Integrated ChIP-seq and Transcriptomic Profiling of Histone Modifications Across Breast Cancer Progression in MCF10A-Derived Cell Lines [ChIP-Seq]
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 60 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
- 60 samples: 28 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.
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 GSE271703_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 PRJNA1132958 and SRA study SRP518504. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 56 samples.
How we read this: 28 replicated groups read from 60 sample titles; they account for 56 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.
- GSM8382859 ChIP_MCF10A_input
- GSM8382860 ChIP_MCF10AT1_input
- GSM8382861 ChIP_MCF10CA1a_input
- GSM8382862 ChIP_MCF10DCIS_input
- GSM8382863 ChIP_MCF10A_H4K5ac_rep1 ChIP_MCF10A_H4K5ac
- GSM8382864 ChIP_MCF10A_H4K5ac_rep2 ChIP_MCF10A_H4K5ac
- GSM8382865 ChIP_MCF10A_H4K8ac_rep1 ChIP_MCF10A_H4K8ac
- GSM8382866 ChIP_MCF10A_H4K8ac_rep2 ChIP_MCF10A_H4K8ac
- GSM8382867 ChIP_MCF10AT1_H4K5ac_rep1 ChIP_MCF10AT1_H4K5ac
- GSM8382868 ChIP_MCF10AT1_H4K5ac_rep2 ChIP_MCF10AT1_H4K5ac
- GSM8382869 ChIP_MCF10AT1_H4K8ac_rep1 ChIP_MCF10AT1_H4K8ac
- GSM8382870 ChIP_MCF10AT1_H4K8ac_rep2 ChIP_MCF10AT1_H4K8ac
- GSM8382871 ChIP_MCF10CA1a_H4K5ac_rep1 ChIP_MCF10CA1a_H4K5ac
- GSM8382872 ChIP_MCF10CA1a_H4K5ac_rep2 ChIP_MCF10CA1a_H4K5ac
- GSM8382873 ChIP_MCF10CA1a_H4K8ac_rep1 ChIP_MCF10CA1a_H4K8ac
- GSM8382874 ChIP_MCF10CA1a_H4K8ac_rep2 ChIP_MCF10CA1a_H4K8ac
- GSM8382875 ChIP_MCF10DCIS_H4K5ac_rep1 ChIP_MCF10DCIS_H4K5ac
- GSM8382876 ChIP_MCF10DCIS_H4K5ac_rep2 ChIP_MCF10DCIS_H4K5ac
- GSM8382877 ChIP_MCF10DCIS_H4K8ac_rep1 ChIP_MCF10DCIS_H4K8ac
- GSM8382878 ChIP_MCF10DCIS_H4K8ac_rep2 ChIP_MCF10DCIS_H4K8ac
- GSM8382879 ChIP_MCF10A_H3K4me1_rep1 ChIP_MCF10A_H3K4me1
- GSM8382880 ChIP_MCF10A_H3K4me1_rep2 ChIP_MCF10A_H3K4me1
- GSM8382881 ChIP_MCF10AT1_H3K4me1_rep1 ChIP_MCF10AT1_H3K4me1
- GSM8382882 ChIP_MCF10AT1_H3K4me1_rep2 ChIP_MCF10AT1_H3K4me1
- GSM8382883 ChIP_MCF10CA1a_H3K4me1_rep1 ChIP_MCF10CA1a_H3K4me1
- GSM8382884 ChIP_MCF10CA1a_H3K4me1_rep2 ChIP_MCF10CA1a_H3K4me1
- GSM8382885 ChIP_MCF10DCIS_H3K4me1_rep1 ChIP_MCF10DCIS_H3K4me1
- GSM8382886 ChIP_MCF10DCIS_H3K4me1_rep2 ChIP_MCF10DCIS_H3K4me1
- GSM8382887 ChIP_MCF10A_H3K27me3_rep1 ChIP_MCF10A_H3K27me3
- GSM8382888 ChIP_MCF10A_H3K27me3_rep2 ChIP_MCF10A_H3K27me3
- GSM8382889 ChIP_MCF10AT1_H3K27me3_rep1 ChIP_MCF10AT1_H3K27me3
- GSM8382890 ChIP_MCF10AT1_H3K27me3_rep2 ChIP_MCF10AT1_H3K27me3
- GSM8382891 ChIP_MCF10DCIS_H3K27me3_rep1 ChIP_MCF10DCIS_H3K27me3
- GSM8382892 ChIP_MCF10DCIS_H3K27me3_rep2 ChIP_MCF10DCIS_H3K27me3
- GSM8382893 ChIP_MCF10CA1a_H3K27me3_rep1 ChIP_MCF10CA1a_H3K27me3
- GSM8382894 ChIP_MCF10CA1a_H3K27me3_rep2 ChIP_MCF10CA1a_H3K27me3
- GSM8382895 ChIP_MCF10A_H3K27ac_rep1 ChIP_MCF10A_H3K27ac
- GSM8382896 ChIP_MCF10A_H3K27ac_rep2 ChIP_MCF10A_H3K27ac
- GSM8382897 ChIP_MCF10AT1_H3K27ac_rep1 ChIP_MCF10AT1_H3K27ac
- GSM8382898 ChIP_MCF10AT1_H3K27ac_rep2 ChIP_MCF10AT1_H3K27ac
+ 20 more — browse all 60 samples with per-sample file links →
- 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
- GSE297914 PU.1-Activated Genomic Regions Define Low-risk MDS Subsets Characterized by Immune Dysregulation and Disease Progression [ChIP-seq] 112 samples shares progression, chip-seq
- GSE337829 Integrated single-cell profiling of RNA and DNA interactomes reveals targetable chromatin architectures in cancer [ChIP-Seq] 32 samples shares integrated, chip-seq
- GSE339456 Integrated bulk and spatial transcriptomic analysis identifies progression-associated molecular signatures in biopsy-proven hypertensive nephropathy [RNA-seq] 35 samples shares progression, integrated
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.