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Determining the chromatin accessibility profiles of functionally distinct SHH-medulloblastoma sub-populations

GSE233993 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 12 samples Submitted 2024/09/11 Platform GPL17021
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 12 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
12 samples: 4 × Primary mouse SHH MB SOX2- tumor cells vs 4 × Primary mouse SHH MB SOX2+ tumor cells vs 2 × Primary mouse SHH MB SOX2+/MKI67- tumor cells vs 2 × Primary mouse SHH MB SOX2+/MKI67+ tumor cellsGroups 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
OLIG2 mediates a rare targetable stem cell fate transition in sonic hedgehog medulloblastomaNature communications · 2025
Summary (written by the submitters)
Using FACS sorting on SOX2-eGFP and MKi67-RFP mice on a Ptch1+/- background, we identified cycling& non-cycling stem cells and tumor bulk subpopulations in endpoint mouse SHH-subgroup medulloblastoma tumors, and determined their chromatin accessibility progiles to identify unique regulators of cell state.
Published in
OLIG2 mediates a rare targetable stem cell fate transition in sonic hedgehog medulloblastoma
Desai K, Wanggou S, Luis E et al. · Nature communications 2025 · PMID 39904987 · doi:10.1038/s41467-024-54858-y
This dataset
Open GSE233993 in finder → Find more mouse 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 GSE233993_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 PRJNA979167 and SRA study SRP440950. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39904987) ↗
Study design
4 × Primary mouse SHH MB SOX2- tumor cells vs 4 × Primary mouse SHH MB SOX2+ tumor cells vs 2 × Primary mouse SHH MB SOX2+/MKI67- tumor cells vs 2 × Primary mouse SHH MB SOX2+/MKI67+ tumor cells

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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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