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Effect of RNF4 depletion on GSK3685032-induced chromatin accessibilty changes in MV4-11 cells [ATAC-seq]

GSE233725 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 11 samples Submitted 2026/05/17 Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 11 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
11 samples: 3 × ATAC-seq_MV4-11, gNT, Day 7 100nM GSK3685032, vs 3 × ATAC-seq_MV4-11, gRNF4, Day 7 DMSO, vs 3 × ATAC-seq_MV4-11, gRNF4, Day 7 100nM GSK3685032, vs 2 × ATAC-seq_MV4-11, gNT, Day 7 DMSO,Groups 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.
Summary (written by the submitters)
GSK3685032-induced DNA hypomethylation results in upregulation of largely viral-responsive gene expression pathways and cell death. We identified that loss of RNF4 causes resistance to GSK3685032. We established RNF4 wild type and deficient MV4-11 cells by CRISPR-Cas9 disruption and treated with vehicle or GSK3685032 to determine how RNF4-deficiency impacts GSK3685032-induced gene expression changes
This dataset
Open GSE233725 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 GSE233725_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 PRJNA977663 and SRA study SRP440190. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
3 × ATAC-seq_MV4-11, gNT, Day 7 100nM GSK3685032, vs 3 × ATAC-seq_MV4-11, gRNF4, Day 7 DMSO, vs 3 × ATAC-seq_MV4-11, gRNF4, Day 7 100nM GSK3685032, vs 2 × ATAC-seq_MV4-11, gNT, Day 7 DMSO,

Supports a between-group comparison across 11 samples.

How we read this: 4 replicated groups read from 11 sample titles; they account for 11 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
Datasets on a similar topic

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