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
Flag a data issue
www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE269545 ↗
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

Open in Vitessce
Visium
Mouse brain
GSM8321875
mouse brain glioma 23.8 MB 2,208 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditionglioma
Size23.8 MB
Spots2,208
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM8321878
mouse brain glioma 43.7 MB 2,769 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditionglioma
Size43.7 MB
Spots2,769
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse brain
GSM8321877
mouse brain glioma 37.5 MB 2,327 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditionglioma
Size37.5 MB
Spots2,327
silver H&E NCBI GEO policy Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.