Collections / Visium spatial gene expression analyses of ovarian clear cell carcinoma (OCCC) [visium OCCC]

Visium spatial gene expression analyses of ovarian clear cell carcinoma (OCCC) [visium OCCC]

We attempted to determine histological localization of chemoresistant cancer subpopulation by performing spatial transcriptomics.

Datasets2
Size~37 MB
AssayVisium
Samplehuman · ovary
KindOther
PMID:38670097 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse224335")
coll.ordered_artifacts.df()                 # the 2 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()}
Open in Vitessce
Visium
Human ovary
GSM7019836
human ovary ovarian clear cell adenocarcinoma 14 MB 898 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian clear cell adenocarcinoma
Size14 MB
Obs898
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM7019835
human ovary ovarian clear cell adenocarcinoma 22 MB 1,514 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian clear cell adenocarcinoma
Size22 MB
Obs1,514
Magnificationother · 3.417 µm/px
bronze H&E Open in Vitessce

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