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ATAC-seq experiment in two versions of Raji cells with inducible BZLF1 variants prior to and after induction of EBV's lytic cycle by doxycycline.

ABSTRACT: ATAC-seq experiment in two versions of Raji cells with inducible BZLF1 variants prior to and after induction of EBV's lytic cycle by doxycycline.

PROVIDER: PRJEB31755 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3225440.fastq.gz	Fastqsanger.gz
	ERR3225441.fastq.gz	Fastqsanger.gz
	ERR3225442.fastq.gz	Fastqsanger.gz
	ERR3225443.fastq.gz	Fastqsanger.gz
	ERR3225444.fastq.gz	Fastqsanger.gz

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ATAC-seq experiment in two versions of Raji cells with inducible BZLF1 variants prior to and after induction of EBV's lytic cycle by doxycycline.

Project description:The aim of the experiment was to identify accessible (open) chromatin regions in the genome prior to and post induction of EBV's lytic phase by the BZLF1 protein. Two versions of BZLF1 were employed: full-length and activation-domain (AD)-truncated BZLF1 non-induced and induced for 15 h. The experiments were performed as triplicates.

2019-04-01 | E-MTAB-7789 | biostudies-arrayexpress

RNA-seq in Raji cells with inducible BZLF1 prior to and after induction of EBV's lytic cycle by doxycycline

Project description:(i) RNA transcripts of Raji iBZLF1 cells (https://www.biorxiv.org/content/10.1101/573659v1) were compared between non-induced cells and cells induced with doxycycline (100 ng/ ml) for 6 h. Human (Hg19) as well as viral (EBV, Raji KF717093.1) transcripts were analyzed. Artificial ERCC Spike-ins (Thermo Scientific) were added to selected samples to control for global changes of RNA levels. (ii) For control purposes, the RNA transcripts in Raji cells equipped with a doxycycline-controlled truncated BZLF1 allele lacking its transactivation domain (Raji iBZLF1 AD-truncated) were prior to and after induction for 6 h. (iii) For another control, the RNA transcripts of parental, unmodified Raji cells were analyzed prior to and after doxycycline induction for 6 h. All experiments were performed as triplicates.

2019-01-01 | E-MTAB-7820 | biostudies-arrayexpress

ChIP-seq against BZLF1 in Raji cells (EBV, Human Herpesvirus 4, GenBank accession KF717093).

Project description:ChIP-seq experiments with the antibody BZ1 directed against the EBV protein BZLF1 prior to and 15 hours post induction with doxycycline (100 ng/ml). The doxycycline regulated conditional BZLF1 allele is encoded by an inducible plasmid stably introduced into Raji cells. Experiments were performed as duplicates.

2019-04-01 | E-MTAB-7788 | biostudies-arrayexpress

RNA-seq in Raji cells with inducible BZLF1 prior to and after induction of EBV's lytic cycle by doxycycline

Project description:RNA-seq in Raji cells with inducible BZLF1 prior to and after induction of EBV's lytic cycle by doxycycline

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RNA-seq data from DG75 cells with inducible BZLF1 prior to and after induction of EBV's lytic cycle by doxycycline.

Project description:(i) Transcripts of DG75 iBZLF1 cells were analyzed comparing non-induced cells and cells induced with doxycycline (100 ng/ ml) for 6 h. Doxycycline induces the expression of the full length viral transcription factor BZLF1. (ii) For control purposes, the transcripts of DG75 cells equipped with a doxycycline-regulated truncated BZLF1 allele lacking its transactivation domain (DG75 iBZLF1 AD-truncated) were analyzed prior to and after induction with doxycycline for 6 h. (iii) For an additional control, the transcripts of parental, unmodified DG75 cells were analyzed prior to and after adding doxycycline for 6 h. All experiments were performed as triplicates. The analysis is based on Homo sapiens (human) genome assembly GRCh37 (hg19) from Genome Reference Consortium. Artificial ERCC Spike-in RNAs (Thermo Scientific) were added as external controls.

2021-02-07 | E-MTAB-8426 | biostudies-arrayexpress

ATAC-seq analyses with results from DG75 cells prior to and post induction of two versions of BZLF1.

Project description:The aim of the experiment was to identify accessible (open) chromatin regions in the genome prior to and post induction of EBV's BZLF1 protein. Two versions of BZLF1 were employed: full-length and activation-domain (AD)-truncated BZLF1 non-induced and induced for 15 h. The experiments were performed as triplicates.

2021-02-07 | E-MTAB-8420 | biostudies-arrayexpress

Capture-C identification of chromatin interactions of 53 selected cellular loci prior to and post induction of EBV's lytic cycle in Raji cells

Project description:Identification of specific chromatin interactions of 53 selected genes with the Capture-C technique in Raji iBZLF1 cells prior to and 6 or 15 h after induction of EBV’s lytic cycle. The experiments were performed as triplicates.

2019-04-05 | E-MTAB-7825 | biostudies-arrayexpress

RNA-seq data from DG75 cells with inducible BZLF1 prior to and after induction of EBV's lytic cycle by doxycycline.

Project description:RNA-seq data from DG75 cells with inducible BZLF1 prior to and after induction of EBV's lytic cycle by doxycycline.

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BET inhibitors suppress BZLF1 expression [MutuI DNA-seq]

Project description:Lytic infection by the Epstein-Barr virus (EBV) poses numerous health risks, such as infectious mononucleosis and lymphoproliferative disorder. We demonstrate that JQ1 and other BET inhibitors block two different steps in the sequential cascade of the EBV life cycle: expression of the immediate-early gene BZLF1 and lytic genome replication. This represents a novel mode of action for antiviral drugs that may increase efficacy and decrease emergence of resistance. The sequenced total DNA data in this series show that JQ1 causes a decrease in EBV genome replication upon antibody induction.

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BET inhibitors suppress BZLF1 expression [MutuI RNA-seq]

Project description:Lytic infection by the Epstein-Barr virus (EBV) poses numerous health risks, such as infectious mononucleosis and lymphoproliferative disorder. We demonstrate that JQ1 and other BET inhibitors block two different steps in the sequential cascade of the EBV life cycle: expression of the immediate-early gene BZLF1 and lytic genome replication. This represents a novel mode of action for antiviral drugs that may increase efficacy and decrease emergence of resistance. The RNA-seq data below show that the first block by JQ1 occurs before transcription of any EBV lytic genes (see wigs of EBV transcriptomes). A subset of the same RNA-seq data (three replicates each of Mutu+vehicle was compared to Mutu+JQ1) was examined for changes in the human transcriptome, and those results are presented in the spreadsheet "Differential_Expression_GEO"

2017-06-30 | GSE84209 | GEO

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