GEO series

MYCN sustains a progenitor-stage differentiation block in human neuroepithelial stem cells to drive ETMR-like tumourigenesis [scRNA-seq]

GSE338545 Homo sapiens (human) Single-cell RNA-seq 1 samples Submitted 2026/07/17 Platform GPL34284

At a glance

Single-cell RNA-seq · human · 1 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)
Samples: 1 samples
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)

Embryonal tumours with multilayered rosettes (ETMRs) are aggressive paediatric brain tumours driven in most cases by amplification of the chromosome 19 microRNA cluster (C19MC), which upregulates the oncogene MYCN. Whether MYCN dysregulation alone is sufficient to produce ETMR-like tumours, independent of the broader C19MC machinery, has not been tested.

Read the full summary ↓

Here, we show that sustained MYCN expression in human neuroepithelial stem (NES) cells, i.e. primitive neural progenitors resembling the proposed cell of origin of ETMR, is sufficient to generate ETMR-like brain tumours in vivo. These tumours share methylation and transcriptional signatures with ETMR and reproduce its primitive, stem-like cellular hierarchy. MYCN-expressing tumour cells are arrested at an early neural progenitor stage, and MYCN withdrawal arrests growth and engages neuronal differentiation. Our findings identify sustained MYCN as sufficient to drive an ETMR-like developmental arrest in primitive human neural cells.

This dataset

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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 GSE338545_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 PRJNA1494943 and SRA study SRP717862. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Samples in this study

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Datasets on a similar topic

GSE339373 MYCN sustains a progenitor-stage differentiation block in human neuroepithelial stem cells to drive ETMR-like tumourigenesis [RNA-seq] 11 samples shares mycn, progenitor-stage, neuroepithelial, tumourigenesis, etmr-like, sustains, block
GSE339375 MYCN sustains a progenitor-stage differentiation block in human neuroepithelial stem cells to drive ETMR-like tumourigenesis. 24 samples shares mycn, progenitor-stage, neuroepithelial, tumourigenesis, etmr-like, sustains, block
GSE211355 The SAGA complex maintains the oncogenic gene expression program in MYCN-amplified neuroblastoma 92 samples shares mycn
GSE268136 MYCN-driven de-differentiation profile identifies a subgroup of aggressive retinoblastoma II 82 samples shares mycn
GSE211354 The SAGA complex maintains the oncogenic gene expression program in MYCN-amplified neuroblastoma [RNA-Seq] 54 samples shares mycn
GSE164455 KDM4 inhibition disrupts the core regulatory transcriptional circuitry in MYCN-driven neuroblastoma [RNA-seq] 33 samples shares mycn
GSE236677 Metformin enhanced the effect of a Ketogenic diet in MYCN amplified Neuroblastoma xenografts 30 samples shares mycn
GSE273349 Kinome reprogramming of G2/M kinases and repression of MYCN contribute to superior efficacy of lorlatinib in ALK-driven neuroblastoma 20 samples shares mycn

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