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Wide-spread disruption of transcription termination in HSV-1 infection: Next-generation sequencing of translational activityd by ribosome profiling

ABSTRACT: Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. Ribosome profiling was performed at various times during infection with minor modification to the protocol described in Stern-Ginossar N et al., Science 2012

ORGANISM(S): Homo sapiens

PROVIDER: GSE60040 | GEO | 2015/05/26

SECONDARY ACCESSION(S): PRJNA257365

REPOSITORIES: GEO

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Wide-spread disruption of transcription termination in HSV-1 infection: Next-generation sequencing of translational activityd by ribosome profiling

Project description:Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. Ribosome profiling was performed at various times during infection with minor modification to the protocol described in Stern-Ginossar N et al., Science 2012 Ribosome profiling was performed a 0, 1, 2, 4, 6 and 8 h post infection. Two biological replicates were analysed.

2015-05-26 | E-GEOD-60040 | biostudies-arrayexpress

Ribosome profiling of HSV-1 infected cells

Project description:Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. Ribosome profiling was performed at various times during infection with minor modification to the protocol described in Stern-Ginossar N et al., Science 2012. Translation start site profiling was performed by culturing cells in presence of Harringtonin or Lactimidomycin for 30 min prior to cell harvest.

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Transcription start site profiling of HSV-1 infected cells using cRNA-seq and dRNA-seq

Project description:Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. Sequencing libraries were prepared using the cRNA-seq and dRNA-seq protocol from the indicated time points of infection.

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Subcellular RNA fractions of HSV-1 infected primary human fibroblasts

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2018-03-08 | GSE100576 | GEO

ATAC-seq on HSV-1 infected primary human fibroblasts (time course)

Project description:Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. ATAC-seq libraries were prepared starting with 50,000 cells per condition following the protocol described by Buenrostro et al., Nature Methods 2013

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Wide-spread disruption of transcription termination in HSV-1 infection: Next generation sequencing of total and newly transcribed (4sU-RNA) RNA

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Wide-spread disruption of transcription termination in HSV-1 infection: Next generation sequencing of total and newly transcribed (4sU-RNA) RNA

Project description:Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. Newly transcribed RNA was labelled by adding 500µM 4-thiouridine (4sU) to the cell culture media for 1h. Total cellular RNA was isolated using Trizol. Newly transcribed RNA was purified following the protocol described in Raedle et al. JoVE 2013. Newly transcribed RNA was labelled in one hour intervals during the first eight hours of HSV-1 infection. All nine 4sU-RNA samples as well as total cellular RNA of every second hour of infection were sent for sequencing. Two independent biological replicates were analysed.

2015-05-26 | E-GEOD-59717 | biostudies-arrayexpress

Subcellular RNA fractions of primary human fibroblasts infected with the HSV-1 delta-ICP27 mutant

Project description:Primary human foreskin fibroblasts (HFF) were infected with the ICP27 null mutant of herpes simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. Subcellular RNA fractions including total RNA, cytoplasmic RNA, nucleoplasmic RNA and chromatin-associated RNA were prepared and subjected to RNA-seq

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Subcellular RNA fractions of HSV-1 infected primary human fibroblasts including infection with delta-Vhs mutant

Project description:Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 or its vhs null mutant at a multiplicity of infection (MOI) of 10. Subcellular RNA fractions including total RNA, cytoplasmic RNA, nucleoplasmic RNA and chromatin-associated RNA were prepared and subjected to RNA-seq.

2020-10-26 | GSE129582 | GEO

Chromatin-associated RNA of HSV-1 infected primary human fibroblasts including infection with vhs mutants

Project description:Primary human foreskin fibroblasts (HFF) were infected with wild-type herpes simplex virus 1 (HSV-1) strain 17 or its vhs null mutant, or with BAC-derived viruses expressing either a wild-type or catalytically inactive vhs with the D195N mutation at a multiplicity of infection (MOI) of 10. Chromatin-associated RNA was prepared and subjected to RNA-seq.

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