Collections / Multimodal spatial transcriptomic characterization of mouse kidney injury and repair [Visium]

Multimodal spatial transcriptomic characterization of mouse kidney injury and repair [Visium]

Spatial transcriptomics (ST) technologies enable the mapping of gene expression to specific regions within tissues. However, current ST platforms present inherent trade-offs between resolution and throughput, which cannot be entirely addressed by a single technology. To unravel the spatiotemporal landscape of gene expression and cellular interactions during kidney injury and repair, we employed an integrated approach combining Xenium's high-resolution in situ sequencing with Visium's whole-transcriptome spatial profiling.

Datasets6
Size~559 MB
AssayVisium
Samplemouse · kidney
KindComparison
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PMID:40813851 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse269622")
cohort.members        # the 6 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/")
Install (Python 3.12+) Docs →
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-gse269622")
coll.ordered_artifacts.to_dataframe()   # the 6 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
Install (Python 3.12+) Docs →
Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse269622 --dest data/
Install (Python 3.12+) Docs →

Licenses: 6 NCBI GEO policy

Member datasets · 6
Open in Vitessce
Visium
Mouse kidney
GSM8323124
mouse kidney acute kidney failure 101 MB 2,772 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuekidney
Conditionacute kidney failure
Size101 MB
Spots2,772
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse kidney
GSM8323122
mouse kidney acute kidney failure 90.1 MB 3,393 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuekidney
Conditionacute kidney failure
Size90.1 MB
Spots3,393
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse kidney
GSM8323121
mouse kidney acute kidney failure 87.0 MB 3,091 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuekidney
Conditionacute kidney failure
Size87.0 MB
Spots3,091
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse kidney
GSM8323123
mouse kidney acute kidney failure 99.9 MB 3,443 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuekidney
Conditionacute kidney failure
Size99.9 MB
Spots3,443
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse kidney
GSM8323120
mouse kidney 80.0 MB 2,858 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuekidney
Size80.0 MB
Spots2,858
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse kidney
GSM8323125
mouse kidney acute kidney failure 101 MB 3,915 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuekidney
Conditionacute kidney failure
Size101 MB
Spots3,915
silver H&E NCBI GEO policy Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.