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Series GSE12014 Query DataSets for GSE12014
Status Public on Dec 01, 2008
Title Expression of EBV miRNAs in numerous EBV-positive cell lines
Platform organisms Arabidopsis thaliana; Homo sapiens; human gammaherpesvirus 4
Sample organism human gammaherpesvirus 4
Experiment type Non-coding RNA profiling by array
Summary EBV-positive cell lines were assayed for expression of EBV miRNAs. The names of the miRNAs are from miRBase from Fall 2007. Microarray probes are tandem complements of the mature miRNA sequence. We assayed Burkitt's lymphoma (BL), Nasopharyngeal carcinoma, post-transplant lymphoproliferative disease (PTLD), primary effusion lymphoma, and lymphoblastoid cell lines. We also assayed primary B cells that were infected with the B95-8 strain of EBV, which was found to express EBV miRNAs as early as 20 hours post infection. We have found PTLD and BLs from HIV-positive donors both express EBV miRNAs. These types of cell lines have not previously been found to express viral miRNAs. We have found that cells that support type I and type II latency express only the BART miRNAs, whereas cells that support type III latency express BART and BHRF1 miRNAs. Furthermore, BL cell lines that spontaneously lose EBV express levels of the viral miRNAs that are at least 5-fold lower than cell lines that do not lose EBV.
Overall design In total, 48 samples have been assayed and included in this study. EBV-negative control samples are not included in this data set, but raw and processed data may be requested from the contributors. These EBV-negative cell lines include the Burkitt's lymphoma cell lines, BJAB and Akata-negative, the gastric carcinoma cell line, AGS, and uninfected primary B cells. Of the 48 samples, we have assayed 22 different EBV-positive cell lines and 4 different time points after infection of primary B cells with EBV. Replicates of the majority of cell lines is included in this data set. Replicates are from independent RNA isolations that were then hybridized to individual microarrays.
Contributor(s) Sugden B, Pratt ZL, Sengupta S, Kuzembayeva M
Citation(s) 19217135
Submission date Jul 06, 2008
Last update date Mar 20, 2012
Contact name Zachary Pratt
Organization name University of Wisconsin-Madison
Department Oncology
Lab Sugden
Street address 1400 University Avenue
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
Platforms (1)
GPL7022 Sugden Lab Epstein-Barr virus (EBV) miRNA microarray
Samples (48)
GSM303592 EBV-positive lymphoblastoid cell line 721, slide 66
GSM303593 EBV-positive lymphoblastoid cell line 721, slide 171
GSM303594 EBV-positive lymphoblastoid cell line 721, slide 181
BioProject PRJNA113285

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Supplementary file Size Download File type/resource
GSE12014_RAW.tar 310.0 Kb (http)(custom) TAR (of TXT)
Processed data included within Sample table

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