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Identification of herpes simplex virus 1 and host targets of miR-138 by comparative PAR-CLIP in Neuro-2a and 293T cells

ABSTRACT: Identification of herpes simplex virus 1 and host targets of miR-138 by comparative PAR-CLIP in Neuro-2a and 293T cells

PROVIDER: PRJNA524884 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8646320.fastq.gz	Fastqsanger.gz
	SRR8646321.fastq.gz	Fastqsanger.gz
	SRR8646316.fastq.gz	Fastqsanger.gz
	SRR8646317.fastq.gz	Fastqsanger.gz
	SRR8646318.fastq.gz	Fastqsanger.gz

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Identification of herpes simplex virus 1 and host targets of miR-138 by comparative PAR-CLIP in Neuro-2a and 293T cells

Project description:This is a part of the study that shows that a host microRNA, miR-138, represses herpes simplex virus 1 (HSV-1) gene expression through both viral and host targets. These PAR-CLIP analyses identified viral and host targets of miR-138 in Neuro-2a (mouse neuroblastoma) and 293T (human embryonic kidney) cells. We constructed two cell lines derived from Neuro-2a cells, one overexpressing miR-138 (N2A138) and one antagonizing miR-138 (N2Aanti138). We also constructed two cell lines derived from 293T cells, one overexpressing miR-138 (293T138) and one control cells (293Tcontrol). Uninfected N2A138 and N2Aanti138 were compared by PAR-CLIP for host targets in Neuro-2A cells. 293T138 and 293Tcontrol cells infected for 4 and 8 hours were compared by PAR-CLIP for HSV-1 targets in 293T cells. 293T138 and 293Tcontrol cells infected for 4 hours were also compared for host targets in 293T cells.

2020-04-27 | GSE127503 | GEO

Identification of viral and host targets of miR-138 by PAR-CLIP analysis of herpes simplex virus 2 infected 293T cells

Project description:Like herpes simplex virus 1 (HSV-1) ICP0 mRNA, HSV-2 ICP0 mRNA is predicted to be targeted by a host neuron-specific microRNA, miR-138. This study was designed to confirm the interaction between HSV-2 ICP0 mRNA and miR-138, and to identify other potential viral and host targets of miR-138 during HSV-2 infection. We performed PAR-CLIP on HSV-2 infected 293T cells overexpressing miR-138 in comparisin to control 293T cells. The results confirmed ICP0 as miR-138's targets, and also identified some other potential viral and host targets of miR-138.

2021-11-01 | GSE155402 | GEO

Identification of targets of miR-138 in Neuro-2a and 293T cells by RNAseq

Project description:We previously showed that miR-138 can repress herpes simplex virus 1 (HSV-1) ICP0 expression by binding to ICP0 mRNA. However, in this study we found that miR-138 can also repress viral gene expression independent of ICP0. We did not find other confirmed viral targets of miR-138. Therefore we conducted these RNAseq experiments (in combination with PAR-CLIP experiments whose results are uploaded separately) to identify host targets of miR-138 in two cell lines to explain the ICP0-independent effects on HSV-1 gene expression.

2020-04-27 | GSE127502 | GEO

Effects of host miR-138 on herpes simplex virus 1 gene expression in Neuro-2a cells and their dependence of the binding sites on ICP0 mRNA

Project description:We previously showed that miR-138 can repress herpes simplex virus 1 (HSV-1) ICP0 expression by binding to ICP0 mRNA. However, in this study we found that miR-138 can also repress viral gene expression independent of ICP0. Therefore we conducted this RNAseq experiment to assess the effects of miR-138 on expression of each individual viral gene to search for other viral targets of miR-138

2020-04-27 | GSE127501 | GEO

RNA-seq identification of herpes simplex virus type 1 transcription in Neuro-2a cells overexpressing ONECUT2

Project description:This is a part of the study that shows that a host gene,ONECUT2 (OC2), promote herpes simplex virus 1 (HSV-1) transcription. These RNA-seq analyses viral genes transcription in Neuro-2a cells. Neuro-2a cells were transfected with pOC2△HOX2 and pcDNA plasmids for 42 hours then infected with herpes simple virus1 for 5 hours.

2023-09-18 | GSE241029 | GEO

Effects of the onecut family on herpes simplex virus 1 and host chromatin accessibility in Neuro-2a cells

Project description:This is a part of the study that shows that a host gene,ONECUT2( OC2), promotes herpes simplex virus 1 (HSV-1) genome accessibility. These ATAC analyses are for viral and host genome accessibility in Neuro-2a cells. Neuro-2a cells were transfected with pOC2△HOX2 and pcDNA plasmids for 42 hours then infected with herpes simple virus1 for 2 hours.

2023-09-18 | GSE240221 | GEO

Identification of viral and host targets of miR-138 by PAR-CLIP analysis of herpes simplex virus 2 infected 293T cells

Project description:Identification of viral and host targets of miR-138 by PAR-CLIP analysis of herpes simplex virus 2 infected 293T cells

| PRJNA649581 | ENA

Identification of genes regulated by Foxc1, which is a host target of miR-138

Project description:In other parts of this study we identified Foxc1 as a host target of miR-138 and found that Foxc1 can promote herpes simplex virus-1 (HSV-1) replication. To understand the mechanisms of this function, we performed an RNAseq experiment comparing vector (pcDNA) and pFoxchuman transfected Neuro-2a cells. After transfection, these cells were infected with HSV-1 for 5 hours at an MOI of 1 to identify viral genes regulated by Foxc1 as well as host genes.

2020-04-27 | GSE145499 | GEO

Identification of targets of miR-138 in Neuro-2a and 293T cells by RNAseq

Project description:Identification of targets of miR-138 in Neuro-2a and 293T cells by RNAseq

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Effects of host miR-138 on herpes simplex virus 1 gene expression in Neuro-2a cells and their dependence of the binding sites on ICP0 mRNA

Project description:Effects of host miR-138 on herpes simplex virus 1 gene expression in Neuro-2a cells and their dependence of the binding sites on ICP0 mRNA

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