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MCF-7 RPMI ERa and FOXA1 ChIP-seq in GDC-9545 and GNE-858

GSE246361 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 18 samples Submitted 2026/03/01 Platform GPL18573
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 18 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
18 samples: 9 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.
Summary (written by the submitters)
We performed ChIPseq for ER, FOXA1 and H3K27ac on MCF-7 cells treated with vehicle (DMSO), GDC-9545 or GNE-858. GNE-858 is a non-ER degrader (SERM) from the same chemical series as GDC-9545.
This dataset
Open GSE246361 in finder → Find more human ChIP / ATAC / CUT&Tag datasets →
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.

Series matrix ↓
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 GSE246361_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓
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.

Raw reads on ENA ↗

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 PRJNA1032610 and SRA study SRP468644. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
9 conditions, mostly in duplicate
MCF-7, FOXA1, ChIP, DMSO ×2 MCF-7, FOXA1, ChIP, GDC-9545 ×2 MCF-7, FOXA1, ChIP, GNE-858 ×2 MCF-7, ERa, ChIP, DMSO ×2 MCF-7, ERa, ChIP, GDC-9545 ×2 MCF-7, ERa, ChIP, GNE-858 ×2 MCF-7, H3K27ac, ChIP, DMSO ×2 MCF-7, H3K27ac, ChIP, GDC-9545 ×2 +1 more

Supports a between-group comparison across 18 samples.

How we read this: 9 replicated groups read from 18 sample titles; they account for 18 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
Datasets on a similar topic

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