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Transcription-Replication conflicts are linked to histone H3K79 methylation and R-loop dependent nucleosome eviction

GSE268017 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 37 samples Submitted 2025/02/28 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 37 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
37 samples: 14 conditions, mostly in duplicateGroups 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
Transcription-replication conflicts drive R-loop-dependent nucleosome eviction and require DOT1L activity for transcription recoveryNucleic acids research · 2025
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Transcription-replication conflicts drive R-loop-dependent nucleosome eviction and require DOT1L activity for transcription recovery
Werner M, Trauner M, Schauer T et al. · Nucleic acids research 2025 · PMID 39988315 · doi:10.1093/nar/gkaf109
This dataset
Open GSE268017 in finder → Find more human 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 GSE268017_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 PRJNA1114052 and SRA study SRP507674. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39988315) ↗
Study design
14 conditions, mostly in duplicate
U-2OS Clone#12 cells, RNAPII Ser2P ChIP ×3 U-2OS Clone#12 cells, RNAPII Ser2P ChIP DOX ×3 U-2OS Clone#12 cells, H3 ChIP ×3 U-2OS Clone#12 cells, H3 ChIP DOX ×3 U-2OS Clone#12 cells, G1 ×2 U-2OS Clone#12 cells, G1 DOX ×2 U-2OS Clone#12 cells, 2h ×2 U-2OS Clone#12 cells, 2h DOX ×2 +11 more

Supports a between-group comparison across 32 samples.

How we read this: 14 replicated groups read from 37 sample titles; they account for 32 of them. 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
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