Chromatin architecture reprogramming reveals novel epigenetic dependencies in breast cancer [Cut&Run]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 24 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
- 24 samples: 12 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
- Chromatin architecture reprogramming reveals novel epigenetic dependencies in breast cancerGenes & development · 2026
Read the full summary ↓
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 GSE296423_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 PRJNA1259259 and SRA study SRP583373. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 12 replicated groups read from 24 sample titles; they account for 24 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.
- GSM8970187 HD_SiC_H3K9me3 Replicate 1 HD_SiC_H3K9me3
- GSM8970188 HD_SiC_H3K9me3 Replicate 2 HD_SiC_H3K9me3
- GSM8970189 HD_SiC_H3K27me3 Replicate 1 HD_SiC_H3K27me3
- GSM8970190 HD_SiC_H3K27me3 Replicate 2 HD_SiC_H3K27me3
- GSM8970191 HD_SiC_IgG Replicate 1 HD_SiC_IgG
- GSM8970192 HD_SiC_IgG Replicate 2 HD_SiC_IgG
- GSM8970193 HD_SiKDM4C_H3K9me3 Replicate 1 HD_SiKDM4C_H3K9me3
- GSM8970194 HD_SiKDM4C_H3K9me3 Replicate 2 HD_SiKDM4C_H3K9me3
- GSM8970195 HD_SiKDM4C_H3K27me3 Replicate 1 HD_SiKDM4C_H3K27me3
- GSM8970196 HD_SiKDM4C_H3K27me3 Replicate 2 HD_SiKDM4C_H3K27me3
- GSM8970197 HD_SiKDM4C_IgG Replicate 1 HD_SiKDM4C_IgG
- GSM8970198 HD_SiKDM4C_IgG Replicate 2 HD_SiKDM4C_IgG
- GSM8970199 E2_SiC_H3K9me3 Replicate 1 E2_SiC_H3K9me3
- GSM8970200 E2_SiC_H3K9me3 Replicate 2 E2_SiC_H3K9me3
- GSM8970201 E2_SiC_H3K27me3 Replicate 1 E2_SiC_H3K27me3
- GSM8970202 E2_SiC_H3K27me3 Replicate 2 E2_SiC_H3K27me3
- GSM8970203 E2_SiC_IgG Replicate 1 E2_SiC_IgG
- GSM8970204 E2_SiC_IgG Replicate 2 E2_SiC_IgG
- GSM8970205 E2_SiKDM4C_H3K9me3 Replicate 1 E2_SiKDM4C_H3K9me3
- GSM8970206 E2_SiKDM4C_H3K9me3 Replicate 2 E2_SiKDM4C_H3K9me3
- GSM8970207 E2_SiKDM4C_H3K27me3 Replicate 1 E2_SiKDM4C_H3K27me3
- GSM8970208 E2_SiKDM4C_H3K27me3 Replicate 2 E2_SiKDM4C_H3K27me3
- GSM8970209 E2_SiKDM4C_IgG Replicate 1 E2_SiKDM4C_IgG
- GSM8970210 E2_SiKDM4C_IgG Replicate 2 E2_SiKDM4C_IgG
- 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
- 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
- GSE337829 Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [ChIP-Seq] 32 samples shares architecture, chromatin
- GSE314776 Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer [ChIP-Seq] 24 samples shares architecture, chromatin
- GSE339365 Genome-wide H3K4me3 profiling of circulating immune cells reveals dynamic epigenetic reprogramming during acute critical COVID-19 120 samples shares reprogramming, epigenetic
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.