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Epigenetic activation of SOX11 is associated with recurrence and progression of DCIS to invasive breast cancer

GSE214094 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 54 samples Submitted 2024/07/17 Platform GPL20301Platform GPL32691
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 54 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
54 samples: 50 distinct titles, 2 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed expression table (series matrix) and the array files, from NCBI.
Paper
Epigenetic activation of SOX11 is associated with recurrence and progression of ductal carcinoma in situ to invasive breast cancerBritish journal of cancer · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Epigenetic activation of SOX11 is associated with recurrence and progression of ductal carcinoma in situ to invasive breast cancer
Treekitkarnmongkol W, Shah V, Kai K et al. · British journal of cancer 2024 · PMID 38760444 · doi:10.1038/s41416-024-02697-5
This dataset
Open GSE214094 in finder → Find more human ChIP / ATAC / CUT&Tag datasets → Breast cancer landscape →
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 GSE214094_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 PRJNA883755 and SRA study SRP398735. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38760444) ↗
Study design
50 distinct titles, 2 of them repeated
SUM225, Control ×3 SUM225, Treated ×3

Supports a case/control comparison: 3 samples read as cases, 3 as controls.

How we read this: Read from 54 sample titles: 50 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.

Samples in this study

+ 14 more — browse all 54 samples with per-sample file links →

More Breast cancer datasets

Search all human ChIP / ATAC / CUT&Tag datasets in GEO →

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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.