GEO series

DNA damage induced by G-quadruplex ligand PyBI and its synthetic lethality with DNA repair inhibitors in cancer cells

GSE270287 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 19 samples Submitted 2025/05/29 Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 19 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: 19 samples: 19 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: Structural basis for nucleolin recognition of MYC promoter G-quadruplexScience (New York, N.Y.) · 2025

Summary (written by the submitters)

The existence of G-quadruplexes (G4s) in vivo verified by diverse techniques, accompanied with their regulatory roles in cellular processes, highlight G4s as a target for various disease treatment. Targeting G-quadruplex DNAs to cause DNA damage has a good prospect for cancer therapy. However, previous studies on DNA damage induced by G4 ligands and its repair response thereof mainly focused on limited scaffolds such as CX series drugs, PDS families, etc.

Read the full summary ↓

Here, we systematically investigated the DNA damage and repair mechanism induced by a good G4 stabilizer with bis(benzimidazole)pyridine as its key scaffold, which we termed as PyBI. PyBI can stabilize G4s both in vitro and in vivo, and cause DNA double strand breaks (DSB) and genome instability during DNA replication, resulting in cell cycle stagnation in G2/M phase and the increase of RAD51 and 53BP1 foci. Significantly, we applied Cleavage Under Targets and Tagmentation (CUT&Tag) for genome-wide mapping DNA damage sites induced by PyBI in cancer cells. Together with its G4 mapping result by CUT&Tag, we revealed that DNA damage caused by PyBI might be mediated by G4 stabilization. Moreover, we thoroughly investigated the synthetic lethality of PyBI with a small library of DNA repair inhibitors. PyBI exhibited good synthetic lethality effects with RAD51 and DNA-PK inhibitor, providing a new prospect for the treatment of genetically defective cancers.

Published in

Structural basis for nucleolin recognition of MYC promoter G-quadruplex

Chen L, Dickerhoff J, Zheng KW et al. · Science (New York, N.Y.) 2025 · PMID 40245140 · doi:10.1126/science.adr1752

This dataset

Open GSE270287 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 GSE270287_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 PRJNA1122302 and SRA study SRP513358. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40245140) ↗

Study design

19 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 19 sample titles: 19 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

GSM8338905 Replicate 1 of G4P CUT&Tag in HeLa, untreated
GSM8338906 Replicate 2 of G4P CUT&Tag in HeLa, untreated
GSM8338907 Replicate 1 of G4P CUT&Tag in HeLa, add PyBI
GSM8338908 Replicate 2 of G4P CUT&Tag in HeLa, add PyBI
GSM8338913 Replicate 1 of RAD51 CUT&Tag in HeLa, untreated
GSM8338914 Replicate 2 of RAD51 CUT&Tag in HeLa, untreated
GSM8338915 Replicate 1 of RAD51 CUT&Tag in HeLa, add PyBI
GSM8338916 Replicate 2 of RAD51 CUT&Tag in HeLa, add PyBI
GSM8338917 Replicate 1 of 53BP1 CUT&Tag in HeLa, untreated
GSM8338918 Replicate 2 of 53BP1 CUT&Tag in HeLa, untreated
GSM8338919 Replicate 1 of 53BP1 CUT&Tag in HeLa, add PyBI
GSM8338920 Replicate 2 of 53BP1 CUT&Tag in HeLa, add PyBI
GSM8338921 IgG control of CUT&Tag in HeLa
GSM8696947 replicate 1 of BG4 CUT&Tag in HeLa, untreated
GSM8696948 replicate 2 of BG4 CUT&Tag in HeLa, untreated
GSM8696949 replicate 1 of BG4 CUT&Tag in HeLa, add PyBI
GSM8696950 replicate 2 of BG4 CUT&Tag in HeLa, add PyBI
GSM8696951 replicate 1 of BG4 CUT&Tag in HeLa, add PDS
GSM8696952 replicate 2 of BG4 CUT&Tag in HeLa, add PDS

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