Molecular characterisation of the metastatic cell state in Breast Cancer
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 101 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)
- Topic
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 101 samples: 21 conditions, mostly in duplicateGroups 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
- A 3D morphogenetic blueprint for metastatic outgrowth in breast cancerCell · 2026
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE281492_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1184134 and SRA study SRP544216. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 9 samples read as cases, 23 as controls.
How we read this: 21 replicated groups read from 101 sample titles; they account for 55 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.
- GSM8621897 MDA-MB-231 CTRL 2D rep1 MDA-MB-231 CTRL 2D
- GSM8621898 MDA-MB-231 CTRL 2D rep2 MDA-MB-231 CTRL 2D
- GSM8621899 MDA-MB-231 ETV KO 2D rep1 MDA-MB-231 ETV KO 2D
- GSM8621900 MDA-MB-231 ETV KO 2D rep2 MDA-MB-231 ETV KO 2D
- GSM8621901 MDA-MB-231 CTRL 3D rep1 MDA-MB-231 CTRL 3D
- GSM8621902 MDA-MB-231 CTRL 3D rep2 MDA-MB-231 CTRL 3D
- GSM8621903 MDA-MB-231 ETV KO 3D rep1 MDA-MB-231 ETV KO 3D
- GSM8621904 MDA-MB-231 ETV KO 3D rep2 MDA-MB-231 ETV KO 3D
- GSM8621905 Human brain metastasis from a HER2+BC patient
- GSM8621906 Lung metastses from a MMTV-PyMT female mouse
- GSM8621907 BBM0 BBM
- GSM8621908 BBM5 BBM
- GSM8621909 BSM1
- GSM8621910 hMG1 hMG
- GSM8621911 hMG2 hMG
- GSM8621912 hMG3 hMG
- GSM8621913 4T1 CTRL 2D rep1 4T1 CTRL 2D
- GSM8621914 4T1 CTRL 2D rep2 4T1 CTRL 2D
- GSM8621915 4T1 ETV4 KO C1 2D rep1 4T1 ETV4 KO C1 2D
- GSM8621916 4T1 ETV4 KO C1 2D rep2 4T1 ETV4 KO C1 2D
- GSM8621917 4T1 ETV4 KO C2 2D rep1 4T1 ETV4 KO C2 2D
- GSM8621918 4T1 ETV4 KO C2 2D rep2 4T1 ETV4 KO C2 2D
- GSM8621919 4T1 CTRL 3D rep1 4T1 CTRL 3D
- GSM8621920 4T1 CTRL 3D rep2 4T1 CTRL 3D
- GSM8621921 4T1 ETV4 KO C1 3D rep1 4T1 ETV4 KO C1 3D
- GSM8621922 4T1 ETV4 KO C1 3D rep2 4T1 ETV4 KO C1 3D
- GSM8621923 4T1 ETV4 KO C2 3D rep1 4T1 ETV4 KO C2 3D
- GSM8621924 4T1 ETV4 KO C2 3D rep2 4T1 ETV4 KO C2 3D
- GSM8623986 BBM7 BBM
- GSM8623987 BBM8 BBM
- GSM8623988 BBM9 BBM
- GSM8623989 BBM10 BBM
- GSM8623990 BBM13 BBM
- GSM8623991 BC3 BC
- GSM8623992 BC4 BC
- GSM8623993 BC16 BC
- GSM8623994 PyMT primary tumor - replicate 1 PyMT primary tumor
- GSM8623995 PyMT primary tumor - replicate 2 PyMT primary tumor
- GSM8623996 PyMT lung metastases - replicate 1 PyMT lung metastases
- GSM8623997 PyMT lung metastases - replicate 2 PyMT lung metastases
+ 61 more — browse all 101 samples with per-sample file links →
- GSE104193 Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF-β signalling and malignant features in vitro and in vivo 32 samples same disease briefing · shares breast
- GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing · shares breast
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing · shares breast
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing · shares breast
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE89309 Chromatin states of tumor-specific T cells 97 samples shares state
- GSE294887 Individual RNA-seq for different prostate cancer cells, tumors treated by LGK974, ENZ, EPZ6438, EED226 or by CTNNB1 gene knockdown and overexpression, and BRN2 gene knockdown 36 samples shares state
- GSE296112 Augment proteasome inhibitor efficacy activates CD8+ T cell-mediated antitumor immunity in breast cancer 27 samples shares breast
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.