GEO DataSets

(Submitter supplied) Lytic activation from latency is a key transition point in the life cycle of herpesviruses. Epstein-Barr virus (EBV) is a human herpesvirus that can cause lymphomas, epithelial cancers, and other diseases, most of which require the lytic cycle. While the lytic cycle of EBV can be triggered by chemicals and immunologic ligands, the lytic cascade is only activated when expression of the EBV latency-to-lytic switch protein ZEBRA is turned on. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platform:

GPL16791

12 Samples

Download data: TXT

(Submitter supplied) We used microarrays to identify genes differentially expressed in EBV-infected human B cells supporting lytic replication vs. those refractory to EBV lytic replication.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL570

2 Samples

Download data: CEL, CHP

(Submitter supplied) We used Precision Nuclear Run-on followed by Deep Sequencing (PRO-Seq) to investigate RNA Polymerase (Pol) activity during Epstein-Barr Virus (EBV) reactivation and its link to CTCF in latently EBV infected ymphoblastoid cell lines (LCLs). Nuclei were harvested from WT LCLs or LCLs containing an 18bp deletion at the LMP CTCF binding site (DCTCF) treated with DMSO or induced to reactivate with the small molecule C60 for 24h. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL21697

8 Samples

Download data: BW

(Submitter supplied) We used Precision Nuclear Run-on followed by Deep Sequencing (PRO-Seq) to investigate RNA Polymerase (Pol) activity during Epstein-Barr Virus (EBV) reactivation in EBV positive Burkitt's lymphoma cell lines Mutu-I and Akata. Nuclei were harvested from latent cells and after treatment with NaB/TPA (Mutu-I) or anti-IgG (akata) to stimulate reactivation at 1 and 4 and 12h. We identified multiple sites on the EBV genome enriched with Pol displaying distinct patterns of activity, which showed an association with CTCF and open chromatin.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

23 Samples

Download data: BW

(Submitter supplied) EBNA1 is the EBV-encoded nuclear antigen required for viral episome maintenance during latency. EBNA1 is a sequence specific DNA binding protein with high affinity binding sites for the viral genome, especially OriP. EBNA1 can also bind sequence specifically to a large number of sites in the host cellular genome, but the function of these binding sites has remained elusive. EBNA1 is also known to provide a host cell survival function, but the molecular mechanisms accounting for this function are not completely understood. more...

Organism:

Homo sapiens

Type:

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

Platforms:

GPL16791 GPL9115

12 Samples

Download data: TXT

(Submitter supplied) RNAseq was used to identify host and EBV viral transcriptome changes in CHAF1B knock-out Akata EBV+ cells. CHAF1B KO Akata EBV+ cells were subjected to RNAseq analysis. The Akata EBV+ cells expressing control sgRNA was used as the control.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: CSV

(Submitter supplied) Burkitt lymphoma cells can be latently infected with Epstein-Barr virus (EBV). The virus may be activated into its lytic cycle by small molecules, such as sodium butyrate. Other molecules, such as valproate and valpromide, block viral lytic reactivation. These pharmacological agents alter the cellular physiology that controls viral lytic gene expression. Changes in the cellular transcription were measured in response to one activator and two inhibitors of the Epstein-Barr virus lytic cycle in order to identify cellular genes that are potential regulators of the viral life cycle.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

12 Samples

Download data: TXT

(Submitter supplied) To understand the changes in global transcriptomic landscape during the EBV lytic cycle reactivation from lymphoblastoid cell lines (LCLs), RNA-seq was performed. By examining the transcriptomic changes, we obtained valuable insights into the molecular events and regulatory mechanisms involved in EBV reactivation into lytic cycle replication. The study also enhances our knowledge of the complex interplay between EBV and the host cells during its lytic cycle.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL24014

6 Samples

Download data: XLSX

(Submitter supplied) In order to gain insights into the intricate molecular alterations taking place following Epstein-Barr virus (EBV) infection in primary B-cells, we employed RNA-Seq to investigate the dynamic changes occurring within the cell transcriptome during the early stages of EBV infection (0, 2, and 4 days post infection). By analysing the transcriptomic data generated, our objective was to find novel pathways and mechanisms that may play pivotal roles in the EBV-induced transformation of B-cells, particularly during early stage of B-cell activation.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

5 Samples

Download data: XLSX

(Submitter supplied) Epstein Barr Virus (EBV) is a potentially oncogenic gammaherpesvirus that establishes a chronic, latent infection in memory B cells. The EBV genome persists in infected host cells as a chromatinized episome and is subject to chromatin-mediated regulation. Binding of the host insulator protein CTCF to the EBV genome has an established role in maintaining viral latency type. CTCF is post-translationally modified by the host enzyme PARP1. more...

