Approximately one-third of melanomas arise from benign nevi, yet the transcriptional and microenvironmental changes accompanying this transition remain incompletely understood. To study the nevus-to-melanoma transition, we employed genome-wide spatial transcriptomics combined with imaging mass cytometry on adjacent nevus-melanoma lesions.
from sddb import Catalog
cohort = Catalog().collection("geo-gse298774")
cohort.members # the 11 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/")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-gse298774")
coll.ordered_artifacts.to_dataframe() # the 11 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse298774 --dest data/Licenses: 11 NCBI GEO policy
@article{Kreuger_2026,
title = {Spatial Analysis Reveals Gene Expression and Microenvironmental Changes in the Transition of Nevus to Melanoma},
volume = {86},
ISSN = {1538-7445},
url = {http://dx.doi.org/10.1158/0008-5472.can-25-2934},
DOI = {10.1158/0008-5472.can-25-2934},
number = {17},
journal = {Cancer Research},
publisher = {American Association for Cancer Research (AACR)},
author = {Kreuger, Inger Z.M. and Merkus, Veerle A. and de Haan, Sanne and Schrader, Anne M.R. and Scheeren, Ferenc A. and van der Burg, Sjoerd H. and van Groningen, Tim and Slieker, Roderick C. and van Doorn, Remco},
year = {2026},
month = June,
pages = {4400–4413}
}