← BioTransfer GEO Dataset Finder
GEO series

Cancer-associated DNA Hypermethylation of Polycomb Targets Requires DNMT3A Dual Recognition of histone H2AK119 Ubiquitination and the Nucleosome Acidic Patch

GSE247019 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 134 samples Submitted 2024/08/28 Platform GPL30172Platform GPL24247Platform GPL21626
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 134 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
Mus musculus (mouse)
Samples
134 samples: 61 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.
Paper
Cancer-associated DNA hypermethylation of Polycomb targets requires DNMT3A dual recognition of histone H2AK119 ubiquitination and the nucleosome acidic patchScience advances · 2024
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
Cancer-associated DNA hypermethylation of Polycomb targets requires DNMT3A dual recognition of histone H2AK119 ubiquitination and the nucleosome acidic patch
Gretarsson KH, Abini-Agbomson S, Gloor SL et al. · Science advances 2024 · PMID 39196936 · doi:10.1126/sciadv.adp0975
This dataset
Open GSE247019 in finder → Find more mouse methylation 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 GSE247019_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 PRJNA1035552 and SRA study SRP470146. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39196936) ↗
Study design
61 conditions, mostly in duplicate
EN Organoid, RRBS, ×3 ESCC Organoid, RRBS, ×3 ESCC Organoid, H3K27me3, Cut&Tag, ×3 ESCC Organoid, H2AK119Ub, Cut&Tag, ×3 ESCC Organoid, H3K4me3, Cut&Tag, ×3 10T, DNMT3A1 WT, RRBS, ×2 10T, DNMT3A1 W330R, RRBS, ×2 10T, DNMT3A1 W330R-R181E, RRBS, ×2 +60 more

Supports a case/control comparison: 17 samples read as cases, 15 as controls.

How we read this: 61 replicated groups read from 134 sample titles; they account for 127 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

+ 94 more — browse all 134 samples with per-sample file links →

Datasets on a similar topic

Search all mouse methylation datasets in GEO →

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.