Birnavirus-infected fish cells

Experimental Protocol


Zebrafish ZF4 cell line was derived from 24h post-fertilization zebrafish embryos. Previous studies have been shown that adult zebrafish and zebrafish cell line could be infected with IPNV. In the present study, ZF4 cells were infected with IPNV, and total RNA was isolated from infected and uninfected control cells at 0 h, 6 h, 12 h, 24 h post-infection. Microarray analysis gene expression between IPNV-infected and uninfected cells relative to internal control on slides. The zebrafish 14K oligo microarray we used comprise 1800 zebrafish gene sequences from the NCBI and a database of 12768 putative open reading frames using NCBI zebrafish EST sequence information. Data files were imported into GeneSpring GX 7.3 for further analysis. Expression data sets must pass all the following quality control categories before used for cluster analysis. Clustering analysis allowed us to observe differences in cellular gene expression. A similar expression pattern was seen when comparing differentially expressed host cell genes between 12 and 24 h post-infection. The expression profiles were significantly different between 6 and 12 h post-infection. Therefore, we conclude that the regulation of host gene expression was changed after 12 h post-infection, and progressed into the late stage. To understand the interactions between host cells and IPNV and the molecular mechanisms involved in IPNV-induced pathogenesis, we used zebrafish oligo microarrays to investigate the gene expression profiles of IPNV-infected zebrafish embryonic cells. We also studied expression of specific genes related to immune response and apoptosis which were not present on the microarray we used by real-time quantitative RT-PCR. We used Pathway Studio’s software to analyze the altered genes in cellular pathway for IPNV, TNFα was shown to be crucial to these genes of host response. Our study proved the variation of transcriptome during infection, which shows the activation of important component of host defense, apoptosis and necrosis through TNFα mediate pathway.

Repositories


GEO

GSE21077

ArrayExpress

E-GEOD-21077

BioProject

PRJNA126715

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Contact


Wei-Lun Wang