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Effect of ZIC1 on group 3 medulloblastoma cell lines and granule neuron progenitor

GSE217639 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 49 samples Submitted 2024/09/19 Platform GPL16791Platform GPL24676Platform GPL30172Platform GPL24247
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 49 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
MedulloblastomaThis series is part of our curated briefing on it.
Samples
49 samples: 39 distinct titles, 8 of them repeatedGroups 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
ZIC1 is a context-dependent medulloblastoma driver in the rhombic lipNature genetics · 2025
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
Published in
ZIC1 is a context-dependent medulloblastoma driver in the rhombic lip
Lee JJY, Tao R, You Z et al. · Nature genetics 2025 · PMID 39753768 · doi:10.1038/s41588-024-02014-z
This dataset
Open GSE217639 in finder → Find more RNA-seq datasets → Medulloblastoma 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 GSE217639_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 PRJNA899864 and SRA study SRP407040. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39753768) ↗
Study design
39 distinct titles, 8 of them repeated
D425_RNA_BFP ×3 D425_RNA_ZIC1_4 ×3 ATOH1_GFP_RNA_mch_bulk ×2 ATOH1_GFP_RNA_mch_sort ×2 ATOH1_GFP_RNA_ZIC1_bulk ×2 ATOH1_GFP_RNA_ZIC1_sort ×2 GNP_ZIC1NF_301_IP ×2 GNP_ZIC1NF_WT1_IP ×2

How we read this: Read from 49 sample titles: 39 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

+ 9 more — browse all 49 samples with per-sample file links →

More Medulloblastoma datasets

Search all RNA-seq 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.