Collections / Spatial transcriptomic profiling of seborrhoeic keratoses

Spatial transcriptomic profiling of seborrhoeic keratoses

Seborrhoeic keratoses (SKs) are common benign skin tumors arising from epidermal keratinocytes and frequently observed in older adults. We used spatial transcriptomics to profile a range of SKs, investigating their cellular composition and gene expression landscapes.

Datasets4
Size~377 MB
AssayVisium
Samplehuman · zone of skin
KindOther
PMID:42413572 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse299660")
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()}
Open in Vitessce
Visium
Human zone of skin
GSM9043135
human zone of skin skin neoplasm 101 MB 4,660 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuezone of skin
Conditionskin neoplasm
Size101 MB
Obs4,660
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human zone of skin
GSM9043136
human zone of skin skin neoplasm 84 MB 3,808 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuezone of skin
Conditionskin neoplasm
Size84 MB
Obs3,808
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human zone of skin
GSM9043134
human zone of skin skin neoplasm 99 MB 4,546 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuezone of skin
Conditionskin neoplasm
Size99 MB
Obs4,546
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human zone of skin
GSM9043133
human zone of skin skin neoplasm 93 MB 4,363 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuezone of skin
Conditionskin neoplasm
Size93 MB
Obs4,363
silver H&E NCBI GEO policy Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.