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Series GSE39913 Query DataSets for GSE39913
Status Public on Aug 28, 2012
Title EBNA1 ChIP-seq and MNase-seq in EBV-positive MUTU cell lines
Organism human gammaherpesvirus 4
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary Epstein-Barr Virus (EBV), which is associated with multiple human tumors, persists as a minichromosome in the nucleus of B-lymphocytes and induces malignancies through incompletely understood mechanisms. Here, we present a large-scale functional genomic analysis of EBV. Our experimentally generated nucleosome positioning maps and viral protein binding data were integrated with over 700 publicly available high-throughput sequencing data sets for human lymphoblastoid cell lines mapped to the EBV genome. We found that viral lytic genes are coexpressed with cellular cancer-associated pathways, suggesting that the lytic cycle may play an unexpected role in virus-mediated oncogenesis. Host regulators of viral oncogene expression and chromosome structure were identified and validated, revealing a role for the B-cell-specific protein Pax5 in viral gene regulation and the cohesin complex in regulating higher order chromatin structure. Our findings provide a deeper understanding of latent viral persistence in oncogenesis and establish a valuable viral genomics resource for future exploration.
 
Overall design Six sequencing experiments were performed. One EBNA1 ChIP-seq was controlled with IgG ChIP-seq. Two MNase-seq biological replicates were each conrolled by input seq using the same cells subjected to MNase digestion.
 
Contributor(s) Tempera I, Lu F, Wikramasinghe P, Arvey A, Lieberman P
Citation(s) 22901543
Submission date Aug 06, 2012
Last update date May 15, 2019
Contact name Aaron Arvey
E-mail(s) aarvey@cbio.mskcc.org
Organization name Memorial Sloan-Kettering Cancer Center
Street address 415 E 68th St ZRC 1441
City New York
State/province NY
ZIP/Postal code 10065
Country USA
 
Platforms (1)
GPL15906 Illumina Genome Analyzer (Human herpesvirus 4)
Samples (6)
GSM982656 Raji EBNA1 ChIP
GSM982657 Raji IgG Control (Matched to EBNA1 ChIP)
GSM982658 MutuI MNase-seq Rep1
Relations
BioProject PRJNA172189
SRA SRP014746

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
GSE39913_RAW.tar 2.9 Mb (http)(custom) TAR (of WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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