Similar studies for GEO DataSets (Select 200239989) - GEO DataSets

Select item 2002399891.

The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC [HiC]

(Submitter supplied) Epstein-Barr virus (EBV) establishes lifelong asymptomatic infection by replication of its chromatinized episomes with the host genome. EBV exhibits different latency-associated transcriptional repertoires, each with distinct three-dimensional structures. CTCF, Cohesin and PARP1 are involved in maintaining viral latency and establishing episome architecture. Epstein-Barr virus-associated gastric cancer (EBVaGC) represents 1.3% to 30.9% of all gastric cancers globally. more...

Organism:: human gammaherpesvirus 4

Type:: Other

Platform:: GPL25190
10 Samples

Download data: TXT

Series

Accession:: GSE239989

ID:: 200239989

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Select item 2002399952.

The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC

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

Organism:: Homo sapiens; human gammaherpesvirus 4

Type:: Genome binding/occupancy profiling by high throughput sequencing; Other; Expression profiling by high throughput sequencing

Platforms:: GPL25190 GPL23185
29 Samples

Download data: BEDPE, BW, NARROWPEAK, TXT

Series

Accession:: GSE239995

ID:: 200239995

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Select item 2002399943.

The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC [RNA-seq]

(Submitter supplied) Epstein-Barr virus (EBV) establishes lifelong asymptomatic infection by replication of its chromatinized episomes with the host genome. EBV exhibits different latency-associated transcriptional repertoires, each with distinct three-dimensional structures. CTCF, Cohesin and PARP1 are involved in maintaining viral latency and establishing episome architecture. Epstein-Barr virus-associated gastric cancer (EBVaGC) represents 1.3% to 30.9% of all gastric cancers globally. more...

Organism:: Homo sapiens; human gammaherpesvirus 4

Type:: Expression profiling by high throughput sequencing

Platform:: GPL23185
3 Samples

Download data: TXT

Series

Accession:: GSE239994

ID:: 200239994

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Select item 2002399924.

The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC [HiChIP]

(Submitter supplied) Epstein-Barr virus (EBV) establishes lifelong asymptomatic infection by replication of its chromatinized episomes with the host genome. EBV exhibits different latency-associated transcriptional repertoires, each with distinct three-dimensional structures. CTCF, Cohesin and PARP1 are involved in maintaining viral latency and establishing episome architecture. Epstein-Barr virus-associated gastric cancer (EBVaGC) represents 1.3% to 30.9% of all gastric cancers globally. more...

Organism:: Homo sapiens; human gammaherpesvirus 4

Type:: Other

Platform:: GPL23185
4 Samples

Download data: BEDPE, TXT

Series

Accession:: GSE239992

ID:: 200239992

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Select item 2002399875.

The three-dimensional structure of the EBV genome plays a crucial role in regulating viral gene expression in EBVaGC [ChIP-seq]

(Submitter supplied) Epstein-Barr virus (EBV) establishes lifelong asymptomatic infection by replication of its chromatinized episomes with the host genome. EBV exhibits different latency-associated transcriptional repertoires, each with distinct three-dimensional structures. CTCF, Cohesin and PARP1 are involved in maintaining viral latency and establishing episome architecture. Epstein-Barr virus-associated gastric cancer (EBVaGC) represents 1.3% to 30.9% of all gastric cancers globally. more...

Organism:: human gammaherpesvirus 4

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL25190
12 Samples

Download data: BW, NARROWPEAK

Series

Accession:: GSE239987

ID:: 200239987

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Select item 2002346586.

Decitabine disrupts EBV genomic epiallele DNA methylation patterns around CTCF binding sites to increase chromatin accessibility and lytic transcription in gastric cancer

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

Organism:: human gammaherpesvirus 4

Type:: Methylation profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL25190 GPL33481
16 Samples

Download data: BW, COV

Series

Accession:: GSE234658

ID:: 200234658

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Select item 2002346037.

Decitabine disrupts EBV genomic epiallele DNA methylation patterns around CTCF binding sites to increase chromatin accessibility and lytic transcription in gastric cancer [ChIP-seq]

(Submitter supplied) To investigate the EBV genome after Decitabine treatment by CTCF ChIP-seq

Organism:: human gammaherpesvirus 4

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL33481
8 Samples

Download data: BW

Series

Accession:: GSE234603

ID:: 200234603

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Select item 2001158298.

PARP1 Stabilizes CTCF Binding and Chromatin Structure to Maintain Epstein Barr Virus Latency Type

(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

Series

Accession:: GSE115829

ID:: 200115829

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Select item 2001609739.

The three-dimensional structure of Epstein-Barr virus genome varies by latency type and is regulated by PARP1 enzymatic activity

(Submitter supplied) Epstein-Barr virus (EBV) establishes life-long latency in human B-cells by maintaining its chromatinized episomes within the nucleus. These circularized mini-chromosomes do not integrate into the host genome. Therefore, it is essential for EBV to organize its chromatin in a manner suitable for genomic stability, DNA replication, and efficient gene expression. Poly [ADP-ribose] polymerase 1 (PARP1) activity is significantly higher in B-cells infected with EBV than those without, and considerably higher in the transcriptionally active type III latency compared to the immunoevasive type I. more...

Organism:: Homo sapiens

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platforms:: GPL16791 GPL18573
8 Samples

Download data: BW, TXT

Series

Accession:: GSE160973

ID:: 200160973

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Select item 20015983710.

