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Optical control of gene expression using a DNA G-quadruplex targeting reversible photoswitch

GSE261837 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 55 samples Submitted 2025/01/30 Platform GPL18573Platform GPL30173
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 55 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
55 samples: 16 conditions, mostly in triplicateGroups 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
Optical control of gene expression using a DNA G-quadruplex targeting reversible photoswitchNature chemistry · 2025
Summary (written by the submitters)
Transcriptional regulation is a dynamic process that coordinates diverse cellular activities, and the use of small molecules to perturb gene expression has propelled our understanding of the fundamental regulatory mechanisms. However, small molecules typically lack the spatiotemporal precision required in highly non-invasive, controlled settings.
Read the full summary ↓
Here, we present the development of a cell-permeable small-molecule DNA G-quadruplex (G4) binder, termed G4switch, that can be reversibly toggled on and off by visible light. We have biophysically characterised the light-mediated control of G4 binding in vitro, followed by cellular, genomic mapping of G4switch to G4 targets in chromatin to confirm G4-selective, light-dependent binding in a cellular context. By deploying G4switch in living cells, we show spatiotemporal control over the expression of a set of G4-containing genes and G4-associated cell proliferation. Our studies demonstrate a chemical tool and approach to interrogate the dynamics of key biological processes directly at the molecular level in cells.
Published in
Optical control of gene expression using a DNA G-quadruplex targeting reversible photoswitch
Zhang X, Dhir S, Melidis L et al. · Nature chemistry 2025 · PMID 40181150 · doi:10.1038/s41557-025-01792-1
This dataset
Open GSE261837 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 GSE261837_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 PRJNA1089188 and SRA study SRP496215. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40181150) ↗
Study design
16 conditions, mostly in triplicate
BG4_CnT_U2OS_DMSO ×5 SLAM-seq_U2OS_DMSO ×4 SLAM-seq_U2OS_G4switch_405nm+525nm ×4 SLAM-seq_U2OS_G4switch_405nm ×4 SLAM-seq_U2OS_G4switch_525nm ×4 SLAM-seq_U2OS_G4switch_dark ×4 G4Switch_Chemmap_405_2h_B1_t ×3 G4Switch_Chemmap_405_2h_B2_t ×3 +8 more

Supports a between-group comparison across 55 samples.

How we read this: 16 replicated groups read from 55 sample titles; they account for 55 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

+ 15 more — browse all 55 samples with per-sample file links →

Datasets on a similar topic

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