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Items: 1 to 20 of 167

1.

Widespread traces of lytic KSHV in primary effusion lymphoma at single-cell resolution

(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; Human gammaherpesvirus 8; Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL28902
2 Samples
Download data: CSV
Series
Accession:
GSE154900
ID:
200154900
2.

RNA sequencing analysis to identify gene targets of Kaposi's sarcoma herpesvirus (KSHV) ORF24

(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:
Human gammaherpesvirus 8; Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25719
9 Samples
Download data: TXT
Series
Accession:
GSE126602
ID:
200126602
3.

Genome-wide map of viral transcription factor ORF34 binding in Kaposi's Sarcoma Herpesvirus (KSHV)

(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
Series
Accession:
GSE126601
ID:
200126601
4.

Comparative Analysis of Gammaherpesvirus Circular RNA

(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:
Human gammaherpesvirus 8; Macacine gammaherpesvirus 4; Macaca mulatta; Murid herpesvirus 68; Homo sapiens; Mus musculus
Type:
Other
Platforms:
GPL26009 GPL25719 GPL26010
10 Samples
Download data: BED
5.

RNA sequencing for KSHV circular RNAs

(Submitter supplied) The purpose was to detect viral circular RNAs from infected cells.
Organism:
Human gammaherpesvirus 8; Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL25719
8 Samples
Download data: BED
Series
Accession:
GSE121756
ID:
200121756
6.

Quantitative RNAseq analysis of Ugandan KS tumors reveals KSHV gene expression dominated by transcription from the LTd downstream latency promoter

(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
Series
Accession:
GSE116160
ID:
200116160
7.

The Epstein-Barr virus episome maneuvers between nuclear chromatin compartments during reactivation [HiC-seq]

(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 4; Human gammaherpesvirus 8; human papillomavirus 31; Human papillomavirus type 16; Homo sapiens
Type:
Other
6 related Platforms
32 Samples
Download data: TXT
8.

K8 CLIP-Seq in KSHV reactivated BCBL-1 cells

(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
9.

ZIC2 ChIP-Seq in KSHV latent and lytic reactivated BCBL-1 cells

(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
Series
Accession:
GSE102462
ID:
200102462
10.

Identification of symmetric methylation of histone H4 arginine 3 on KSHV genome (H4R3me2s ChIP-Seq)

(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
Series
Accession:
GSE100044
ID:
200100044
11.

Virus-like vesicles of Kaposi’s Sarcoma-Associated Herpesvirus activate lytic replication through triggering differentiation signaling (microRNA)

(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:
Human gammaherpesvirus 8; Homo sapiens
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL19367
1 Sample
Download data: XLSX
Series
Accession:
GSE91385
ID:
200091385
12.

Virus-like vesicles of Kaposi’s Sarcoma-Associated Herpesvirus activate lytic replication through triggering differentiation signaling (mRNA)

(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:
Human gammaherpesvirus 8; Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL11154 GPL19367
14 Samples
Download data: XLSX
Series
Accession:
GSE91384
ID:
200091384
13.

Identification of symmetric methylation of histone H4 arginine 3 on KSHV genome (iSLKBac16WT ChIP-Seq)

(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
4 Samples
Download data: WIG
Series
Accession:
GSE98087
ID:
200098087
14.

Identification of symmetric methylation of histone H4 arginine 3 on KSHV genome (TREx Und 12h 24hInd ChIP-Seq)

(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
10 Samples
Download data: WIG
Series
Accession:
GSE98057
ID:
200098057
15.

KSHV Infection Mimics the Hypoxic Response Based on Next-Generation Sequencing [miRNA-Seq]

(Submitter supplied) Purpose: Kaposi’s sarcoma associated-herpesvirus (KSHV) causes several hyperproliferative disorders, including Kaposi’s sarcoma, primary effusion lymphoma and multicentric Castleman’s disease. KSHV encodes for a number of microRNAs (miRNAs), and KSHV infection can affect the expression of cellular miRNAs. Hypoxia has been shown to induce KSHV reactivation, directly induce several KSHV lytic genes, and also induce the most abundant latent viral protein, LANA. more...
Organism:
Homo sapiens; Human gammaherpesvirus 8
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL11154
6 Samples
Download data: BEDGRAPH, CSV
Series
Accession:
GSE79030
ID:
200079030
16.

Next-Generation Sequencing Analysis Reveals Differential Expression Profiles of miRNA-mRNA Target Pairs in KSHV-Infected Cells [mRNA-Seq]

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. Purpose: Kaposi’s sarcoma (KS)-associated herpesvirus (KSHV) causes several lymphoproliferative disorders, including KS, a common AIDS-associated malignancy. Cellular and viral microRNAs (miRNAs) have been shown to play important roles in regulating the expression of genes in oncogenesis. Herpesviruses, including KSHV, encode for miRNAs that are involved in angiogenesis, inflammation and apoptosis. more...
Organism:
Human gammaherpesvirus 8; Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL19367 GPL11154
6 Samples
Download data: BEDGRAPH
Series
Accession:
GSE62829
ID:
200062829
17.

Next-Generation Sequencing Analysis Reveals Differential Expression Profiles of miRNA-mRNA Target Pairs in KSHV-Infected Cells [microRNA-Seq]

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below. Purpose: Kaposi’s sarcoma (KS)-associated herpesvirus (KSHV) causes several lymphoproliferative disorders, including KS, a common AIDS-associated malignancy. Cellular and viral microRNAs (miRNAs) have been shown to play important roles in regulating the expression of genes in oncogenesis. Herpesviruses, including KSHV, encode for miRNAs that are involved in angiogenesis, inflammation and apoptosis. more...
Organism:
Homo sapiens; Human gammaherpesvirus 8
Type:
Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL19367 GPL11154
6 Samples
Download data: BEDGRAPH
Series
Accession:
GSE62828
ID:
200062828
18.

Transcriptome Analysis of KSHV virions produced from BCBL1 and BAC36 in 293L cells

(Submitter supplied) The objective of this study was to identify the viral transcripts packaged into the virion particles produced from BCBL1 cells as well as virions from 293L cells containing BAC36 BACs
Organism:
Human gammaherpesvirus 8
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17680
3 Samples
Download data: CSV
Series
Accession:
GSE62343
ID:
200062343
19.

Transcriptome Analysis of KSHV during de novo primary infection of endothelial (TIVE) cells

(Submitter supplied) The objective of this study was to identify the viral transcripts packaged into the virion particles and the transcription profiles of the viral genome during early infection, till the virus establishes latent infection in endothelial (TIVE) cells
Organism:
Human gammaherpesvirus 8
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17680
5 Samples
Download data: CSV
Series
Accession:
GSE62342
ID:
200062342
20.

Transcriptome Analysis of KSHV during de novo primary infection of human B cells (PBMCs)

(Submitter supplied) The objective of this study was to identify the viral transcripts packaged into the virion particles and the transcription profiles of the viral genome during early infection, till the virus establishes latent infection in human PBMCs
Organism:
Human gammaherpesvirus 8
Type:
Expression profiling by high throughput sequencing
Platform:
GPL17680
5 Samples
Download data: CSV
Series
Accession:
GSE62341
ID:
200062341
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