Mouse small intestine
GSM7106693
mouse small intestine 47.3 MB 4,190 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuesmall intestine
Spots4,190
silver H&E NCBI GEO policy
Collections / Time-series spatial transcriptomic analysis of murine small intestine (SI) undergoing irradiation induced injury-repair with and without LXR activation
Time-series spatial transcriptomic analysis of murine small intestine (SI) undergoing irradiation induced injury-repair with and without LXR activation
To unbiasedly characterize the spatial transcriptomics landscape of murine small intestine damage and repair, we performed a time-series spatial transcriptional analysis of total small intestinal tissue during the course of irradiation damage from mice receiving standard diet. Additionally, to understand the role of LXR activation during damage and repair, we also collected small intestine tissues from mice fed with GW3965 diet.
Datasets4
Size~222 MB
AssayVisium
Samplemouse · small intestine
KindComparison
Download the whole collection
Python · sddb client
from sddb import Catalog
cohort = Catalog().collection("geo-gse227742")
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/") 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-gse227742")
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()] Shell
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse227742 --dest data/Licenses: 4 NCBI GEO policy
Member datasets · 4
Mouse small intestine
GSM7106691
mouse small intestine 58.4 MB 4,585 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuesmall intestine
Spots4,585
silver H&E NCBI GEO policy
Mouse small intestine
GSM7106692
mouse small intestine 51.9 MB 4,881 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuesmall intestine
Spots4,881
silver H&E NCBI GEO policy
Mouse small intestine
GSM7106694
mouse small intestine 64.7 MB 4,859 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuesmall intestine
Spots4,859
silver H&E NCBI GEO policy
Cite this collection
No linked publication found — please cite the data source.