Squamous cell carcinoma arising from mature teratoma (SCC-MT) is one of the rare ovarian malignancies. Therefore, the molecular background of SCC-MT remains largely unelucidated. In this study, we performed the spatial transcriptomics for SCC-MT.
from sddb import Catalog
cohort = Catalog().collection("geo-gse272833")
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/")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-gse272833")
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()]# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse272833 --dest data/Licenses: 4 NCBI GEO policy
@article{Yoshida_2025,
title = {Single‐Nucleus <scp>RNA</scp> Sequencing and Spatial Transcriptomics for Squamous Cell Carcinoma Arising From Ovarian Mature Teratoma},
volume = {116},
ISSN = {1349-7006},
url = {http://dx.doi.org/10.1111/cas.70022},
DOI = {10.1111/cas.70022},
number = {5},
journal = {Cancer Science},
publisher = {Wiley},
author = {Yoshida, Kosuke and Yokoi, Akira and Suzuki, Hironori and Tamauchi, Satoshi and Kitagawa, Masami and Inami, Eri and Nakayama, Jun and Mori, Yutaro and Okamoto, Koji and Suzuki, Yutaka and Yoshida, Hiroshi and Kato, Tomoyasu and Kajiyama, Hiroaki and Yamamoto, Yusuke},
year = {2025},
month = Feb,
pages = {1339–1351}
}