GEO series
Dose-dependent Effects of Estrogen on Genomic Regulation in Breast Cancer Cells [PRO-seq]
Summary
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. 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
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Direct links to NCBI, no account and no request form: the whole study as GSE298770_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 15 samples.
Also filed as BioProject PRJNA1271075. Searching any of these in the dataset finder brings you back here.
Study design
5 conditions, mostly in triplicate
MCF-7_PRO-seq_DMSO 30min ×3
MCF-7_PRO-seq_10 pM E2 30min ×3
MCF-7_PRO-seq_100 pM E2 30min ×3
MCF-7_PRO-seq_1 nM E2 30min ×3
MCF-7_PRO-seq_10 nM E2 30min ×3
Supports a between-group comparison across 15 samples.
5 replicated groups read from 15 sample titles; they account for 15 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9022901 MCF-7_PRO-seq_DMSO 30min_rep1
- GSM9022902 MCF-7_PRO-seq_DMSO 30min_rep2
- GSM9022903 MCF-7_PRO-seq_DMSO 30min_rep3
- GSM9022904 MCF-7_PRO-seq_10 pM E2 30min_rep1
- GSM9022905 MCF-7_PRO-seq_10 pM E2 30min_rep2
- GSM9022906 MCF-7_PRO-seq_10 pM E2 30min_rep3
- GSM9022907 MCF-7_PRO-seq_100 pM E2 30min_rep1
- GSM9022908 MCF-7_PRO-seq_100 pM E2 30min_rep2
- GSM9022909 MCF-7_PRO-seq_100 pM E2 30min_rep3
- GSM9022910 MCF-7_PRO-seq_1 nM E2 30min_rep1
- GSM9022911 MCF-7_PRO-seq_1 nM E2 30min_rep2
- GSM9022912 MCF-7_PRO-seq_1 nM E2 30min_rep3
- GSM9022913 MCF-7_PRO-seq_10 nM E2 30min_rep1
- GSM9022914 MCF-7_PRO-seq_10 nM E2 30min_rep2
- GSM9022915 MCF-7_PRO-seq_10 nM E2 30min_rep3
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