GEO series

Transcriptional consequences of herpes simplex virus 1 ICP4 inducible expression in uninfected cells

GSE311056 Homo sapiens (human) RNA-seq (gene expression) 22 samples Submitted 2026/03/13 Platform GPL34284

At a glance

RNA-seq (gene expression) · human · 22 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Homo sapiens (human)
Samples: 22 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

Successful viral infections reflect the balanced outcome of a tightly regulated program of viral gene expression and manipulation of the host cell to favor production of new infectious particles. The productive replication cycle of herpes simplex virus 1 (HSV-1) is dependent on the immediate-early essential transcription factor ICP4, which positively or negatively regulates transcription of immediate-early, early, and late HSV-1 genes at different steps in the temporal cascade, largely through sequence-specific binding to cis-acting regulatory elements.

Read the full summary ↓

In contrast, direct regulation of host transcription programming by ICP4 is less well understood. In this study we exogenously expressed doxycycline-inducible wild-type and mutant ICP4 proteins in uninfected primary human fibroblasts and performed RNA-Seq to identify ICP4-driven changes to the host transcriptome. Cross-referencing our findings to a published dataset of ICP4-dependent changes to the host transcriptome in cells infected with HSV-1 provided validation for a subset of ICP4-regulated differentially-expressed genes. Furthermore, mutations in ICP4 that disrupt interactions with the host transcriptional machinery or interfere with site-specific DNA binding further modified this ICP4-driven remodeling of host transcription programming. Taken together, these data provide a comprehensive transcriptomic analysis of ICP4-driven dysregulation of host gene expression in uninfected cells.

This dataset

Open GSE311056 in finder → Find more human RNA-seq datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE311056_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1368599 and SRA study SRP648012. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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+ 22 more — browse all 22 samples with per-sample file links →

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.