← BioTransfer GEO Dataset Finder
GEO series

Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level

GSE243796 Homo sapiens (human) DNA methylation 90 samples Submitted 2024/04/22 Platform GPL13534Platform GPL23976Platform GPL30173
At a glance

DNA methylation · human · 90 samples

What it is
DNA methylationChemical marks on DNA that help switch genes on or off.
Organism
Homo sapiens (human)
Topic
MedulloblastomaThis series is part of our curated briefing on it.
Samples
90 samples: 6 conditions, mostly with about 40 replicates eachGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed expression table (series matrix) and the array files, from NCBI.
Paper
Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan levelNature communications · 2024
Summary (written by the submitters)
Medulloblastomas (MBs) are malignant pediatric brain tumors that are molecularly and clinically heterogenous. The application of omics technologies – mainly studying nucleic acids – has significantly improved MB classification and stratification, but treatment options are still unsatisfactory. The proteome and their N-glycans hold the potential to discover clinically relevant phenotypes and targetable pathways.
Read the full summary ↓
We compile a harmonized proteome dataset of 167 MBs and integrate findings with DNA methylome, transcriptome and N-glycome data. We show six proteome MB subtypes, that can be assigned to two main molecular programs: transcription/translation (pSHHt, pWNT and pGroup3myc), and synapses/immunological processes (pSHHs, pGroup3 and pGroup4). Multiomic analysis reveals different conservation levels of proteome features across MB subtypes at the DNA methylome level. Aggressive pGroup3myc MBs and favourable pWNT MBs are most similar in cluster hierarchies concerning overall proteome patterns but show different protein abundances of the vincristine resistance-associated multiprotein complex TriC/CCT and of N-glycan turnover-associated factors. The N-glycome reflects proteome subtypes and complex-bisecting N-glycans characterize pGroup3myc tumors. Our results shed light on targetable alterations in MB and set a foundation for potential immunotherapies targeting glycan structures. This SuperSeries is composed of the SubSeries listed below.
Published in
Multiomic profiling of medulloblastoma reveals subtype-specific targetable alterations at the proteome and N-glycan level
Godbole S, Voß H, Gocke A et al. · Nature communications 2024 · PMID 39043693 · doi:10.1038/s41467-024-50554-z
This dataset
Open GSE243796 in finder → Find more human methylation 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 GSE243796_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 beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA1020062 and SRA study SRP462679. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39043693) ↗
Study design
6 conditions, mostly with about 40 replicates each
genomic DNA from FFPE material of MB patient … ×40 genomic DNA from FFPE material of MB patient … ×29 SHH MB ×7 WNT MB ×6 GR4 MB ×4 GR3 MB ×3 GR3 MB ×1

Supports a between-group comparison across 89 samples.

How we read this: 6 replicated groups read from 90 sample titles; they account for 89 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

+ 50 more — browse all 90 samples with per-sample file links →

More Medulloblastoma datasets

Search all human 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.