Collections / Spatial RNA sequencing of bleomycin-treated young and old mice lungs at day 14 and day 28 post injection
Spatial RNA sequencing of bleomycin-treated young and old mice lungs at day 14 and day 28 post injection
We monitored lung fibrosis formation and resolution in young and old mice by generating a series of spatial transcriptomics datasets using the 10x Genomics Visium platform
Datasets8
Size~148 MB
AssayVisium
Samplemouse · lung
KindTime course
Download the whole collection
Python · sddb client
from sddb import Catalog
cohort = Catalog().collection("geo-gse234198")
cohort.members # the 8 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-gse234198")
coll.ordered_artifacts.to_dataframe() # the 8 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-gse234198 --dest data/ Licenses: 8 NCBI GEO policy
Member datasets · 8
Mouse lung
GSM7454048
mouse lung pulmonary fibrosis 27.1 MB 2,383 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuelung
Conditionpulmonary fibrosis
Spots2,383
silver H&E NCBI GEO policy
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No linked publication found — please cite the data source.