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| 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
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| 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.
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| 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.
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| Contributor(s) |
Sugden B, Pratt ZL, Sengupta S, Kuzembayeva M |
| Citation(s) |
19217135 |
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| Submission date |
Jul 06, 2008 |
| Last update date |
Mar 20, 2012 |
| Contact name |
Zachary Pratt |
| E-mail(s) |
zpratt@wisc.edu
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| Organization name |
University of Wisconsin-Madison
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| Department |
Oncology
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| Lab |
Sugden
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| Street address |
1400 University Avenue
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
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| Platforms (1) |
| GPL7022 |
Sugden Lab Epstein-Barr virus (EBV) miRNA microarray |
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| Samples (48)
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| 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 |
| GSM303595 |
EBV-positive lymphoblastoid cell line 721, slide 189 |
| GSM303596 |
Gastric Carcinoma cell line, AGS, stably maintaining recombinant Akata EBV-GFP |
| GSM303597 |
Recombinant Akata GFP, Burkitt's lymphoma cell line stably maintaining recombinant Akata EBV-GFP, miRNA expression |
| GSM303598 |
Akata, a type I Burkitt's lymphoma cell line maintaining EBV |
| GSM303599 |
B958IID4, an EBV-positive marmoset cell clone |
| GSM303600 |
BL-5, an EBV-positive type I Burkitt's lymphoma cell line, slide 63 |
| GSM303601 |
BL-5, an EBV-positive type I Burkitt's lymphoma cell line, slide 182 |
| GSM303602 |
BL-8, an EBV-positive, type I Burkitt's lymphoma cell line, slide 70 |
| GSM303603 |
BL-8, an EBV-positive, type I Burkitt's lymphoma cell line, slide 183 |
| GSM303604 |
C666-1 Nasopharyngeal carcinoma cell line, EBV-positive |
| GSM303605 |
Dante, an EBV-positive, type I Burkitt's lymphoma cell line |
| GSM303606 |
Daudi, an EBV-positive, Burkitt's lymphoma cell line, slide 102 |
| GSM303607 |
Daudi, an EBV-positive, Burkitt's lymphoma cell line, slide 173 |
| GSM303608 |
Daudi, an EBV-positive, Burkitt's lymphoma cell line, slide 180 |
| GSM303621 |
GG68, an EBV-positive, type III Burkitt's lymphoma cell line, slide 93 |
| GSM303622 |
GG68, an EBV-positive, type III Burkitt's lymphoma cell line, slide 174 |
| GSM303623 |
JSC-1, an EBV- and KSHV-positive primary effusion lymphoma cell line |
| GSM303624 |
Kem1, an EBV-positive, type I Burkitt's lymphoma cell line |
| GSM303625 |
MutuI, an EBV-positive, type I Burkitt's lymphoma cell line, slide 61 |
| GSM303626 |
MutuI, an EBV-positive, type I Burkitt's lymphoma cell line, slide 174 |
| GSM303627 |
MutuIII, an EBV-positive, type III Burkitt's lymphoma cell line, slide 61 |
| GSM303628 |
MutuIII, an EBV-positive, type III Burkitt's lymphoma cell line, slide 175 |
| GSM303629 |
MutuIII, an EBV-positive, type III Burkitt's lymphoma cell line, slide 186 |
| GSM303630 |
OkuI, an EBV-positive, Wp-restricted Burkitt's lymphoma cell line, slide 92 |
| GSM303631 |
OkuI, an EBV-positive, Wp-restricted Burkitt's lymphoma cell line, slide 173 |
| GSM303632 |
OkuI, an EBV-positive, Wp-restricted Burkitt's lymphoma cell line, slide 177 |
| GSM303633 |
OkuI, an EBV-positive, Wp-restricted Burkitt's lymphoma cell line, slide 186 |
| GSM303634 |
Primary B cells, infected with B95-8 EBV, 20 hours post infection |
| GSM303635 |
Primary B cells, infected with B95-8 EBV, 44 hours post infection |
| GSM303636 |
Primary B cells, infected with B95-8 EBV, 66 hours post infection |
| GSM303637 |
Primary B cells, infected with B95-8 EBV, 90 hours post infection |
| GSM303638 |
PTLD1, an EBV-positive, post-transplant lymphoproliferative disease cell line, slide 62 |
| GSM303639 |
PTLD1, an EBV-positive, post-transplant lymphoproliferative disease cell line, slide 183 |
| GSM303640 |
PTLD3, an EBV-positive, post-transplant lymphoproliferative disease cell line |
| GSM303641 |
PTLD5, an EBV-positive, post-transplant lymphoproliferative disease cell line, slide 62 |
| GSM303642 |
PTLD5, an EBV-positive, post-transplant lymphoproliferative disease cell line, slide 185 |
| GSM303643 |
Raji, an EBV-positive, type III Burkitt's lymphoma cell line, slide 72 |
| GSM303644 |
Raji, an EBV-positive, type III Burkitt's lymphoma cell line, slide 176 |
| GSM303645 |
Raji, an EBV-positive, type III Burkitt's lymphoma cell line, slide 187 |
| GSM303646 |
SavI, an EBV-positive, type I Burkitt's lymphoma cell line, slide 70 |
| GSM303647 |
SavI, an EBV-positive, type I Burkitt's lymphoma cell line, slide 178 |
| GSM303648 |
SM-1, an EBV-positive, type I Burkitt's lymphoma cell line from an HIV-positive donor, slide 65 |
| GSM303649 |
SM-1, an EBV-positive, type I Burkitt's lymphoma cell line from an HIV-positive donor, slide 181 |
| GSM303650 |
Recombinant Akata GFP, Burkitt's lymphoma cell line stably maintaining recombinant Akata EBV-GFP, slide 178 |
| GSM303651 |
Daudi, a type I Burkitt's lymphoma cell line, slide 189 |
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| Relations |
| BioProject |
PRJNA113285 |
| 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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