Collections / geo-gse302642

geo-gse302642

Datasets6
Size~4.2 GB
TechnologyXenium
Samplehuman · brain
KindPublication
Flag a data issue
10.1126/science.adt0559 ↗
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Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse302642")
cohort.members        # the 6 datasets as a table

print(cohort.licenses())              # check the terms before you download

sdatas = cohort.to_dict()             # {uid: SpatialData}, cached locally
# or keep the .zarr files in a folder of your choice:
# sdatas = cohort.to_dict(dest="data/")
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")
coll = db.Collection.get(key="geo-gse302642")
coll.ordered_artifacts.to_dataframe()   # the 6 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
Install (Python 3.12+) Docs →
Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse302642 --dest data/
Install (Python 3.12+) Docs →

Licenses: 6 NCBI GEO policy

About the study

IDH-mutant gliomas arise from glial progenitor cells harboring the initial driver mutation.

Read the abstract at the source →
Member datasets · 6
Open in Vitessce
Xenium
Human brain
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)
human brain astrocytoma (excluding glioblastoma) 984 MB 45,749 cells 339 genes bronze NCBI GEO policy
TechnologyXenium
Organismhuman
Tissuebrain
Conditionastrocytoma (excluding glioblastoma)
Size984 MB
Cells45,749
Genes339
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
Xenium
Human brain
IDH-mutant gliomas arise from glial progenitor cells harboring the initial driver mutation (Related accession no. GSE275791) - Spatial transcriptomics dataset: HumanBrain-PeritumoralTissue-3 (Patient-derived peritumoral tissue, Normal Peritumoral tissue, 48 years)
human brain 245 MB 4,411 cells 339 genes bronze NCBI GEO policy
TechnologyXenium
Organismhuman
Tissuebrain
Size245 MB
Cells4,411
Genes339
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
Xenium
Human brain
IDH-mutant gliomas arise from glial progenitor cells harboring the initial driver mutation (Related accession no. GSE275791) - Spatial transcriptomics dataset: HumanBrain-PeritumoralTissue-5 (Patient-derived peritumoral tissue, Normal Peritumoral tissue, 61 years)
human brain 401 MB 9,615 cells 339 genes bronze NCBI GEO policy
TechnologyXenium
Organismhuman
Tissuebrain
Size401 MB
Cells9,615
Genes339
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
Xenium
Human brain
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)
human brain oligodendroglioma 866 MB 29,655 cells 339 genes bronze NCBI GEO policy
TechnologyXenium
Organismhuman
Tissuebrain
Conditionoligodendroglioma
Size866 MB
Cells29,655
Genes339
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
Xenium
Human brain
IDH-mutant gliomas arise from glial progenitor cells harboring the initial driver mutation (Related accession no. GSE275791) - Spatial transcriptomics dataset: HumanBrain-PeritumoralTissue-2 (Patient-derived peritumoral tissue, Normal Peritumoral tissue, 42 years)
human brain 872 MB 23,123 cells 339 genes bronze NCBI GEO policy
TechnologyXenium
Organismhuman
Tissuebrain
Size872 MB
Cells23,123
Genes339
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
Xenium
Human brain
IDH-mutant gliomas arise from glial progenitor cells harboring the initial driver mutation (Related accession no. GSE275791) - Spatial transcriptomics dataset: HumanBrain-PeritumoralTissue-1 (Patient-derived peritumoral tissue, Normal Peritumoral tissue, 29 years)
human brain 833 MB 21,799 cells 339 genes bronze NCBI GEO policy
TechnologyXenium
Organismhuman
Tissuebrain
Size833 MB
Cells21,799
Genes339
bronze NCBI GEO policy Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.