Collections / Specific oncogenic drivers differently shaped the composition and functional diversity of immune cells in the microenvironment of experimental gliomas
Specific oncogenic drivers differently shaped the composition and functional diversity of immune cells in the microenvironment of experimental gliomas
We performed spatial transcriptomics to profile spatial localization and intercations of cell populations within GL261 glioma mouse model. Funding: The Polish National Science Center 2020/39/B/NZ4/02683 (BK).
Datasets3
Size~105 MB
AssayVisium
Samplemouse · brain
KindComparison
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Python · sddb client
from sddb import Catalog
cohort = Catalog().collection("geo-gse269545")
cohort.members # the 3 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/") 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-gse269545")
coll.ordered_artifacts.to_dataframe() # the 3 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()] Shell
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse269545 --dest data/ Licenses: 3 NCBI GEO policy
Member datasets · 3
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