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Series GSE59842 Query DataSets for GSE59842
Status Public on Aug 01, 2014
Title Genome wide DNA methylation of Epstein-Barr virus infected immortalized normal oral keratinocytes
Organism Homo sapiens
Experiment type Methylation profiling by high throughput sequencing
Summary The oral cavity is the persistent reservoir for EBV with lifelong infection of resident epithelial and B cells. Infection of these cell types results in distinct EBV gene expression patterns that are regulated by epigenetic modifications involving DNA methylation and chromatin structure. Such regulation of EBV gene expression relies on viral manipulation of the host epigenetic machinery that may inadvertently result in long-lasting, oncogenic host epigenetic reprogramming. To test this hypothesis in the context of EBV infection of epithelial cells, we established a transient infection model to identify the epigenetic consequences after EBV infection of immortalized normal oral keratinocytes and subsequent viral loss.
Overall design NOK cells were single cell cloned (designated as cl1) and EBV infected by co-culture with a recombinant Akata EBV strain carrying neomcycin resistance and GFP expression cassette in place of EBV BXLF1. Cells were selected with 350 ug/ml G418. As a selection control, cells were transfected a plasmid carrying a neomycin resistance cassette. Cells were passaged 10 times with G418, followed by removal of selection pressure. After an additional 10 passages, cells were single cell cloned and the presence of EBV was determined by various methods. Three clones were identified as being EBV negative and said to be transiently infected. Uninfected parental and vector transfected cells were passaged in the same manner and also single cell cloned. The DNA methylation profiles were examined using reduced representation bisulfite sequencing.
Contributor(s) Scott RS
Citation(s) 25056883
Submission date Jul 28, 2014
Last update date May 15, 2019
Contact name Rona S. Scott
Phone 318-675-6263
Organization name Louisiana State University Health Sciences Center-Shreveport
Department Microbiology and Immunology
Street address 1501 Kings Highway
City Shreveport
State/province LA
ZIP/Postal code 71130
Country USA
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (6)
GSM1447374 NOK cl1 uninfected p30
GSM1447375 NOK cl1 pTURF transfected p22
GSM1447376 NOK cl1 AkataBX-1 cl4 p31 EBV+
This SubSeries is part of SuperSeries:
GSE59843 Genome wide DNA methylation and expression profiling of Epstein-Barr virus infected immortalized normal oral keratinocytes
BioProject PRJNA256343
SRA SRP044960

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

Supplementary file Size Download File type/resource
GSE59842_EBV_CpG_methylation.csv.gz 60.5 Kb (ftp)(http) CSV
GSE59842_RAW.tar 359.1 Mb (http)(custom) TAR (of BED, CSV)
GSE59842_hdiff.csv.gz 87.1 Kb (ftp)(http) CSV
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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