Head and neck squamous cell carcinoma is the 6th most common malignancy worldwide. We performed spatial transcriptomics to profile intra- and inter-tumor heterogeneity. We identified recurring patterns of spatial gene expression that co-localize in subsets of tumors.
from sddb import Catalog
cohort = Catalog().collection("geo-gse268014")
cohort.members # the 26 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-gse268014")
coll.ordered_artifacts.to_dataframe() # the 26 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-gse268014 --dest data/Licenses: 26 NCBI GEO policy
@article{Simkin_2026,
title = {Spatial analysis of head and neck cancer identifies two ecosystems with distinct modes of epithelial-to-mesenchymal transition},
volume = {58},
ISSN = {1546-1718},
url = {http://dx.doi.org/10.1038/s41588-026-02723-7},
DOI = {10.1038/s41588-026-02723-7},
number = {9},
journal = {Nature Genetics},
publisher = {Springer Science and Business Media LLC},
author = {Simkin, Dor and Barrett, Thomas F. and Zhang, Lingling and Moore, Michael J. and Greenwald, Alissa C. and Galili, Noam and Mints, Michael and Ramadan, Salma and Yu, Victoria and Mullins, Riley D. Z. and Zaretsky, Jesse and Bischoff, Porter and Adkins, Douglas and Thorstad, Wade L. and Karam, Sana D. and Paniello, Randall C. and Rich, Jason T. and Jackson, Ryan S. and Pipkorn, Patrik and Zolkind, Paul A. and Peng, Guangyong and Harbison, R. Alex and Chernock, Rebecca and Parikh, Anuraag S. and Puram, Sidharth V. and Tirosh, Itay},
year = {2026},
month = Aug,
pages = {2240–2253}
}