GEO DataSets

(Submitter supplied) Expression profiling of latently infected cells using a custom tiling microarray HUVEC and TIME cells were infected BCBL-1-derived KSHV. Mock infected HUVEC and TIME cells served as controls for each of these two stably infected cells, respectively. BJAB cells served as uninfected controls for the BCBL-1 cells. KSHV-infected cells are induced to enter lytic cycle with valproate or Adenovirus-RTA. Cells were harvested at indicated time points and analyzed.

Organism:

Homo sapiens; Human herpesvirus 8 type M

Type:

Expression profiling by genome tiling array

Platform:

GPL10083

20 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) 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) The purpose was to measure expression changes in human circular RNAs. Total RNA was harvested from KSHV-infected HUVEC and MC116 cells. A portion of the RNA was digested with RNase R to enrich for circular RNAs.

Organism:

Homo sapiens

Type:

Non-coding RNA profiling by array

Platform:

GPL19977

12 Samples

Download data: GPR

(Submitter supplied) The purpose was to measure expression changes in human and viral circular RNAs.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16791

20 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:

Homo sapiens; Human gammaherpesvirus 8

Type:

Other

Platforms:

GPL24095 GPL16791

4 Samples

Download data: TXT

(Submitter supplied) CTCF and the cohesin complex modify chromatin by binding to DNA and interacting with each other and with other cellular proteins. Both proteins regulate transcription by a variety of local effects on transcription and by long range topological effects. CTCF and cohesin also bind to herpesvirus genomes at specific sites and regulate viral transcription during latent and lytic cycles of replication. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16791

9 Samples

Download data: TXT

(Submitter supplied) CTCF and the cohesin complex modify chromatin by binding to DNA and interacting with each other and with other cellular proteins. Both proteins regulate transcription by a variety of local effects on transcription and by long range topological effects. CTCF and cohesin also bind to herpesvirus genomes at specific sites and regulate viral transcription during latent and lytic cycles of replication. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL16791

9 Samples

Download data: BW

(Submitter supplied) Kaposi's sarcoma-associated herpesvirus (KSHV) is a human oncogenic virus, which maintains the persistent infection of the host by intermittently reactivating from latently infected cells to produce viral progenies. Here, we performed a comprehensive time course transcriptome analysis during KSHV reactivation in KSHV+ primary effusion B-cell lymphoma cells (PEL). For this we used a recombinant PEL cell line called TRExBCBL1-3xFLAG-RTA. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

12 Samples

Download data: TXT

(Submitter supplied) Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) analysis was performed during Kaposi's sarcoma-associated herpesvirus (KSHV) reactivation in KSHV+ recombinant primary effusion B-cell lymphoma cells (PEL). RTA binding sites were identified genome-wide in a recombinant PEL cell line called TRExBCBL1-3xFLAG-RTA cells at 12 hours post-induction (hpi) of RTA expression.

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL18573

2 Samples

Download data: TXT

(Submitter supplied) BCBL-1 cells were induced with 20 ng/ml TPA either in the absence (U) or presence (+) of 100 µM cidofovir (CDV) treatment and collected at 0, 6, 8, 10, 12, 24, 36, 48, 72, 96 hours (h) post-TPA addition, and compared against untreated (U), uninduced latent BCBL-1 reference cells. Three biological repeats were performed. Keywords = Kaposi's sarcoma-associated herpesvirus Keywords = KSHV Keywords = human herpesvirus type 8 Keywords = HHV-8 Keywords = primary effusion lymphoma (PEL) cells Keywords = body-cavity based lymphoma-1 (BCBL-1) cells Keywords = lytic induction Keywords = 12-O-tetradecanoylphorbol-13-acetate (TPA) Keywords = viral replication inhibition Keywords = cidofovir (CDV) Keywords: time-course

Organism:

Human gammaherpesvirus 8; Homo sapiens

Type:

Expression profiling by array

Platform:

GPL1386

60 Samples

Download data: TIFF

(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) KS lesions consist of endothelial cells latently infected with KSHV which express the KSHV miRNAs. Identifying the targets of the KSHV miRNAs will help us understand their role in viral oncogenesis. Cross-Linking and Sequencing of Hybrids (CLASH) is a method for unambiguously identifying miRNA targetomes. We developed a streamlined version of CLASH, called quick CLASH (qCLASH). qCLASH requires a lower initial input of cells than its parent protocol. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL16791

9 Samples

Download data: TXT

(Submitter supplied) We have previously shown that the Epstein-Barr virus (EBV) likely encodes hundreds of viral long non-coding RNAs (vlncRNAs) that are expressed during reactivation. Here we show that the EBV latency origin of replication (oriP) is transcribed bi-directionally during reactivation and that both leftward (oriPtLs) and rightward transcripts (oriPtRs) are largely localized in the nucleus. While the oriPtLs are most likely non-coding, at least some of the oriPtRs contain the BCRF1/vIL10 open reading frame. more...

Organism:

human gammaherpesvirus 4

Type:

Expression profiling by high throughput sequencing

Platform:

GPL20090

16 Samples

Download data: XLS

(Submitter supplied) [original title] Mock or latently infected KSHV cells (BCBL, SLK and HFF) vs common reference (mixture of RNA from both infected and uninfected cells). Expression profiling of latently infected cells using a custom tiling microarray. SLK and HFF cells were infected and selected for rKSHV.219. Mock infected SLK and HFF cells served as controls for each of these two stably infected cells, respectively. more...

Organism:

Homo sapiens; Human gammaherpesvirus 8; Human herpesvirus 8 type M; Human herpesvirus 8 strain rKSHV.219

Type:

Expression profiling by genome tiling array

Platform:

GPL10083

12 Samples

Download data: TXT