GEO series

Single-nucleus and spatial landscape of the sub-ventricular zone in human glioblastoma

GSE259378 Homo sapiens (human) Single-nucleus RNA-seq 28 samples Submitted 2024/11/20 Platform GPL24676

At a glance

Single-nucleus RNA-seq · human · 28 samples

What it is: Single-nucleus RNA-seqGene activity measured in individual nuclei (used when whole cells are hard to isolate, for example from frozen tissue).
Organism: Homo sapiens (human)
Topic: GlioblastomaThis series is part of our curated briefing on it.
Samples: 28 samples: 27 distinct titles, 1 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: Single-nucleus and spatial landscape of the sub-ventricular zone in human glioblastomaCell reports · 2025

Summary (written by the submitters)

Glioblastoma (GBM) clinical management is challenging due to its heterogeneous nature, invasive potential, and poor response to radio- and chemo-therapy. As a result, GBM inevitably recurs and only a minority of patients survive 5 years post-diagnosis. We were the first to show that in the majority of GBM patients, the sub-ventricular zone (SVZ) of the lateral ventricles is a reservoir of cancer stem-like cells (CSCs) that show distinct patterns of treatment resistance when compared to matched CSCs from the tumor mass and contribute to the seeding of the recurrent tumor.

Read the full summary ↓

However, the sampling and the characterization of the SVZ in GBM patients pose several challenges, as this area is extremely small and needs to be objectively identified during tumor surgical resection.

Published in

Single-nucleus and spatial landscape of the sub-ventricular zone in human glioblastoma

Licón-Muñoz Y, Avalos V, Subramanian S et al. · Cell reports 2025 · PMID 39752252 · doi:10.1016/j.celrep.2024.115149

This dataset

Open GSE259378 in finder → Find more human RNA-seq datasets → Glioblastoma 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 GSE259378_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 PRJNA1081384 and SRA study SRP492102. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39752252) ↗

Study design

27 distinct titles, 1 of them repeated

Nsvz_HNS ×2

How we read this: Read from 28 sample titles: 27 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

GSM8115039 Nsvz_HNS1
GSM8115040 Nsvz_HNS2
GSM8115041 TMASS_GBM10A
GSM8115042 TMASS_GBM12A
GSM8115043 TMASS_GBM14A
GSM8115044 TMASS_GBM16A
GSM8115045 TMASS_GBM17A
GSM8115046 TMASS_GBM18A
GSM8115047 TMASS_GBM20A
GSM8115048 TMASS_GBM22A
GSM8115049 TMASS_GBM7A
GSM8115050 TMASS_GBM8A
GSM8115051 TMASS_GBM9A
GSM8115052 TMASS_MIS1A
GSM8115053 TMASS_MIS2A
GSM8115054 TMASS_MIS3A
GSM8115055 TSVZ_GBM10B
GSM8115056 TSVZ_GBM12B
GSM8115057 TSVZ_GBM16B
GSM8115058 TSVZ_GBM17B
GSM8115059 TSVZ_GBM20B
GSM8115060 TSVZ_GBM22B
GSM8115061 TSVZ_GBM7B
GSM8115062 TSVZ_GBM8B
GSM8115063 TSVZ_GBM9B
GSM8115064 TSVZ_MIS1B
GSM8115065 TSVZ_MIS2B
GSM8115066 TSVZ_MIS3B

More Glioblastoma datasets

GSE112648 SOXC factors as suppressors modulate Rho activity to promote neuronal reprogramming of human glioblastoma cells 18 samples same disease briefing · shares glioblastoma
GSE131928 single cell RNA-seq analysis of adult and paediatric IDH-wildtype Glioblastomas 2 samples same disease briefing · shares glioblastoma
GSE107560 Ivy Glioblastoma Atlas Project 305 samples same disease briefing · shares glioblastoma
GSE13041 Gene expression analysis of glioblastomas identifies the major molecular basis for the prognostic benefit of younger age 267 samples same disease briefing · shares glioblastoma
GSE112645 SOXC factors as suppressors modulate Rho activity to promote neuronal reprogramming of human glioblastoma cells 12 samples same disease briefing · shares glioblastoma
GSE10878 Integrative Genome-wide Analysis of Glioblastoma. 60 samples same disease briefing · shares glioblastoma
GSE112650 SOX4/11 Enhances NGN2 Reprogramming Glioblastoma Cells into Neuron Cells by Modulating RhoA and CDC42/RAC1 Pathway Activity 30 samples same disease briefing · shares glioblastoma
GSE115459 Exosome-transmitted RVT1 from reactive astrocytes promotes recurrence glioblastoma proliferation 9 samples same disease briefing · shares glioblastoma

Search all human 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.