GEO DataSets

(Submitter supplied) Human SLK cells were infected with wildtype (wt) and LANA knockout (KO) Kaposi's sarcoma-associated herpesvirus (KSHV), separately for 3 days. Cellular gene expression changes were identified upon the wild type and LANA KO KSHV virus infection compared to the uninfected SLK cells using the human gene expression microarray U133plus2.0.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

6 Samples

Download data: CEL

(Submitter supplied) Latency-associated nuclear antigen (LANA), a multifunctional protein expressed by the Kaposi sarcoma-associated herpesvirus (KSHV) in latently-infected cells, is required for stable maintenance of the viral episome. This is mediated by two interactions: LANA binds to specific sequences (LBS1 and 2) on viral DNA, and also engages host histones, tethering the viral genome to host chromosomes in mitosis. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9115 GPL16791

33 Samples

Download data: BED, GTF, TXT

(Submitter supplied) Kaposi’s sarcoma-associated herpesvirus (KSHV) is a g-herpesvirus which persists as circular extrachromasomal DNA in the nucleus during latent infection. During latency a limited number of viral proteins are expressed, including LANA (latency-associated nuclear antigen). LANA is a multi-functional protein known to interact with transcriptional regulators and chromatin remodelers, and to regulate the LANA and RTA promoters. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL10999

18 Samples

Download data: TDF, WIG

(Submitter supplied) The establishment of latency is an essential step for the life-long persistent infection and pathogenesis of Kaposi’s sarcoma-associated herpesvirus (KSHV). While the KSHV genome is chromatin-free in the virions, the viral DNA in latently infected cells has a chromatin structure that is characterized by a specific pattern of activating and repressive histone modifications that ultimately promote latent gene expression while suppressing lytic gene expression. more...

Organism:

Human herpesvirus 8 type M; Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL17838

16 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Human gammaherpesvirus 8

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17680

24 Samples

Download data: CSV

(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

(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

(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

(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 B-cells as well as in endothelial cells

Organism:

Human gammaherpesvirus 8

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17680

5 Samples

Download data: CSV

(Submitter supplied) The objective of this study was to identify the transcription profiles of wild type KSHV and ORF59 deleted KSHV (Kaposi's sarcoma-associated herpesvirus) 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

6 Samples

Download data: CSV

(Submitter supplied) LANA is essential for tethering the KSHV genome to metaphase chromosomes and for modulating host-cell gene expression, but the binding sites in the host-chromosome remain unknown. Here, we use LANA-specific chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) to identify LANA binding sites in the viral and host-cell genomes of a latently infected pleural effusion lymphoma cell line BCBL1. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL9115

4 Samples

Download data: BED

(Submitter supplied) Kaposi’s Sarcoma-associated herpesvirus (KSHV) transcripts are subject to degradation by at least two host-mediated nuclear RNA decay pathways, PABPN1 and PAPα/γ-mediated RNA decay (PPD) and an ARS2-dependent decay pathway. KSHV expresses the multifunctional protein ORF57, which increases viral transcripts stability by protecting them preferentially from ARS2-dependent decay. However, a subset of viral transcripts succumb to PPD even in the presence of ORF57, but the role of PPD during KSHV infection is not completely understood. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

12 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; Human gammaherpesvirus 8

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

Platform:

GPL25719

42 Samples

Download data: BW, 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:

Homo sapiens; Human gammaherpesvirus 8

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) Higher order genome structure influences the transcriptional regulation of cellular genes through the juxtaposition of regulatory elements, such as enhancers, close to promoters of target genes. While enhancer activation has emerged as an important facet of Kaposi’s sarcoma-associated herpesvirus (KSHV) biology, mechanisms controlling enhancer-target gene expression remain obscure. Here, we discover that the KSHV genome tethering protein latency-associated nuclear antigen (LANA) potentiates enhancer-target gene expression in primary effusion lymphoma (PEL), a highly aggressive B cell lymphoma causally associated with KSHV. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL24676

67 Samples

Download data: BW, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Human gammaherpesvirus 8; Homo sapiens

Type:

Methylation profiling by genome tiling array; Genome binding/occupancy profiling by genome tiling array

Platform:

GPL9942

19 Samples

Download data: GPR

(Submitter supplied) Herpesvirus latency is generally thought to be governed by epigenetic modifications, but the dynamics of viral chromatin at early timepoints of latent infection are poorly understood. Here, we report a comprehensive spatial and temporal analysis of epigenetic modifications during latent infection with Kaposi's sarcoma associated herpesvirus (KSHV), the etiologic agent of Kaposi's sarcoma and primary effusion lymphoma (PEL). more...

Organism:

Human gammaherpesvirus 8; Homo sapiens

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL9942

12 Samples

Download data: GPR

(Submitter supplied) Herpesvirus latency is generally thought to be governed by epigenetic modifications, but the dynamics of viral chromatin at early timepoints of latent infection are poorly understood. Here, we report a comprehensive spatial and temporal analysis of epigenetic modifications during latent infection with Kaposi's sarcoma associated herpesvirus (KSHV), the etiologic agent of Kaposi's sarcoma and primary effusion lymphoma (PEL). more...

Organism:

Human gammaherpesvirus 8; Homo sapiens

Type:

Methylation profiling by genome tiling array

Platform:

GPL9942

8 Samples

Download data: GPR