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Series GSE28420 Query DataSets for GSE28420
Status Public on May 01, 2011
Title The dynamics of E1A in regulating networks and canonical pathways in quiescent cells
Organism Mus musculus
Experiment type Expression profiling by array
Summary Adenoviruses force quiescent cells to re-enter the cell cycle to replicate their DNA, and for the most part, this is accomplished after they express the E1A protein immediately after infection. In this context, E1A is believed to inactivate cellular proteins (e.g., p130) that are known to be involved in the silencing of E2F-dependent genes that are required for cell cycle entry. However, the potential perturbation of these types of genes by E1A relative to their functions in regulatory networks and canonical pathways remains poorly understood. We have used DNA microarrays analyzed with Bayesian ANOVA for microarray (BAM) to assess changes in gene expression after E1A alone was introduced into quiescent cells from a regulated promoter. Approximately 2,401 genes were significantly modulated by E1A, and of these, 385 and 1033 met the criteria for generating networks and functional and canonical pathway analysis respectively, as determined by using Ingenuity Pathway Analysis software. After focusing on the highest-ranking cellular processes and regulatory networks that were responsive to E1A in quiescent cells, we observed that many of the up-regulated genes were associated with DNA replication, the cell cycle and cellular compromise. We also identified a cadre of up regulated genes with no previous connection to E1A; including genes that encode components of global DNA repair systems and DNA damage checkpoints. Among the down-regulated genes, we found that many were involved in cell signalling, cell movement, and cellular proliferation. Remarkably, a subset of these was also associated with p53-independent apoptosis, and the putative suppression of this pathway may be necessary in the viral life cycle until sufficient progeny have been produced. These studies have identified for the first time a large number of genes that are relevant to E1A’s activities in promoting quiescent cells to re-enter the cell cycle in order to create an optimum environment for adenoviral replication.
 
Overall design Six independent cell cultures (n = 6) were randomly assigned to two treatment groups with three independent biological replicates per group. The control group, denoted ‘Q’, are quiescent cells without Doxycycline, i.e. no E1A expression (untreated for 8 hr, total RNA harvested 1 hour after). The stimulated group, denoted ‘S’, are stimulated cells with Doxycycline, i.e. with E1A expression (treated with Doxycycline for 8 hr, total RNA harvested 1 hour after treatment).
 
Contributor(s) Dazard J, Zhang K, Sha J, Yasin O, Cai L, Nguyen C, Ghosh M, Bongorno J, Harter M
Citation(s) 21615925
Submission date Apr 06, 2011
Last update date Jan 18, 2013
Contact name Jean-Eudes Dazard
Organization name Case Western Reserve University
Department Proteomics and Bioinformatics
Lab Bioinformatics
Street address 10900 Euclid Avenue
City Cleveland
State/province Ohio
ZIP/Postal code 44106
Country USA
 
Platforms (1)
GPL6103 Illumina mouseRef-8 v1.1 expression beadchip
Samples (6)
GSM702345 Quiescent Q1
GSM702346 Quiescent Q2
GSM702347 Quiescent Q3
Relations
BioProject PRJNA139095

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

Supplementary file Size Download File type/resource
GSE28420_RAW.tar 3.4 Mb (http)(custom) TAR
GSE28420_non-normalized.txt.gz 633.4 Kb (ftp)(http) TXT
Processed data included within Sample table

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