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SAMPLES (11)

mace:id
Technology # Array version
Species
Organ
Tissue
Physiopathology
Type
Name

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User name	Arndt Benecke
Email	arndt@ihes.fr
Phone / Fax number	+33160926665 / +33160926609
Location	Institut des Hautes Etudes Scientifiques (Integrative Biology) - 35, route de Chartres - 91440 Bures sur Yvette, France

Scientific description

Little is known about the physiological role of the EBER1 and 2 nuclear RNAs during Epstein Barr viral infection. The cellular transcription response to EBER2 expression using the wild-type and an internal deletion mutant was determined. Significant changes in gene expression patterns were observed. A functional meta-analysis of the regulated genes points to inhibition of stress and immune responses, as well as activation of cellular growth and cytoskeletal reorganization as potential targets for EBER2 RNA. Different functions can be assigned to different parts of the RNA. These results provide new avenues to the understanding of EBER2 and EBV biology.
Keywords: Overexpression of non-translated RNA

Technical description

Biological relicates, 3 conditions: empty expression vector (pUC-18), pUC-18-EBER2, pUC-18-EBER2-L2

Sample type 	RNA
  	
Source Name 	HEK293 cell line
Organism(s) 	Homo sapiens
Extracted molecule 	total RNA
Extraction protocol 	RNA was extracted from the cell lines using RNeasy Midi Kit (Quiagen) according to the instructions provided by the manufacturer
Label 	DIG-UTP
Label protocol 	Digoxigenin-UTP labeled cRNA was generated and amplified from 2 Î¼g of total RNA from each sample using Applied Biosystems NanoAmp RT-IVT Labeling Kit (P/N 4365715) according to the manufacturerâ€™s protocol(P/N 4365710).
  	
Hybridization protocol 	Array hybridization was performed for 16 hrs at 55 oC. Pre-Hybridization, Hybridization, antibody binding and Chemiluminescence reaction were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) following the manufacturerâ€™s protocol (P/N 4339627).
Scan protocol 	image acquisition and analysis were performed using Applied Biosystems Chemiluminescence Detection Kit (P/N 4342142) and Applied Biosystems 1700 Chemiluminescent Microarray Analyzer (P/N 4338036) following the manufacturerâ€™s protocol (P/N 4339629).
Data processing 	Images were auto-gridded and the chemiluminescent signals were quantified, corrected for background, and finally, spot- and spatially-normalized using the Applied Biosystems 1700 Chemiluminescent Microarray Analyzer software v 1.1 (P/N 4336391). Median normalization and Probabilty for a gene to be expressed(A) were calculated with proprietary software.

References

Eilebrecht S, Pellay FX, OdenwÃ¤lder P, Brysbaert G et al. EBER2 RNA-induced transcriptome changes identify cellular processes likely targeted during Epstein Barr Virus infection. BMC Res Notes 2008 Oct 28;1:100.

Pubmed : http://www.ncbi.nlm.nih.gov/pubmed/18957101

This dataset was previously published on NCBI/GEO with accession no.: GSE11093