GEO DataSets

(Submitter supplied) We used ac4C-seq to detedc cellular and KSHV transcripts in iSLK-Puro, iSLK-KSHV, iSLK-KSHV (WT), iSLK-KSHV (ΔNAT10) cells after after doxycycline and sodium butyrate treatment.

Organism:

Homo sapiens; Human gammaherpesvirus 8

Type:

Other

Platform:

GPL30065

24 Samples

Download data: TXT, XLS

(Submitter supplied) Flag-RIP-seq was performed in NAT10-Flag overexpressing iSLK-KSHV cells.

Organism:

Homo sapiens; Human gammaherpesvirus 8

Type:

Other

Platform:

GPL30065

12 Samples

Download data: TXT

(Submitter supplied) Historically, ribosomes have been viewed as unchanged homogeneous macromolecular machines with no intrinsic regulatory capacity for mRNA translation. However, an emerging concept is that heterogeneity of ribosomal composition exists, which can exert a regulatory function or specificity in translational control. This is supported by recent discoveries identifying compositionally distinct ‘specialized ribosomes’ that actively regulate mRNA translation. more...

Organism:

Homo sapiens; Human gammaherpesvirus 8

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL30065

8 Samples

Download data: TSV

(Submitter supplied) Control of RNA Polymerase II (pol II) elongation is a critical component of gene expression in mammalian cells. The PNUTS-protein phosphatase 1 (PP1) complex controls elongation rates, slowing pol II after polyadenylation sites to promote termination. The Kaposi's sarcoma-associated herpesvirus (KSHV) co-opts pol II to express its genes, but little is known about its regulation of pol II elongation. more...

Organism:

Homo sapiens; Human gammaherpesvirus 8

Type:

Other

Platform:

GPL24095

4 Samples

Download data: BW

(Submitter supplied) Control of RNA Polymerase II (pol II) elongation is a critical component of gene expression in mammalian cells. The PNUTS-protein phosphatase 1 (PP1) complex controls elongation rates, slowing pol II after polyadenylation sites to promote termination. The Kaposi's sarcoma-associated herpesvirus (KSHV) co-opts pol II to express its genes, but little is known about its regulation of pol II elongation. more...

Organism:

Human gammaherpesvirus 8; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24095

24 Samples

Download data: TXT

(Submitter supplied) Eukaryotic genomes are structurally organized via the formation of multiple loops that create gene expression regulatory units called topologically associating domains (TADs). Here we revealed the KSHV TAD structure at 500 base pair resolution and constructed a 3D KSHV genomic structural model. The latent KSHV genome formed very similar TAD structures among three different naturally infected PEL cell lines. more...

Organism:

Human gammaherpesvirus 8; Homo sapiens

Type:

Other

Platform:

GPL25719

10 Samples

Download data: HIC

(Submitter supplied) lncRNAs regulate protein functions via formation of protein-RNA complexes. Previous studies have shown that expression of viral lncRNA, polyadenylated nuclear RNA (PAN RNA) is essential for inducible viral genomic looping and distal gene activation during Kaposi's sarcoma-associated herpesvirus (KSHV) reactivation. Here we show an underlying molecular mechanism and regulation of KSHV latency by a viral lncRNA-CHD4 (chromodomain helicase DNA binding protein 4) interaction. more...

Organism:

Human gammaherpesvirus 8; Homo sapiens

Type:

Other

Platform:

GPL25719

12 Samples

Download data: HIC

(Submitter supplied) lncRNAs regulate protein functions via formation of protein-RNA complexes. Previous studies have shown that expression of viral lncRNA, polyadenylated nuclear RNA (PAN RNA) is essential for inducible viral genomic looping and distal gene activation during Kaposi's sarcoma-associated herpesvirus (KSHV) reactivation. Here we show an underlying molecular mechanism and regulation of KSHV latency by a viral lncRNA-CHD4 (chromodomain helicase DNA binding protein 4) interaction. more...

Organism:

Human gammaherpesvirus 8; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25719

30 Samples

Download data: BW

(Submitter supplied) Herpesviruses rely on host cell transcription and translation machineries for replication. Viral proteins thus function to redirect multiple cellular proteins for viral replication. In herpesvirus replicating cells, host cell gene transcription is frequently down-regulated because important transcriptional apparatuses are appropriated by viral transcription factors. Here we show that an evolutionally-shaped viral protein sequence is a great starting material for unique drug development to modulate cellular transcription. more...

