GEO series

G-Quadruplex DNA suppresses Transcription during DNA Replication [CUT&Tag]

GSE306391 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 264 samples Submitted 2025/09/10 Platform GPL29480

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 264 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: 264 samples: 222 distinct titles, 42 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.

Summary (written by the submitters)

G-quadruplex DNA (G4-DNA) structures play crucial but incompletely understood roles in coordinating DNA replication and transcription. Here, we investigate the dynamics of G4-DNA during DNA replication and its functional interplay with transcription machinery in synchronized tumor cells. Using a double-thymidine block to arrest cells in early S phase, we profile G4-DNA structures and associated transcription factors through CUT&Tag, while monitoring transcriptional changes via PRO-seq.

Read the full summary ↓

To mechanistically dissect these relationships, we perturb the system by overexpressing G4-DNA helicases (DHX36 and BRIP1), treating with the G4-destabilizing agent PhpC, and knocking down the novel G4-binding protein RFC3. Our integrated analysis reveals how G4-DNA spatially and temporally regulates replication-transcription coupling, with important implications for understanding genome stability in cancer. These findings provide new insights into the role of G4-DNA as a regulatory nexus between DNA replication and gene expression.

This dataset

Open GSE306391 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 GSE306391_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 PRJNA1310565 and SRA study SRP612347. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

222 distinct titles, 42 of them repeated

CUT&Tag of NELFA in cells ×2 CUT&Tag of NELFA in cells treated with delta_… ×2 CUT&Tag of NELFA in cells treated with L-thyr… ×2 CUT&Tag of NELFA in cells treated with piperl… ×2 CUT&Tag of NELFA in cells treated with spermi… ×2 CUT&Tag of NELFB in cells ×2 CUT&Tag of NELFB in cells treated with delta_… ×2 CUT&Tag of NELFB in cells treated with L-thyr… ×2 +34 more

Supports a case/control comparison: 64 samples read as cases, 48 as controls.

How we read this: Read from 264 sample titles: 222 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

GSM9198535 CUT&Tag of G4-DNA in Early_S cells rep1.
GSM9198537 CUT&Tag of G4-DNA in Early_S cells rep2.
GSM9198538 CUT&Tag of BRIP1 in Early_S cells rep1.
GSM9198539 CUT&Tag of BRIP1 in Early_S cells rep2.
GSM9198540 CUT&Tag of DHX36 in Early_S cells rep1.
GSM9198541 CUT&Tag of DHX36 in Early_S cells rep2.
GSM9198542 CUT&Tag of NELFA in Early_S cells rep1.
GSM9198543 CUT&Tag of NELFA in Early_S cells rep2.
GSM9198545 CUT&Tag of NELFB in Early_S cells rep1.
GSM9198546 CUT&Tag of NELFB in Early_S cells rep2.
GSM9198547 CUT&Tag of RFC3 in Early_S cells rep1.
GSM9198548 CUT&Tag of RFC3 in Early_S cells rep2.
GSM9198550 CUT&Tag of RNAPS2P in Early_S cells rep1.
GSM9198551 CUT&Tag of RNAPS2P in Early_S cells rep2.
GSM9198552 CUT&Tag of RNAPS5P in Early_S cells rep1.
GSM9198553 CUT&Tag of RNAPS5P in Early_S cells rep2.
GSM9198554 CUT&Tag of G4-DNA in G1_S cells rep1.
GSM9198556 CUT&Tag of G4-DNA in G1_S cells rep2.
GSM9198557 CUT&Tag of BRIP1 in G1_S cells rep1.
GSM9198558 CUT&Tag of BRIP1 in G1_S cells rep2.
GSM9198559 CUT&Tag of DHX36 in G1_S cells rep1.
GSM9198560 CUT&Tag of DHX36 in G1_S cells rep2.
GSM9198561 CUT&Tag of NELFA in G1_S cells rep1.
GSM9198563 CUT&Tag of NELFA in G1_S cells rep2.
GSM9198564 CUT&Tag of NELFB in G1_S cells rep1.
GSM9198565 CUT&Tag of NELFB in G1_S cells rep2.
GSM9198566 CUT&Tag of RFC3 in G1_S cells rep1.
GSM9198567 CUT&Tag of RFC3 in G1_S cells rep2.
GSM9198569 CUT&Tag of RNAPS2P in G1_S cells rep1.
GSM9198570 CUT&Tag of RNAPS2P in G1_S cells rep2.
GSM9198571 CUT&Tag of RNAPS5P in G1_S cells rep1.
GSM9198572 CUT&Tag of RNAPS5P in G1_S cells rep2.
GSM9198573 CUT&Tag of G4-DNA in Late_S cells rep1.
GSM9198574 CUT&Tag of G4-DNA in Late_S cells rep2.
GSM9198575 CUT&Tag of BRIP1 in Late_S cells rep1.
GSM9198577 CUT&Tag of BRIP1 in Late_S cells rep2.
GSM9198578 CUT&Tag of DHX36 in Late_S cells rep1.
GSM9198579 CUT&Tag of DHX36 in Late_S cells rep2.
GSM9198580 CUT&Tag of NELFA in Late_S cells rep1.
GSM9198581 CUT&Tag of NELFA in Late_S cells rep2.

+ 224 more — browse all 264 samples with per-sample file links →

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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.