A 3D genome atlas of breast cancer progression
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 31 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)
- Topic
- Breast cancerThis series is part of our curated briefing on it.
- Samples
- 31 samples: 31 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
- A 3D genome compendium of breast cancer progressioniScience · 2025
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 GSE273999_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 PRJNA1144432. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 31 sample titles: 31 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.
- GSM8441307 P01_HB_ERa
- GSM8441308 P01_LM_ERa
- GSM8441309 P01_PB_ERa
- GSM8441310 P02_HB_ERa
- GSM8441311 P02_LM_ERa
- GSM8441312 P02_PB_ERa
- GSM8441313 P02_RPB_ERa
- GSM8441314 P03_LM_ERa
- GSM8441315 P03_PB_ERa
- GSM8441316 P04_LM_ERa
- GSM8441317 P04_PB_ERa
- GSM8441318 P01_HB_HiC
- GSM8441319 P01_LM_HiC
- GSM8441320 P01_PB_HiC
- GSM8441321 P02_HB_HiC
- GSM8441322 P02_PB_HiC
- GSM8441323 P03_LM_HiC
- GSM8441324 P03_PB_HiC
- GSM8441325 P04_LM_HiC
- GSM8441326 P04_PB_HiC
- GSM8441327 P05_PB_HiC
- GSM8441328 P06_PE_HiC
- GSM8441329 P07_PE_HiC
- GSM8441330 P08_PE_HiC
- GSM8441331 P09_PE_HiC
- GSM8441332 P10_PE_HiC
- GSM8441333 P11_PE_HiC
- GSM8441334 P12_PE_HiC
- GSM8441335 P13_PE_HiC
- GSM8441336 P14_PE_HiC
- GSM8441337 P15_PE_HiC
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing · shares progression, 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
- 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
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE261713 Linking single cell genomes and transcriptomes at scale to decode breast cancer progression [scRNA-seq] 35 samples shares progression, breast
- GSE309697 Generation of a Comprehensive Epigenomic Atlas in Clear Cell Renal Cell Carcinoma Informs Kidney Cancer Progression and Heritability 265 samples shares progression
- GSE283522 The spatially informed mFISHseq assay resolves biomarker discordance and predicts treatment response in breast cancer 1254 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.