Human papillomavirus (HPV) is a major causative factor of head and neck squamous cell carcinoma (HNSCC), and the incidence of HPV-associated HNSCC is increasing. The role of tumor microenvironment (TME) in viral infection and metastasis needs to be explored further. Thus we studied the molecular characteristics of primary tumors (PTs) and lymph node metastatic tumors (LNMTs) by stratifying them based on their HPV status using spatial transcriptomics.
from sddb import Catalog
cohort = Catalog().collection("geo-gse281978")
cohort.members # the 5 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-gse281978")
coll.ordered_artifacts.to_dataframe() # the 5 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-gse281978 --dest data/Licenses: 5 NCBI GEO policy
@article{Lee_2024,
title = {Deciphering head and neck cancer microenvironment: Single‐cell and spatial transcriptomics reveals human papillomavirus‐associated differences},
volume = {96},
ISSN = {1096-9071},
url = {http://dx.doi.org/10.1002/jmv.29386},
DOI = {10.1002/jmv.29386},
number = {1},
journal = {Journal of Medical Virology},
publisher = {Wiley},
author = {Lee, Hansong and Park, Sohee and Yun, Ju Hyun and Seo, Chorong and Ahn, Ji Mi and Cha, Hyun‐Young and Shin, Yoo Seob and Park, Hae Ryoun and Lee, Dongjun and Roh, Jin and Heo, Hye Jin and Baek, Seung Eun and Kim, Eun Kyoung and Lee, Hae Seul and Kim, Chul‐Ho and Kim, Yun Hak and Jang, Jeon Yeob},
year = {2024},
month = Jan
}