We collected HNSCC primary tumor sections from head and neck squamous cell carcinoma patients at the Taipei Veterans General Hospital (TVGH) for 10x Genomics Visium analysis.
from sddb import Catalog
cohort = Catalog().collection("geo-gse181300")
cohort.members # the 8 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-gse181300")
coll.ordered_artifacts.to_dataframe() # the 8 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-gse181300 --dest data/Licenses: 8 NCBI GEO policy
@article{Cheng_2022,
title = {Snail-regulated exosomal microRNA-21 suppresses NLRP3 inflammasome activity to enhance cisplatin resistance},
volume = {10},
ISSN = {2051-1426},
url = {http://dx.doi.org/10.1136/jitc-2022-004832},
DOI = {10.1136/jitc-2022-004832},
number = {8},
journal = {Journal for ImmunoTherapy of Cancer},
publisher = {BMJ},
author = {Cheng, Han-Ying and Hsieh, Chia-Hsin and Lin, Po-Han and Chen, Yu-Tung and Hsu, Dennis Shin-Shian and Tai, Shyh-Kuan and Chu, Pen-Yuan and Yang, Muh-Hwa},
year = {2022},
month = Aug,
pages = {e004832}
}