Estrogen Receptor alpha CUT&RUN analysis of estrogen receptor positive breast cancer cell lines MCF7 and UCD12 with 1h hormone E2 treatment
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 40 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
- 40 samples: 40 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
- Estradiol (E2) concentration shapes the chromatin binding landscape of estrogen receptor alphaThe Journal of biological chemistry · 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 GSE210007_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 PRJNA863298 and SRA study SRP388628. 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 40 sample titles: 40 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.
- GSM6413381 MCF7 ETOH 1h replicate 1 ERα CUT&RUN
- GSM6413382 MCF7 ETOH 1h replicate 2 ERα CUT&RUN
- GSM6413383 MCF7 ETOH 1h replicate 3 ERα CUT&RUN
- GSM6413384 MCF7 10^-12M E2 1h replicate 1 ERα CUT&RUN
- GSM6413385 MCF7 10^-12M E2 1h replicate 2 ERα CUT&RUN
- GSM6413386 MCF7 10^-12M E2 1h replicate 3 ERα CUT&RUN
- GSM6413387 MCF7 10^-10M E2 1h replicate 1 ERα CUT&RUN
- GSM6413388 MCF7 10^-10M E2 1h replicate 2 ERα CUT&RUN
- GSM6413389 MCF7 10^-10M E2 1h replicate 3 ERα CUT&RUN
- GSM6413390 MCF7 10^-8M E2 1h replicate 1 ERα CUT&RUN
- GSM6413391 MCF7 10^-8M E2 1h replicate 2 ERα CUT&RUN
- GSM6413392 MCF7 10^-8M E2 1h replicate 3 ERα CUT&RUN
- GSM6413393 UCD12 ETOH 1h replicate 1 ERα CUT&RUN
- GSM6413394 UCD12 ETOH 1h replicate 2 ERα CUT&RUN
- GSM6413395 UCD12 ETOH 1h replicate 3 ERα CUT&RUN
- GSM6413396 UCD12 10^-12M E2 1h replicate 1 ERα CUT&RUN
- GSM6413397 UCD12 10^-12M E2 1h replicate 2 ERα CUT&RUN
- GSM6413398 UCD12 10^-12M E2 1h replicate 3 ERα CUT&RUN
- GSM6413399 UCD12 10^-10M E2 1h replicate 1 ERα CUT&RUN
- GSM6413400 UCD12 10^-10M E2 1h replicate 2 ERα CUT&RUN
- GSM6413401 UCD12 10^-10M E2 1h replicate 3 ERα CUT&RUN
- GSM6413402 UCD12 10^-8M E2 1h replicate 1 ERα CUT&RUN
- GSM6413403 UCD12 10^-8M E2 1h replicate 2 ERα CUT&RUN
- GSM6413404 UCD12 10^-8M E2 1h replicate 3 ERα CUT&RUN
- GSM6413405 MCF7 10^-10M E2 1h replicate 1 IgG CUT&RUN
- GSM6413406 MCF7 10^-10M E2 1h replicate 2 IgG CUT&RUN
- GSM6413407 UCD12 10^-10M E2 1h replicate 1 IgG CUT&RUN
- GSM6413408 UCD12 10^-10M E2 1h replicate 2 IgG CUT&RUN
- GSM7744754 MCF7 ETOH 1h replicate 1 RNA-seq
- GSM7744755 MCF7 ETOH 1h replicate 2 RNA-seq
- GSM7744756 MCF7 ETOH 1h replicate 3 RNA-seq
- GSM7744757 MCF7 10^-12M E2 1h replicate 1 RNA-seq
- GSM7744758 MCF7 10^-12M E2 1h replicate 2 RNA-seq
- GSM7744759 MCF7 10^-12M E2 1h replicate 3 RNA-seq
- GSM7744760 MCF7 10^-10M E2 1h replicate 1 RNA-seq
- GSM7744761 MCF7 10^-10M E2 1h replicate 2 RNA-seq
- GSM7744762 MCF7 10^-10M E2 1h replicate 3 RNA-seq
- GSM7744763 MCF7 10^-8M E2 1h replicate 1 RNA-seq
- GSM7744764 MCF7 10^-8M E2 1h replicate 2 RNA-seq
- GSM7744765 MCF7 10^-8M E2 1h replicate 3 RNA-seq
- GSE10885 An integromic analysis reveals that metaplastic carcinomas are distinct from basal-like tumors. 244 samples same disease briefing
- GSE10886 A Supervised Risk Predictor of Breast Cancer Based on Biological Subtypes 226 samples same disease briefing
- GSE11121 The humoral immune system has a key prognostic impact in node-negative breast cancer 200 samples same disease briefing
- 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
- GSE104675 Role for the Transcriptional Activator ZRF1 in Breast Cancer Progression and Endocrine Resistance 6 samples same disease briefing
- GSE287902 BPTF regulstes androgen receptor activity by enhancing chromatin accessibility and stabilizing the AR-FOXA1 interaction [Cut&Run] 40 samples shares cut, run, receptor
- GSE270125 Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency [CUT&Run] 169 samples shares cut, run
- GSE270503 Epigenetic heterogeneity and state-specific transcriptional programs determine differential drug response in osteosarcoma [Cut&Run] 56 samples shares cut, run
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.