Collections / Spatial transcriptomic analysis of patient- and cell line-derived high grade serous ovarian cancer spheroids

Spatial transcriptomic analysis of patient- and cell line-derived high grade serous ovarian cancer spheroids

In vitro models of high grade serous ovarian cancer spheroids are often used to study mechanisms of cell dormancy and resistance to chemotherapy, but their ability to accurately mimic spheroid biology in patients is unclear. We performed spatial transcriptomic profiling of in vitro cell line- and in vivo patient-derived high grade serous ovarian cancer spheroids to profile spheroid cell composition and gene expression programs between models. Our analysis reveals the predominant cell types that make up patient spheroids and common expression patterns that shared between models.

Datasets2
Size~59 MB
AssayVisium
Samplehuman · ovary
KindOther
www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE335181 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse335181")
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()}
Member datasets · 2
Open in Vitessce
Visium
Human ovary
GSM9807708
human ovary ovarian serous adenocarcinoma 38 MB 4,674 obs silver H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian serous adenocarcinoma
Size38 MB
Obs4,674
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM9807709
human ovary ovarian serous adenocarcinoma 21 MB 4,963 obs silver H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian serous adenocarcinoma
Size21 MB
Obs4,963
silver H&E Open in Vitessce

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