GEO DataSets

(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) Chromatin-organizing factors, like CTCF and cohesins, have been implicated in the control of complex viral regulatory programs. We investigated the role of CTCF and cohesin in the control of the latent to lytic switch for Kaposi's Sarcoma-Associated Herpesvirus (KSHV). We found that cohesin subunits, but not CTCF, were required for the repression of KSHV immediate early gene transcription. Depletion of cohesin subunits Rad21, SMC1, or SMC3 resulted in lytic cycle gene transcription and viral DNA replication. more...

Organism:

Human gammaherpesvirus 8; Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL9115 GPL15642

5 Samples

Download data: BED, WIG

(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) Purpose: RNA sequencing (RNA-seq) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. In addition, we have already registered the transcriptome analysis results of HMGB1 KO iSLK BAC16 cell in GSE157275, and this registration is to reproduce it.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: XLSX

(Submitter supplied) Purpose: RNA sequencing (RNA-seq) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

4 Samples

Download data: XLSX

(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) To investigate the regulation of ER stress-related gene expression by KSHV-ORF45 during lytic replication, we performed RNA-sequencing analysis of iSLK-BAC16 vs. iSLK-STOP45 cells under lytic induction for 72h. When the differentially expressed genes were filtered and analyzed, we found that ER stress-related gene expression was much low in iSLK-STOP45 cells compared with iSLK-BAC16 cells, indicating that ORF45 expression is required for induction of ER stress.To further reveal the signal transduction of LAMP3 in KSHV lytic replication, RNA-sequencing analysis was performed to identify the differentially expressed genes (DEGs) in normal vs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24676

8 Samples

Download data: TXT

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

Organism:

Homo sapiens; Human gammaherpesvirus 8

Type:

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

Platforms:

GPL19367 GPL11154

15 Samples

Download data: XLSX

(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

(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:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL19367

14 Samples

Download data: XLSX

(Submitter supplied) The Kaposi's sarcoma-associated herpesvirus (KSHV) genome consists of an approximately 140 kb unique coding region flanked by 30-40 copies of 0.8 kb terminal repeat (TR) sequence. KSHV genomes persist in latently infected cells as episomes via tethering to the host cell chromosomes, and KSHV latency associated nuclear antigen (LANA) plays a crucial role in latent episomal DNA replication and segregation during host cell mitosis by binding to TR. more...

Organism:

Homo sapiens

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL24676

44 Samples

Download data: BIGWIG, BW

(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) 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