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~395 MB
AssayVisium
Samplehuman · zone of skin
KindOther
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PMID:42413572 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse299660")
cohort.members        # the 4 datasets as a table

print(cohort.licenses())              # check the terms before you download

sdatas = cohort.to_dict()             # {uid: SpatialData}, cached locally
# or keep the .zarr files in a folder of your choice:
# sdatas = cohort.to_dict(dest="data/")
Install (Python 3.12+) Docs →
Python · lamindb

Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
coll = db.Collection.get(key="geo-gse299660")
coll.ordered_artifacts.to_dataframe()   # the 4 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
Install (Python 3.12+) Docs →
Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse299660 --dest data/
Install (Python 3.12+) Docs →

Licenses: 4 NCBI GEO policy

Member datasets · 4
Open in Vitessce
Visium
Human zone of skin
GSM9043135
human zone of skin skin neoplasm 106 MB 4,660 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuezone of skin
Conditionskin neoplasm
Size106 MB
Spots4,660
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human zone of skin
GSM9043136
human zone of skin skin neoplasm 88.0 MB 3,808 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuezone of skin
Conditionskin neoplasm
Size88.0 MB
Spots3,808
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human zone of skin
GSM9043134
human zone of skin skin neoplasm 104 MB 4,546 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuezone of skin
Conditionskin neoplasm
Size104 MB
Spots4,546
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human zone of skin
GSM9043133
human zone of skin skin neoplasm 97.4 MB 4,363 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuezone of skin
Conditionskin neoplasm
Size97.4 MB
Spots4,363
silver H&E NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.1016/j.jid.2026.03.048 ↗
BibTeX 
@article{Oey_2026,
  title = {The genomic and spatial transcriptomic landscape of seborrheic keratoses},
  ISSN = {0022-202X},
  url = {http://dx.doi.org/10.1016/j.jid.2026.03.048},
  DOI = {10.1016/j.jid.2026.03.048},
  journal = {Journal of Investigative Dermatology},
  publisher = {Elsevier BV},
  author = {Oey, Harald M. and Kao, Yung-Ching and Lee, Katie J. and Zhou, Chenhao and Brysland, Simone A. and Jagirdar, Kasturee and Sunnefeldt, Erik and Hammerlindl, Sabrina and Tom, Lisa N. and Tan, Jean-Marie and Lambie, Duncan and Sturm, Richard A. and Schaider, Helmut and Dicker, Tony and Khosrotehrani, Kiarash and Soyer, H. Peter and Stark, Mitchell S.},
  year = {2026},
  month = July
}