Spatial transcriptomics (10x Genomics Visium) was performed on fresh-frozen liver tissue (left lobe) from Mgmt-/- mice treated with N-nitrosodimethylamine (NDMA) or saline vehicle during the juvenile period. The study includes male and female mice sacrificed at 10 weeks or 10 months post-birth to characterize spatially resolved transcriptomic changes associated with NDMA-induced liver damage and potential carcinogenesis over time. Mice carried the RaDR+/+; GPT+/+ genotype enabling detection of recombination and mutation events. Tissue sections were processed using the 10x Visium workflow, H&E stained, imaged, permeabilized for spatially barcoded cDNA synthesis, and sequenced on an Illumina NextSeq 500.
from sddb import Catalog
cohort = Catalog().collection("geo-gse332601")
cohort.members # the 4 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/")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-gse332601")
coll.ordered_artifacts.to_dataframe() # the 4 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse332601 --dest data/Licenses: 4 NCBI GEO policy
No linked publication found — please cite the data source.