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Tumor-associated neutrophil precursors impair homologous DNA repair and promote sensitivity to PARP-inhibition.

GSE288570 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 18 samples Submitted 2025/03/18 Platform GPL18573Platform GPL24676
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 18 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
18 samples: 3 × MCF7 cells, control, 24h, H3K9me3 IP, vs 3 × MCF7 cells, succinate 2mM, 24h, H3K9me3 IP, vs 3 × MCF7 cells, vehicle controls, 72h, vs 3 × MCF7 cells, treated with CM obtained from PreNeu (cm-PreNeu), 72h,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.
Paper
Tumor-associated neutrophil precursors impair homologous DNA repair and promote sensitivity to PARP inhibitionNature communications · 2025
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Tumor-associated neutrophil precursors impair homologous DNA repair and promote sensitivity to PARP inhibition
Mukherjee S, Garda C, Boffa L et al. · Nature communications 2025 · PMID 40738898 · doi:10.1038/s41467-025-61422-9
This dataset
Open GSE288570 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 GSE288570_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 PRJNA1218452 and SRA study SRP561119. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40738898) ↗
Study design
3 × MCF7 cells, control, 24h, H3K9me3 IP, vs 3 × MCF7 cells, succinate 2mM, 24h, H3K9me3 IP, vs 3 × MCF7 cells, vehicle controls, 72h, vs 3 × MCF7 cells, treated with CM obtained from PreNeu (cm-PreNeu), 72h,

Supports a case/control comparison: 7 samples read as cases, 7 as controls.

How we read this: 4 replicated groups read from 18 sample titles; they account for 12 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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