The three-dimensional structure of Epstein-Barr virus genome varies by latency type and is regulated by PARP1 enzymatic activity

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

Organism:: Homo sapiens; human gammaherpesvirus 4

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

Platforms:: GPL9052 GPL25190
16 Samples

Download data: BEDGRAPH, BROADPEAK, BW

Series

Accession:: GSE159837

ID:: 200159837

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Select item 20015983611.

The three-dimensional structure of Epstein-Barr virus genome varies by latency type and is regulated by PARP1 enzymatic activity [RNA-Seq]

(Submitter supplied) PARP does have an essential role in the regulation of global EBV episome chromatin structure. We have functionally characterized the effect of PARP enzymatic inhibition on total episomal structure and we mapped intragenomic contact changes after PARP inhibition to global binding of the chromatin looping factors CTCF and cohesin across the EBV genome. The altered expression profile after the structural rearrangement induced by PARP inhibition supports the model where PARP1 helps maintain EBV latency programs.

Organism:: Homo sapiens

Type:: Expression profiling by high throughput sequencing

Platform:: GPL9052
8 Samples

Download data: CSV

Series

Accession:: GSE159836

ID:: 200159836

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Select item 20015983412.

The three-dimensional structure of Epstein-Barr virus genome varies by latency type and is regulated by PARP1 enzymatic activity [ChIP-Seq]

(Submitter supplied) PARP does have an essential role in the regulation of global EBV episome chromatin structure. We have functionally characterized the effect of PARP enzymatic inhibition on total episomal structure and we mapped intragenomic contact changes after PARP inhibition to global binding of the chromatin looping factors CTCF and cohesin across the EBV genome. The altered expression profile after the structural rearrangement induced by PARP inhibition supports the model where PARP1 helps maintain EBV latency programs.

Organism:: human gammaherpesvirus 4

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL25190
8 Samples

Download data: BEDGRAPH, BROADPEAK, BW

Series

Accession:: GSE159834

ID:: 200159834

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Select item 20015405213.

Epstein-Barr Virus episome physically interacts with active regions of the host genome in lymphoblastoid cells

(Submitter supplied) Epstein-Barr virus (EBV) episome is known to interact with the three-dimensional structure of human genome in infected cells. However, the exact locations of these interactions and their potential functional consequences remain unclear. Recently the high-resolution chromatin interaction capture (Hi-C) assays in lymphoblastoid cells have become available enabling us to precisely map the contacts between the EBV episome(s) and the human host genome. more...

Organism:: Homo sapiens

Type:: Other

Platform:: GPL11154
2 Samples

Download data: BED

Series

Accession:: GSE154052

ID:: 200154052

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Select item 20021124714.

Dysregulation of RNA Pol activity at CTCF binding sites in EBV LCL ΔCTCF mutant

(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

Series

Accession:: GSE211247

ID:: 200211247

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Select item 20018858415.

Increased RNA Polymerase Activity at CTCF binding sites on the Epstein Barr Virus Genome During Reactivation from Latency

(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

Series

Accession:: GSE188584

ID:: 200188584

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Select item 20019895416.

The Nuclear Lamina Binds the EBV Genome During Latency and Regulates Viral Gene Expression

(Submitter supplied) Several cellular factors, including the nuclear lamina, regulate chromatin composition and architecture. While the interaction of the viral genome with the nuclear lamina has been studied in the context of EBV lytic reactivation, the role of the nuclear lamina in controlling EBV latency has not been investigated. Here, we report that the nuclear lamina is an essential epigenetic regulator of the EBV episome.

Organism:: human gammaherpesvirus 4

Type:: Genome binding/occupancy profiling by high throughput sequencing

Platform:: GPL25190
5 Samples

Download data: BEDGRAPH

Series

Accession:: GSE198954

ID:: 200198954

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Select item 20019841317.

Nuclear Lamina binds the EBV genome during latency and regulates viral gene expression

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

Organism:: Homo sapiens; human gammaherpesvirus 4

Type:: Expression profiling by high throughput sequencing; Other

Platform:: GPL30446
14 Samples

Download data: MATRIX

Series

Accession:: GSE198413

ID:: 200198413

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Select item 20019841218.

Nuclear lamina binds the EBV genome during latency and regulates viral gene expression [Hi-C]

(Submitter supplied) Approximately 90% of the world population is infected with EBV and carries the virus in a silent, asymptomatic state for life. In immunocompromised individuals, EBV infection can cause B-cell transformation and malignancies. One approach to control EBV infectivity is by changing the expression of viral genes. We are interested in how epigenetics contributes to regulating the gene expression patterns adopted by EBV during latency. more...

Organism:: Homo sapiens; human gammaherpesvirus 4

Type:: Other

Platform:: GPL30446
4 Samples

Download data: BED, MATRIX

Series

Accession:: GSE198412

ID:: 200198412

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Select item 20018101219.

Nuclear Lamina binds the EBV genome during latency and regulates viral gene expression [RNA-seq]

(Submitter supplied) Approximately 90% of the world population is infected with EBV and carries the virus in a silent, asymptomatic state for life. In immunocompromised individuals, EBV infection can cause B-cell transformation and malignancies. One approach to control EBV infectivity is by changing the expression of viral genes. We are interested in how epigenetics contributes to regulating the gene expression patterns adopted by EBV during latency. more...