GEO series
The Multi-Layered Transcriptional Architecture of Glioblastoma Ecosystems [10X]
GSE274546
Homo sapiens
Expression profiling by high throughput sequencing
121 samples
Submitted 2025/01/01
Platform GPL24676
Summary
To comprehensively define the cellular heterogeneity of glioblastoma (GBM), the GBM CARE (Cellular Analysis of Resistance and Evolution) consortium set out to profile 121 GBMs with extensive clinical annotation, by single-nucleus RNA-sequencing and bulk tumor DNA sequencing. The resulting dataset enabled us to characterize GBM heterogeneity at three levels. First, GBMs are classified by their cellular composition, encompassing malignant, immune, neuronal and glial cell types. Second, within each cell type, and particularly among the malignant cells, we describe the diversity of cellular states and their pathway-based functional activities. Third, after controlling for the frequencies of cellular states, we find that the remaining variation between GBMs highlights three baseline gene expression programs which we labeled Neuronal, Glial, and Extracellular Matrix. These three layers of heterogeneity are inter-related and partially associated with specific genetic aberrations, thereby defining three stereotypic ecosystems in GBM. This work provides an unparalleled view of the multi-layered transcriptional architecture of GBM.
Published in
Spitzer A, Johnson KC, Nomura M et al.
· Nature genetics 2025
· PMID 40346362
· doi:10.1038/s41588-025-02168-4
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE274546_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 121 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1147185. Searching any of these in the dataset finder brings you back here.
Study design
40 conditions, each sampled once — no replicated groups
Read from the first 40 of 121 sample titles: 40 distinct titles with little repetition. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM8452584 Patient 1, Timepoint 1, Chromium gene expression
- GSM8452585 Patient 1, Timepoint 2, Chromium gene expression
- GSM8452586 Patient 2, Timepoint 1, Chromium gene expression
- GSM8452587 Patient 2, Timepoint 2, Chromium gene expression
- GSM8452588 Patient 3, Timepoint 1, Chromium gene expression
- GSM8452589 Patient 3, Timepoint 2, Chromium gene expression
- GSM8452590 Patient 4, Timepoint 1, Chromium gene expression
- GSM8452591 Patient 4, Timepoint 2, Chromium gene expression
- GSM8452592 Patient 5, Timepoint 1, Chromium gene expression
- GSM8452593 Patient 5, Timepoint 2, Chromium gene expression
- GSM8452594 Patient 6, Timepoint 1, Chromium gene expression
- GSM8452595 Patient 6, Timepoint 2, Chromium gene expression
- GSM8452596 Patient 8, Timepoint 1, Chromium gene expression
- GSM8452597 Patient 8, Timepoint 2, Chromium gene expression
- GSM8452598 Patient 9, Timepoint 1, Chromium gene expression
- GSM8452599 Patient 9, Timepoint 2, Chromium gene expression
- GSM8452600 Patient 20, Timepoint 1, Chromium gene expression
- GSM8452601 Patient 20, Timepoint 2, Chromium gene expression
- GSM8452602 Patient 20, Timepoint 3, Chromium gene expression
- GSM8452603 Patient 21, Timepoint 1, Chromium gene expression
- GSM8452604 Patient 21, Timepoint 2, Chromium gene expression
- GSM8452605 Patient 22, Timepoint 1, Chromium gene expression
- GSM8452606 Patient 22, Timepoint 2, Chromium gene expression
- GSM8452607 Patient 23, Timepoint 1, Chromium gene expression
- GSM8452608 Patient 23, Timepoint 2, Chromium gene expression
- GSM8452609 Patient 24, Timepoint 1, Chromium gene expression
- GSM8452610 Patient 24, Timepoint 2, Chromium gene expression
- GSM8452611 Patient 25, Timepoint 1, Chromium gene expression
- GSM8452612 Patient 25, Timepoint 2, Chromium gene expression
- GSM8452613 Patient 26, Timepoint 1, Chromium gene expression
- GSM8452614 Patient 26, Timepoint 2, Chromium gene expression
- GSM8452615 Patient 27, Timepoint 1, Chromium gene expression
- GSM8452616 Patient 27, Timepoint 2, Chromium gene expression
- GSM8452617 Patient 28, Timepoint 1, Chromium gene expression
- GSM8452618 Patient 28, Timepoint 2, Chromium gene expression
- GSM8452619 Patient 29, Timepoint 1, Chromium gene expression
- GSM8452620 Patient 29, Timepoint 2, Chromium gene expression
- GSM8452621 Patient 30, Timepoint 1, Chromium gene expression
- GSM8452622 Patient 30, Timepoint 2, Chromium gene expression
- GSM8452623 Patient 31, Timepoint 1, Chromium gene expression
+ 81 more — browse all 121 samples with per-sample file links →
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