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Series GSE124711 Query DataSets for GSE124711
Status Public on Jan 07, 2019
Title Comparative Analysis of Gammaherpesvirus Circular RNA
Organisms Macaca mulatta; Homo sapiens; Mus musculus; Human gammaherpesvirus 8; Macacine gammaherpesvirus 4; Murid herpesvirus 68
Experiment type Other
Summary Recent studies have identified circular RNAs (circRNAs) expressed from the Epstein-Barr virus (EBV) and Kaposi’s sarcoma herpesvirus (KSHV) human DNA tu- mor viruses. To gain initial insights into the potential relevance of EBV circRNAs in virus biology and disease, we assessed the circRNAome of the interspecies homologue rhesus macaque lymphocryptovirus (rLCV) in a naturally occurring lymphoma from a simian immunodeficiency virus (SIV)-infected rhesus macaque. This analysis revealed rLCV orthologues of the latency-associated EBV circular RNAs circRPMS1_E4_E3a and circEBNA_U. Also identified in two samples displaying unusually high lytic gene expres- sion was a novel rLCV circRNA that contains both conserved and rLCV-specific RPMS1 exons and whose backsplice junctions flank an rLCV lytic origin of replication (OriLyt). Analysis of a lytic infection model for the murid herpesvirus 68 (MHV68) rhadinovirus identified a cluster of circRNAs near an MHV68 lytic origin of replication, with the most abundant of these, circM11_ORF69, spanning the OriLyt. Lastly, analysis of KSHV la- tency and reactivation models revealed the latency associated circRNA originating from the vIRF4 gene as the predominant viral circRNA. Together, the results of this study broaden our appreciation for circRNA repertoires in the Lymphocryptovirus and Rhadinovirus genera of gammaherpesviruses and provide evolutionary support for vi- ral circRNA functions in latency and viral replication.
Overall design RNA-sequencing of Ribodepleted + RNase R treated, and Poly-A selection libraries of gammaherpesviral samples
Contributor(s) Flemington E
Citation(s) 30567979
Submission date Jan 06, 2019
Last update date Apr 08, 2019
Contact name Erik K Flemington
Phone 504 988-1167
Organization name Tulane Health Sciences Center
Department Pathology
Street address 1430 Tulane Ave., SL79
City New Orleans
State/province LA
ZIP/Postal code 70112
Country USA
Platforms (3)
GPL25719 Illumina HiSeq 4000 (Homo sapiens; Human gammaherpesvirus 8)
GPL26009 Illumina HiSeq 4000 (Murid herpesvirus 68; Mus musculus)
GPL26010 Illumina HiSeq 4000 (Macaca mulatta; Macacine gammaherpesvirus 4)
Samples (10)
GSM3543748 HE2.1
GSM3543749 NIH3T12
GSM3543750 BCBL1 (induced)
BioProject PRJNA513195
SRA SRP176282

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
GSE124711_RAW.tar 3.2 Mb (http)(custom) TAR (of BED)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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