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Understanding and reversing mammary tumour-driven reprogramming of myelopoieisis to reduce metastatic spread [ATAC-seq]

GSE264085 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 84 samples Submitted 2025/04/08 Platform GPL21626
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 84 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
Mus musculus (mouse)
Samples
84 samples: 28 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
Understanding and reversing mammary tumor-driven reprogramming of myelopoiesis to reduce metastatic spreadCancer cell · 2025
Summary (written by the submitters)
Tumour-induced systemic accumulation and polarisation of neutrophils to an immunosuppressive phenotype is a potent driver of metastasis formation. Yet how mammary tumours reprogram granulopoiesis at the molecular level and when tumour imprinting occurs during neutrophil development remains underexplored. Here we combined single cell, chromatin and functional analyses to unravel the tumour-driven reprogramming of granulopoiesis, along with intervention studies aimed at reversing this process.
Read the full summary ↓
We observe that mammary tumours accelerate commitment to the neutrophil lineage at the expense of lymphopoiesis and erythropoiesis without stimulating the development of a novel myeloid lineage. Moreover, tumour-directed immunosuppressive imprinting of neutrophils starts early in haematopoiesis. Treatment with anti-IL-1β normalised tumour-induced granulopoiesis, reduced neutrophil production of T cell suppressive superoxides and mitigated metastatic spread. Together, these data provide molecular insights into the aberrant tumour-driven neutrophil differentiation pathway leading to metastasis-promoting chronic inflammation and how it can be reversed to reduce metastatic spread.
Published in
Understanding and reversing mammary tumor-driven reprogramming of myelopoiesis to reduce metastatic spread
Garner H, Martinovic M, Liu NQ et al. · Cancer cell 2025 · PMID 40345190 · doi:10.1016/j.ccell.2025.04.007
This dataset
Open GSE264085 in finder → Find more mouse 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 GSE264085_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 PRJNA1100963 and SRA study SRP502126. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40345190) ↗
Study design
28 conditions, mostly in triplicate
ATAC_MatN_WT_CTRL ×4 ATAC_LTHSC_WT_CTRL ×3 ATAC_LTHSC_KEP_CTRL ×3 ATAC_LTHSC_WT_aIL1B ×3 ATAC_LTHSC_KEP_aIL1B ×3 ATAC_MPP_WT_CTRL ×3 ATAC_MPP_KEP_CTRL ×3 ATAC_MPP_WT_aIL1B ×3 +20 more

Supports a between-group comparison across 84 samples.

How we read this: 28 replicated groups read from 84 sample titles; they account for 84 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

+ 44 more — browse all 84 samples with per-sample file links →

Datasets on a similar topic

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

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