GEO series
Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells [ChIP-seq]
GSE298767
Homo sapiens (human)
ChIP-seq / ATAC-seq (genome binding and open chromatin)
63 samples
Submitted 2026/04/18
Platform GPL30173
At a glance
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 63 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)
- Samples
- 63 samples: 21 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
- Dose-dependent hormone actions at estrogen receptor enhancers specify distinct molecular and biological outcomesScience advances · 2026
Summary (written by the submitters)
Estrogen is the primary mitogen for ER+ BC cells. However, most studies prior to this examining the genomic effects of E2-regulated signaling in cell-based assays used supraphysiological levels of hormone. While this has allowed us to understand the extremes of E2 signaling, it has limited our ability to examine cellular functions which operate at lower hormone concentrations.
Read the full summary ↓
In particular, the genomic actions of ligand-bound ERa through transcriptional enhancer formation and function are not understood at physiological E2 doses. Here, we use an integrated genomic approach with RNA-seq, PRO-seq, ChIP-seq, and ATAC-seq to identify gene sets that express preferentially at either picomolar or nanomolar concentrations of E2. Expression of these genes is regulated mainly at the transcriptional level and is associated with distinct enhancer features, including chromatin accessibility and H3K27ac enrichment, as well as differential binding of FOXA1 and GATA3 co-transcription factors.
Published in
Kim HB, Nandu T, Kim YJ et al.
· Science advances 2026
· PMID 42234735
· doi:10.1126/sciadv.aec2424
This dataset
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.
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 GSE298767_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1271073 and SRA study SRP589377. Searching any of these in the dataset finder brings you back here.
Study design
21 conditions, mostly in triplicate
MCF7_ChIP-seq input_DMSO 30 min ×3
MCF7_ER-ChIP-seq_DMSO 30 min ×3
MCF7_ChIP-seq input_10 pM E2 30 min ×3
MCF7_ER-ChIP-seq_10 pM E2 30 min ×3
MCF7_ChIP-seq input_100 pM E2 30 min ×3
MCF7_ER-ChIP-seq_100 pM E2 30 min ×3
MCF7_ChIP-seq input_1 nM E2 30 min ×3
MCF7_ER-ChIP-seq_1 nM E2 30 min ×3
+13 more
Supports a between-group comparison across 63 samples.
How we read this: 21 replicated groups read from 63 sample titles; they account for 63 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
- GSM9022817 MCF7_ChIP-seq input_DMSO 30 min_set 1 MCF7_ChIP-seq input_DMS…
- GSM9022818 MCF7_ChIP-seq input_DMSO 30 min_set 2 MCF7_ChIP-seq input_DMS…
- GSM9022819 MCF7_ChIP-seq input_DMSO 30 min_set 3 MCF7_ChIP-seq input_DMS…
- GSM9022820 MCF7_ER-ChIP-seq_DMSO 30 min_set 1 MCF7_ER-ChIP-seq_DMSO 3…
- GSM9022821 MCF7_ER-ChIP-seq_DMSO 30 min_set 2 MCF7_ER-ChIP-seq_DMSO 3…
- GSM9022822 MCF7_ER-ChIP-seq_DMSO 30 min_set 3 MCF7_ER-ChIP-seq_DMSO 3…
- GSM9022823 MCF7_ChIP-seq input_10 pM E2 30 min_set 1 MCF7_ChIP-seq input_10 …
- GSM9022824 MCF7_ChIP-seq input_10 pM E2 30 min_set 2 MCF7_ChIP-seq input_10 …
- GSM9022825 MCF7_ChIP-seq input_10 pM E2 30 min_set 3 MCF7_ChIP-seq input_10 …
- GSM9022826 MCF7_ER-ChIP-seq_10 pM E2 30 min_set 1 MCF7_ER-ChIP-seq_10 pM …
- GSM9022827 MCF7_ER-ChIP-seq_10 pM E2 30 min_set 2 MCF7_ER-ChIP-seq_10 pM …
- GSM9022828 MCF7_ER-ChIP-seq_10 pM E2 30 min_set 3 MCF7_ER-ChIP-seq_10 pM …
