Collections / Spatial characterization of the transcriptome of the adult healthy and mutant FUS mouse spinal cords [Spatial transcriptomics]

Spatial characterization of the transcriptome of the adult healthy and mutant FUS mouse spinal cords [Spatial transcriptomics]

Here we investigated the spatial transcriptome of the aged mouse spinal cord using 10X Genomics Visium platform. We produced local transcriptomes of the full spinal cord with a resolution of 100 um, characterizing ventral and dorsal horn regions, in addition to grey and white matter regions. With these spatial data, it is possible to explore the spatial transcriptome of the aged mouse spinal cord, extrapolating information on the cellular composition of this tissue.

Datasets4
Size~45 MB
AssayVisium
Samplemouse · spinal cord
KindOther
PMID:41430470 ↗
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Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse269377")
coll.ordered_artifacts.df()                 # the 4 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 · 4
Open in Vitessce
Visium
Mouse spinal cord
GSM8314106
mouse spinal cord 11 MB 4,992 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuespinal cord
Size11 MB
Obs4,992
Magnificationother · 4.059 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse spinal cord
GSM8314109
mouse spinal cord 11 MB 4,992 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuespinal cord
Size11 MB
Obs4,992
Magnificationother · 4.059 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse spinal cord
GSM8314108
mouse spinal cord 9.5 MB 4,992 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuespinal cord
Size9.5 MB
Obs4,992
Magnificationother · 4.057 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse spinal cord
GSM8314107
mouse spinal cord 14 MB 4,992 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuespinal cord
Size14 MB
Obs4,992
Magnificationother · 4.060 µm/px
bronze H&E Open in Vitessce

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