Organism:

Human gammaherpesvirus 8; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL30065

15 Samples

Download data: BW

(Submitter supplied) Cancer cells of primary effusion lymphoma (PEL) often contain both Kaposi sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV). We measured the interplay of human, KSHV, and EBV transcription in a cell culture model of PEL using single-cell RNA sequencing. The data detect widespread trace expression of lytic KSHV genes.

Organism:

human gammaherpesvirus 4; Homo sapiens; Human gammaherpesvirus 8

Type:

Expression profiling by high throughput sequencing

Platform:

GPL28902

2 Samples

Download data: CSV

(Submitter supplied) ORF24 is the core component of a virally encoded transcription complex in KSHV that is active during later stages of infection. ORF24 makes interactions with both promoter DNA and host RNA polymerase II. The aim of this study was to identify the targets of the virally encoded transcription complex by sequencing total RNA from cells that express a mutant ORF24 that does not interact with RNA polymerase II and compare it to RNA from a mutant rescue cell line (WT). more...

Organism:

Homo sapiens; Human gammaherpesvirus 8

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25719

9 Samples

Download data: TXT

(Submitter supplied) We report the mapping of the genome-wide binding sites of a central component of a viral transcription complex from KSHV. We find that ORF34 binds at several locations on the viral genome but observed no detectable binding to the host genome. A majority of binding sites on the viral genome were upstream of known transcription start sites of mapped genes.

Organism:

Human gammaherpesvirus 8; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25719

8 Samples

Download data: TDF

(Submitter supplied) 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. more...

Organism:

Macacine gammaherpesvirus 4; Homo sapiens; Mus musculus; Human gammaherpesvirus 8; Macaca mulatta; Murid herpesvirus 68

Type:

Other

Platforms:

GPL25719 GPL26009 GPL26010

10 Samples

Download data: BED

(Submitter supplied) The purpose was to detect viral circular RNAs from infected cells.

Organism:

Homo sapiens; Human gammaherpesvirus 8

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25719

8 Samples

Download data: BED

(Submitter supplied) Purpose: We used RNA deep sequencing to characterize KSHV expression in a large collection of KS biopsies (n=41) from HIV-infected Ugandans. Using a novel approach to quantitate expression in complex genomes like KSHV, we found that RNA from a single KSHV promoter within the latency region constituted the majority of KSHV transcripts in the KS tumors. Alternate RNA processing produced different spliced and un-spliced transcripts with different coding potentials. more...

Organism:

Human gammaherpesvirus 8

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25233

41 Samples

Download data: GFF, TXT, XLS

(Submitter supplied) Using chromatin conformation capture methods, we learned that the latent episome of the human Epstein-Barr virus (EBV) displays preferential chromosome association that correlates with gene density. The episome avoids gene-rich chromosomes and favors gene-poor chromosomes. Kaposi’s sarcoma-associated herpesvirus behaves similarly, but human papillomavirus does not, suggesting limited evolutionary conservation of this strategy. more...

Organism:

Human gammaherpesvirus 8; Homo sapiens; Human papillomavirus 16; human gammaherpesvirus 4; human papillomavirus 31

Type:

Other

6 related Platforms

32 Samples

Download data: TXT

(Submitter supplied) KSHV K8 is required for KSHV DNA replication and is found to be an RNA binding protein. To understand the molecular mechanism of K8 in regulation of DNA replication, we examine the binding RNAs of K8 protein in BCBL-1 cells using CLIP-Seq analysis.

Organism:

Human gammaherpesvirus 8; Homo sapiens

Type:

Other

Platforms:

GPL24095 GPL16791

4 Samples

Download data: TXT

(Submitter supplied) ZIC2 is required for the maintenance of KSHV latency in human host cells. To understand the molecular action of ZIC2, we map ZIC2 binding sites across the KSHV genome in BCBL-1 cells using ChIP-Seq analysis.

Organism:

Human gammaherpesvirus 8; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23888

4 Samples

Download data: BED

(Submitter supplied) The objective of this study was to identify the symmetric methylation sites on KSHV genome during latency and lytic reactivation

Organism:

Human gammaherpesvirus 8

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL23366

8 Samples

Download data: WIG

(Submitter supplied) Virus-like vesicles (VLVs) are membrane derived cellular vesicles that resemble native envelope viruses in organization and conformation, but lack viral capsid and/or genome. During productive virus infection, both infectious virions and non-infectious VLVs are produced and released into the extracellular space. VLVs have been shown to play a role in intercellular communication and in facilitating virus infection. more...

Organism:

Homo sapiens; Human gammaherpesvirus 8

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19367

1 Sample

Download data: XLSX