Collections / Single-nucleus and spatial transcriptomics of human ovary: Molecular insights into signaling pathways underlying primary ovarian insufficiency in classic galactosemia [Spatial transcriptomics]

Single-nucleus and spatial transcriptomics of human ovary: Molecular insights into signaling pathways underlying primary ovarian insufficiency in classic galactosemia [Spatial transcriptomics]

Classic galactosemia (CG) is a rare inborn error of galactose metabolism caused by mutations in GALT gene. Primary ovarian insufficiency (POI) is a later complication that affects 80% of women with CG due to significant decline in ovarian follicle reserve. The definite mechanisms underlying the early onset of POI in CG patients is not fully understood. We utilized spatial transcriptomics from 10x Visium to generate spatial landscape of human ovaries from pre-pubertal girls with CG to investigate dynamic gene expression profiles in the ovarian follicles and stromal cells.

Datasets6
Size~312 MB
AssayVisium
Samplehuman · ovary
KindComparison
PMID:39440457 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse268523")
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
Human ovary
GSM8292465
human ovary classic galactosemia 35 MB 1,225 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionclassic galactosemia
Size35 MB
Obs1,225
Magnificationother · 5.496 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM8292464
human ovary classic galactosemia 49 MB 2,000 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionclassic galactosemia
Size49 MB
Obs2,000
Magnificationother · 5.503 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM8292466
human ovary 25 MB 946 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueovary
Size25 MB
Obs946
Magnificationother · 5.496 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM8292467
human ovary 98 MB 5,067 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueovary
Size98 MB
Obs5,067
Magnificationother · 6.412 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM8292463
human ovary classic galactosemia 67 MB 2,828 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionclassic galactosemia
Size67 MB
Obs2,828
Magnificationother · 5.495 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM8292468
human ovary 39 MB 1,739 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueovary
Size39 MB
Obs1,739
Magnificationother · 5.497 µm/px
bronze H&E Open in Vitessce

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