GEO series

Human cerebellar organoids to study medulloblastoma pathogenesis and treatment. [scRNA-Seq]

GSE263652 Homo sapiens (human) Single-cell RNA-seq 17 samples Submitted 2026/04/30 Platform GPL24676

At a glance

Single-cell RNA-seq · human · 17 samples

What it is: Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart.
Organism: Homo sapiens (human)
Topic: MedulloblastomaThis series is part of our curated briefing on it.
Samples: 17 samples: 17 samples, each with a distinct title — no replicated groupsGroups 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)

Faithful in vivo models of Group 4 medulloblastoma (G4 MB) are currently unavailable and recent studies showed the unique role of human-specific progenitors in the development of G3 and G4 MB. Here, we obtained cerebellar organoid (CbO) from expanded potential stem cells (EPSC) and developed them in vitro as 3D structures.

Read the full summary ↓

We performed extensive characterisation of the epigenetic and transcriptomic profile of the mature CbO confirming the presence of sub compartment-specific cerebellar lineages linked to MB formation, including populations expressing signature genes reminiscent of the G3 and G4 MB cell-of-origin never described before. In parallel we have established a protocol to co-culture primary MB cells with our CbO to generate CbO-MB models. We confirmed that CbO sustains MB cells proliferation and invasion while preserving their molecular identity, and that CbO-MB recapitulated the efficacy of in vivo anti-tumour therapy, hence representing a suitable model to gain insight into G3/G4 MB pathogenesis and to set up pre-clinical drug screening.

This dataset

Open GSE263652 in finder → Find more human 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 GSE263652_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1098648 and SRA study SRP500761. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

17 samples, each with a distinct title — no replicated groups

Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.

How we read this: Read from 17 sample titles: 17 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

GSM8196014 Cb019_D7_GEX
GSM8196015 Cb019_D35_GEX
GSM8196016 Cb061_D7_GEX
GSM8196017 Cb061_D35_GEX
GSM8196018 Cb061_D49_GEX
GSM8196019 Cb0_MB_C_GEX
GSM8196020 Cb0_MB_S_GEX
GSM8879326 CbO+Med211FH_invitro
GSM8879327 CbO+Med211FH_PDX
GSM8879328 CbO+NSC73.5
GSM8879329 CbO19_D63_Pax6-dox.cntrl
GSM8879330 CbO19_D63_Pax6-MycOE
GSM8879331 CbO19_D63_Eomes-dox.cntrl
GSM8879332 CbO19_D63_Eomes-MycOE
GSM8879333 Med211FH-2D
GSM9475511 CbO+Eomes.MYC.MB
GSM9475512 CbO+Pax6.MYC.MB

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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.