- GSM9022829 MCF7_ChIP-seq input_100 pM E2 30 min_set 1 MCF7_ChIP-seq input_100…
- GSM9022830 MCF7_ChIP-seq input_100 pM E2 30 min_set 2 MCF7_ChIP-seq input_100…
- GSM9022831 MCF7_ChIP-seq input_100 pM E2 30 min_set 3 MCF7_ChIP-seq input_100…
- GSM9022832 MCF7_ER-ChIP-seq_100 pM E2 30 min_set 1 MCF7_ER-ChIP-seq_100 pM…
- GSM9022833 MCF7_ER-ChIP-seq_100 pM E2 30 min_set 2 MCF7_ER-ChIP-seq_100 pM…
- GSM9022834 MCF7_ER-ChIP-seq_100 pM E2 30 min_set 3 MCF7_ER-ChIP-seq_100 pM…
- GSM9022835 MCF7_ChIP-seq input_1 nM E2 30 min_set 1 MCF7_ChIP-seq input_1 n…
- GSM9022836 MCF7_ChIP-seq input_1 nM E2 30 min_set 2 MCF7_ChIP-seq input_1 n…
- GSM9022837 MCF7_ChIP-seq input_1 nM E2 30 min_set 3 MCF7_ChIP-seq input_1 n…
- GSM9022838 MCF7_ER-ChIP-seq_1 nM E2 30 min_set 1 MCF7_ER-ChIP-seq_1 nM E…
- GSM9022839 MCF7_ER-ChIP-seq_1 nM E2 30 min_set 2 MCF7_ER-ChIP-seq_1 nM E…
- GSM9022840 MCF7_ER-ChIP-seq_1 nM E2 30 min_set 3 MCF7_ER-ChIP-seq_1 nM E…
- GSM9022841 MCF7_ChIP-seq input_10 nM E2 30 min_set 1 MCF7_ChIP-seq input_10 …
- GSM9022842 MCF7_ChIP-seq input_10 nM E2 30 min_set 2 MCF7_ChIP-seq input_10 …
- GSM9022843 MCF7_ChIP-seq input_10 nM E2 30 min_set 3 MCF7_ChIP-seq input_10 …
- GSM9022844 MCF7_ER-ChIP-seq_10 nM E2 30 min_set 1 MCF7_ER-ChIP-seq_10 nM …
- GSM9022845 MCF7_ER-ChIP-seq_10 nM E2 30 min_set 2 MCF7_ER-ChIP-seq_10 nM …
- GSM9022846 MCF7_ER-ChIP-seq_10 nM E2 30 min_set 3 MCF7_ER-ChIP-seq_10 nM …
- GSM9022847 MCF7_H3K27ac-ChIP-seq_DMSO 30 min_set 1 MCF7_H3K27ac-ChIP-seq_D…
- GSM9022848 MCF7_H3K27ac-ChIP-seq_DMSO 30 min_set 2 MCF7_H3K27ac-ChIP-seq_D…
- GSM9022849 MCF7_H3K27ac-ChIP-seq_DMSO 30 min_set 3 MCF7_H3K27ac-ChIP-seq_D…
- GSM9022850 MCF7_H3K27ac-ChIP-seq_10 pM E2 30 min_set 1 MCF7_H3K27ac-ChIP-seq_1…
- GSM9022851 MCF7_H3K27ac-ChIP-seq_10 pM E2 30 min_set 2 MCF7_H3K27ac-ChIP-seq_1…
- GSM9022852 MCF7_H3K27ac-ChIP-seq_10 pM E2 30 min_set 3 MCF7_H3K27ac-ChIP-seq_1…
- GSM9022853 MCF7_H3K27ac-ChIP-seq_100 pM E2 30 min_set 1 MCF7_H3K27ac-ChIP-seq_1…
- GSM9022854 MCF7_H3K27ac-ChIP-seq_100 pM E2 30 min_set 2 MCF7_H3K27ac-ChIP-seq_1…
- GSM9022855 MCF7_H3K27ac-ChIP-seq_100 pM E2 30 min_set 3 MCF7_H3K27ac-ChIP-seq_1…
- GSM9022856 MCF7_H3K27ac-ChIP-seq_1 nM E2 30 min_set 1 MCF7_H3K27ac-ChIP-seq_1…
+ 23 more — browse all 63 samples with per-sample file links →
Datasets on a similar topic
- GSE298770 Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells [PRO-seq] 15 samples shares dose-dependent, estrogen, breast
- GSE318617 Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells [Hi-C] 6 samples shares dose-dependent, estrogen, breast
- GSE289805 Histone H4 lysine 20 tri-methylation safeguards breast cancer lineage fidelity and unfolded protein response [ChIP-seq/ATAC-seq] 126 samples shares chip-seq, breast
- GSE259248 ZBTB7A is a modulator of KDM5-driven transcriptional networks in basal breast cancer (ChIP-Seq) 36 samples shares chip-seq, breast
- GSE280574 mChIP-seq for high-throughput epigenomic profiling reveals a decoupling of H2A.Z and H3K4me3 in cancer 576 samples shares chip-seq
- GSE314776 Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer [ChIP-Seq] 24 samples shares chip-seq
- GSE296831 Epigenetic Context Defines the Transcriptional Activity of Canonical and Noncanonical NF-kappaB Signaling in Pancreatic Cancer [ChIP-Seq] 48 samples shares chip-seq
- GSE316389 Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [ATAC-seq] 36 samples shares breast
Share this dataset
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.