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~534 MB
AssayVisium
Samplemouse · kidney
KindComparison
PMID:40813851 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse269622")
coll.ordered_artifacts.df()                 # the 6 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]

# …or load each straight into memory as a SpatialData object:
sdatas = {a.key: sd.read_zarr(a.cache()) for a in coll.ordered_artifacts.all()}
Member datasets · 6
Open in Vitessce
Visium
Mouse kidney
GSM8323124
mouse kidney acute kidney failure 97 MB 2,772 obs silver H&E
TechnologyVisium
Organismmouse
Tissuekidney
Conditionacute kidney failure
Size97 MB
Obs2,772
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse kidney
GSM8323122
mouse kidney acute kidney failure 86 MB 3,393 obs silver H&E
TechnologyVisium
Organismmouse
Tissuekidney
Conditionacute kidney failure
Size86 MB
Obs3,393
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse kidney
GSM8323121
mouse kidney acute kidney failure 83 MB 3,091 obs silver H&E
TechnologyVisium
Organismmouse
Tissuekidney
Conditionacute kidney failure
Size83 MB
Obs3,091
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse kidney
GSM8323123
mouse kidney acute kidney failure 95 MB 3,443 obs silver H&E
TechnologyVisium
Organismmouse
Tissuekidney
Conditionacute kidney failure
Size95 MB
Obs3,443
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse kidney
GSM8323120
mouse kidney 76 MB 2,858 obs silver H&E
TechnologyVisium
Organismmouse
Tissuekidney
Size76 MB
Obs2,858
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse kidney
GSM8323125
mouse kidney acute kidney failure 97 MB 3,915 obs silver H&E
TechnologyVisium
Organismmouse
Tissuekidney
Conditionacute kidney failure
Size97 MB
Obs3,915
silver H&E Open in Vitessce

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