GEO series

Indirect identification of genomic G-quadruplexes via a small protein probe that specifically recognizes C-rich single-stranded DNA

GSE296647 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 24 samples Submitted 2026/03/01 Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 24 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: 24 samples: 24 samples, each with a distinct title — no replicated groupsGroups 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: Indirect identification of genomic G-quadruplexes via a small protein probe that specifically recognizes C-rich single-stranded DNANucleic acids research · 2026

Summary (written by the submitters)

Detecting intracellular genomic G-quadruplexes (G4s) is crucial for understanding their biological functions. Although various G4 recognition probes have been developed, there remains a need for new G4 detection technologies to create detailed and reliable genomic G4 maps. In this study, we developed a small protein (CK13) that specifically recognizes the complementary C-rich single-stranded DNA (ssDNA) released during the formation of G4.

Read the full summary ↓

Based on CK13 and CUT&Tag technology, we identified tens of thousands of C-rich ssDNA sites within human genomic DNA. These sites contain the vast majority of G4 sites detected by G4 probes, indicating that CK13 can well confirm the results of traditional G4 probes. Since CK13’s binding to C-rich ssDNA is minimally influenced by G4-binding proteins, it produces strong signals at the sites where intracellular G4-binding proteins are present. This indicates that, beyond free G4 structures, CK13 can also detect G4s occupied by G4-binding proteins within cells. Our findings demonstrate that C-rich ssDNA complementary to G4 can serve as an indirect marker for G4 formation, offering a promising approach to further explore the regulatory roles of G4s and their interacting proteins.

Published in

Indirect identification of genomic G-quadruplexes via a small protein probe that specifically recognizes C-rich single-stranded DNA

Chen JN, Xie ML, Yan JY et al. · Nucleic acids research 2026 · PMID 41614300 · doi:10.1093/nar/gkag068

This dataset

Open GSE296647 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 GSE296647_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 PRJNA1259701 and SRA study SRP583478. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41614300) ↗

Study design

24 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 24 sample titles: 24 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

GSM8974165 replicate 2 of IgG CUT&Tag in HeLa
GSM8974166 replicate 1 of IgG CUT&Tag in HeLa
GSM8974167 replicate 2 of TOP1 CUT&Tag in HeLa
GSM8974168 replicate 1 of TOP1 CUT&Tag in HeLa
GSM8974169 replicate 2 of NCL CUT&Tag in HeLa
GSM8974170 replicate 1 of NCL CUT&Tag in HeLa
GSM8974171 replicate 2 of CK13 CUT&Tag in HeLa
GSM8974172 replicate 1 of CK13 CUT&Tag in HeLa
GSM8974173 replicate 2 of IgG CUT&Tag in HCT116
GSM8974174 replicate 1 of IgG CUT&Tag in HCT116
GSM8974175 replicate 2 of NCL CUT&Tag in HCT116
GSM8974176 replicate 1 of NCL CUT&Tag in HCT116
GSM8974177 replicate 2 of G4P CUT&Tag in HCT116
GSM8974178 replicate 1 of G4P CUT&Tag in HCT116
GSM8974179 replicate 2 of CK13 CUT&Tag in HCT116
GSM8974180 replicate 1 of CK13 CUT&Tag in HCT116
GSM9334633 replicate 2 of CK13 CUT&Tag in HEK293T
GSM9334634 replicate 1 of CK13 CUT&Tag in HEK293T
GSM9334635 replicate 2 of ZnTTAPc G4P CUT&Tag in HCT116
GSM9334636 replicate 1 of ZnTTAPc G4P CUT&Tag in HCT116
GSM9334637 replicate 2 of ZnTTAPc CK13 CUT&Tag in HCT116
GSM9334638 replicate 1 of ZnTTAPc CK13 CUT&Tag in HCT116
GSM9334639 replicate 2 of CTRL CK13 CUT&Tag in HCT116
GSM9334640 replicate 1 of CTRL CK13 CUT&Tag in HCT116

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Search all human ChIP / ATAC / CUT&Tag datasets in GEO →

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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.