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3D genome topology distinguishes molecular subgroups of medulloblastoma

GSE246125 Homo sapiens (human) RNA-seq (gene expression) 55 samples Submitted 2024/09/29 Platform GPL20795Platform GPL16791
At a glance

RNA-seq (gene expression) · human · 55 samples

What it is
RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism
Homo sapiens (human)
Topic
MedulloblastomaThis series is part of our curated briefing on it.
Samples
55 samples: 55 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)
Four main medulloblastoma (MB) molecular subtypes have been identified based on transcriptional, DNA methylation and genetic profiles. However, it is currently not known whether MB subtypes have their own specific 3D genome architecture. Hi-C maps were globally stable across MB subtypes. However, among the 3D genome features we tested, boundary strengths of topologically associating domains (TADs) were the best at classifying MB samples – including Group 3 and Group 4 specimens - according to their known molecular subtypes.
Read the full summary ↓
Although boundary strength was not generally associated with differential gene expression between subtypes, we found that Group 3 and Group 4 specimens had differential TAD boundary strengths near genes that are uniquely expressed in their respective lineages of origin. Accordingly, we provide examples of TAD boundary reorganization that clearly distinguish Group 3 and 4 samples at these developmentally important genomic sites. TAD boundary strength allows classification of MB molecular subtypes, indicating that the shape of the 3D genome is unique to each molecular subtype. Genome topologies of Group 3 and 4 tumors are shaped differently at key lineage genes, but these differences are not strongly predictive of changes in gene expression. 3D genome architecture might be a fossil of the lineages of origin of MB subtypes.
This dataset
Open GSE246125 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 GSE246125_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1031604. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
55 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 55 sample titles: 55 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

+ 15 more — browse all 55 samples with per-sample file links →

More Medulloblastoma datasets

Search all human RNA-seq datasets in GEO →

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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.