Collections / Spatial transcriptomics of human brain metastases

Spatial transcriptomics of human brain metastases

Spatial transcriptomics of six surgically-resected human brain metastasis samples

Datasets6
Size~118 MB
AssayVisium
Samplehuman · brain
KindReplicates
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PMID:35584630 ↗
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Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse179572")
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-gse179572")
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-gse179572 --dest data/
Install (Python 3.12+) Docs →

Licenses: 6 NCBI GEO policy

Member datasets · 6
Open in Vitessce
Visium
Human brain
GSM5420753
human brain breast carcinoma 35.2 MB 4,342 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuebrain
Conditionbreast carcinoma
Size35.2 MB
Spots4,342
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM5420749
human brain lung adenocarcinoma 14.3 MB 2,112 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuebrain
Conditionlung adenocarcinoma
Size14.3 MB
Spots2,112
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM5420752
human brain clear cell renal carcinoma 12.7 MB 1,298 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuebrain
Conditionclear cell renal carcinoma
Size12.7 MB
Spots1,298
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM5420754
human brain lung adenocarcinoma 20.7 MB 2,152 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuebrain
Conditionlung adenocarcinoma
Size20.7 MB
Spots2,152
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM5420750
human brain melanoma 19.8 MB 1,716 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuebrain
Conditionmelanoma
Size19.8 MB
Spots1,716
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM5420751
human brain lung adenocarcinoma 15.7 MB 946 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuebrain
Conditionlung adenocarcinoma
Size15.7 MB
Spots946
silver H&E NCBI GEO policy Open in Vitessce

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No linked publication found — please cite the data source.