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IDH-mutant gliomas arise from glial progenitor cells harboring the initial driver mutation (Related accession no. GSE275791) - Spatial transcriptomics dataset: HumanBrain-Tumor-Oligodendroglioma (IDH-mutant glioma, 48 years)

bronze Interactive viewer oligodendroglioma Provisional
Xenium
print(sdata) 
SpatialData object
├── Images
│     └── 'morphology_mip': DataTree[cyx] (1, 23964, 31254), (1, 11982, 15627), (1, 5991, 7813), (1, 2995, 3906), (1, 1497, 1953)
├── Labels
│     ├── 'cell_labels': DataTree[yx] (21162, 30472), (10581, 15236), (5290, 7618), (2645, 3809), (1322, 1904)
│     └── 'nucleus_labels': DataTree[yx] (21116, 30426), (10558, 15213), (5279, 7606), (2639, 3803), (1319, 1901)
├── Points
│     └── 'transcripts': DataFrame with shape: (16845110, 13) (3D points)
├── Shapes
│     ├── 'cell_boundaries': GeoDataFrame shape: (29655, 1) (2D shapes)
│     ├── 'cell_circles': GeoDataFrame shape: (29655, 2) (2D shapes)
│     └── 'nucleus_boundaries': GeoDataFrame shape: (29655, 2) (2D shapes)
└── Tables
      └── 'table': AnnData (29655, 339)
with coordinate systems:
    ▸ 'global', with elements:
        morphology_mip (Images), cell_labels (Labels), nucleus_labels (Labels), transcripts (Points), cell_boundaries (Shapes), cell_circles (Shapes), nucleus_boundaries (Shapes)
Install (Python 3.12+) Docs →
Python · sddb client 
from sddb import Catalog

ds = Catalog().dataset("krDQ02XmS3Aq9QFC0000")
ds.elements()          # inspect without downloading
sdata = ds.to_sdata()  # cached locally, reused
print(sdata)
Install (Python 3.12+) Docs →
Python · lamindb

Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
artifact = db.Artifact.get("krDQ02XmS3Aq9QFC")   # stem uid: Lamin resolves it to the latest version

sdata = artifact.load()   # cache, then load into memory
group = artifact.open()   # stream without downloading
path  = artifact.cache()  # sync into the local cache, returns the path
Install (Python 3.12+) Docs →
Shell 
# sddb client: download the .zarr into data/
sddb-cli download krDQ02XmS3Aq9QFC0000 --dest data/

# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/krDQ02XmS3Aq9QFC

# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid krDQ02XmS3Aq9QFC
Install (Python 3.12+) Docs →

License: NCBI GEO policy

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Part of collection
geo-gse302642→
6 datasets · publication

Metadata

Technology
Xenium
Vendor
10x Genomics
Organism
human
Tissue
brain
Condition
oligodendroglioma
Modality
RNA
Observations (cells)
29,655
Transcripts
16,845,110
Target genes
339
Tier
bronze
Size
866 MB
Sample ID
GSM9107838
License
NCBI GEO policy
Published
Jan 13, 2026

Cite this dataset

doi.org/10.1126/science.adt0559 ↗
BibTeX 
@article{geo:GSE302642,
  doi = {10.1126/science.adt0559},
  title = {IDH-mutant gliomas arise from glial progenitor cells harboring the initial driver mutation (Related accession no. GSE275791) - Spatial transcriptomics dataset: HumanBrain-Tumor-Astrocytoma (IDH-mutant glioma, 61 years)},
  year = {2026}
}

Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB