Collections / Spatial transcriptomics reveals ovarian cancer subclones with different microenvironments

Spatial transcriptomics reveals ovarian cancer subclones with different microenvironments

8 spatial RNA-seq experiments (10x Genomics Visium) and 5 single-cell RNA-seq experiments (10x Genomics Chromium) using high-grade serous ovarian carcinoma (HGSOC) samples obtained from the ovaries during the interval debulking surgery

Datasets8
Size~238 MB
AssayVisium
Samplehuman · ovary
KindComparison
PMID:38570491 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse211956")
coll.ordered_artifacts.df()                 # the 8 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
GSM6506110
human ovary ovarian serous adenocarcinoma 34 MB 2,940 obs silver H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian serous adenocarcinoma
Size34 MB
Obs2,940
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM6506114
human ovary ovarian serous adenocarcinoma 27 MB 2,124 obs silver H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian serous adenocarcinoma
Size27 MB
Obs2,124
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM6506115
human ovary ovarian serous adenocarcinoma 23 MB 1,801 obs silver H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian serous adenocarcinoma
Size23 MB
Obs1,801
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM6506112
human ovary ovarian serous adenocarcinoma 21 MB 1,504 obs silver H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian serous adenocarcinoma
Size21 MB
Obs1,504
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM6506116
human ovary ovarian serous adenocarcinoma 38 MB 3,632 obs silver H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian serous adenocarcinoma
Size38 MB
Obs3,632
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM6506113
human ovary ovarian serous adenocarcinoma 34 MB 3,007 obs silver H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian serous adenocarcinoma
Size34 MB
Obs3,007
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM6506117
human ovary ovarian serous adenocarcinoma 36 MB 3,180 obs silver H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian serous adenocarcinoma
Size36 MB
Obs3,180
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human ovary
GSM6506111
human ovary ovarian serous adenocarcinoma 25 MB 1,935 obs silver H&E
TechnologyVisium
Organismhuman
Tissueovary
Conditionovarian serous adenocarcinoma
Size25 MB
Obs1,935
silver H&E Open in Vitessce

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