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Herpes simplex virus type 1 (HSV-1) R-loops are targets for APOBEC-mediated mutagenesis

GSE312648 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 14 samples Submitted 2026/03/09 Platform GPL16791
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 14 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Homo sapiens (human)
Samples
14 samples: 12 distinct titles, 2 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
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.
Paper
Herpes simplex virus type 1 R-loops are targets for APOBEC-mediated mutagenesisGenome biology · 2026
Summary (written by the submitters)
APOBEC3 enzymes are key components of antiviral immunity that introduce mutations into viral genomes. We show that R-loops serve as preferred substrates for APOBEC3 mutagenesis during herpes simplex virus type 1 infection. APOBEC3 enzymes are recruited to viral R-loops, where they generate clustered C-to-T mutations in genes critical for viral assembly.
Read the full summary ↓
Importantly, R-loops alone are not mutagenic, and APOBECA3 enzymes do not edit HSV-1 without an R-loop; mutagenesis occurs when R-loops and APOBEC3 enzymes interact. These findings identify endogenous R-loops formed during the HSV-1 life cycle as focal vulnerabilities and highlight R-loop–APOBEC3 coupling as a mechanism for antiviral mutagenesis.
Published in
Herpes simplex virus type 1 R-loops are targets for APOBEC-mediated mutagenesis
Miskei M, Varga D, Hornyák L et al. · Genome biology 2026 · PMID 41981657 · doi:10.1186/s13059-026-04078-y
This dataset
Open GSE312648 in finder → Find more human ChIP / ATAC / CUT&Tag 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 GSE312648_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA1375651 and SRA study SRP651710. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41981657) ↗
Study design
12 distinct titles, 2 of them repeated
HSV1 A3A induced RPE-1 ChIP-seq IP ×2 HSV1 A3A induced RPE-1 DRIP-seq IP ×2

How we read this: Read from 14 sample titles: 12 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study
Datasets on a similar topic

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