Organism:

human gammaherpesvirus 4

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL25190

8 Samples

Download data: BED, BEDGRAPH, BW, NARROWPEAK

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

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

30 Samples

Download data

(Submitter supplied) RNAseq was used to identify host and viral transcriptome changes in xenograft tumors treated with DMSO or CBL0137. Mouse xenograft experiments were regulated by Institutional Animal Care & Use Committee (IACUC# 2017-0035) of Weill Cornell Medical Center(WCMC). Non-obese diabetic/severe combined immunodeficiency (NOD-SCID) mice were obtained from Jackson Laboratories. Six to eight-week-old male and female mice (10 male/18 female) were injected in the flank with 1 x 107 BL cells in PBS with Matrigel eleven days before the treatment. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

6 Samples

Download data: XLSX

(Submitter supplied) To gain insights into how EBV latency is maintained, we performed a human genome-wide CRISPR screen in latently EBV-infected Burkitt lymphoma B-cells. Our analyses identified a network of host factors that repress EBV lytic reactivation, centered on the transcription factor MYC and including cohesins, FACT, STAGA and Mediator. RNAseq was used to identify host and viral transcriptome changes in P3HR-1 Burkitt lymphoma cells expressing control, smc1a, supt16h, med12, or tada2b sgRNAs. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18573

24 Samples

Download data: CSV

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

Organism:

Human gammaherpesvirus 8; Homo sapiens

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:

Human gammaherpesvirus 8; Homo sapiens

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:

Human gammaherpesvirus 8; Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL11154 GPL19367

14 Samples

Download data: XLSX

(Submitter supplied) Epstein-Barr virus (EBV) Rta is a latent-lytic molecular switch evolutionarily conserved in all gamma-herpesviruses. In previous studies, doxycycline-inducible Rta was shown to potently produce an irreversible G1 arrest followed by cellular senescence in 293 cells. Here, we demonstrate that in this system the inducible Rta not only reactivates resident genome of EBV but also that of Kaposi’s sarcoma-associated herpesvirus (KSHV), to similar efficiency. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

7 Samples

Download data: CEL

(Submitter supplied) EBV Rta is a transcriptional activator that functions to disrupt EBV latency in cells of epithelial origin. This series of experiment is to identify host genes that are moduated by the expression of doxycycline-inducible EBV Rta in nasopharyngeal carcinoma cells. Designations for the two EBV Rta inducible cell lines are TW01TetER_cl7 (lower expression level) and TW01TetER_cl19 (higher expression level); for the control line is TW01Tet.

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

3 Samples

Download data: CEL, TXT

(Submitter supplied) EBV Rta is a transcriptional activator that functions to disrupt EBV latency in cells of epithelial origin. This series of experiment is to identify host genes that are moduated by the expression of doxycycline-inducible EBV Rta in HEK293 cells. Designations for the pooled EBV Rta inducible cell lines is 293TetER; pooled luciferase inducible lines is 293TetLuc (control).

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL6244

4 Samples

Download data: CEL, TXT

(Submitter supplied) Epstein-Barr virus (EBV) is a human gamma-herpesvirus that is causally associated with various lymphomas and carcinomas. Although EBV is not typically associated with multiple myeloma (MM), it can be found in some B-cell lines derived from multiple myeloma patients. Here, we analyzed two EBV+ MM-patient derived cell lines IM9 and ARH77 and found defective viral genomes and atypical viral gene expression patterns. more...

Organism:

Homo sapiens

Type:

Other

Platform:

GPL18573

2 Samples

Download data: TXT