Objective: To spatially resolve the identified celltypes, subtypes and transcriptomic profiles from single-nuclei RNA-seq with matched 12 infrapatellar fat pad of knee OA patients using spatial transcriptomics sequencing.
from sddb import Catalog
cohort = Catalog().collection("geo-gse253199")
cohort.members # the 12 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-gse253199")
coll.ordered_artifacts.to_dataframe() # the 12 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-gse253199 --dest data/Licenses: 12 NCBI GEO policy
@article{Peters_2025,
title = {Cell and transcriptomic diversity of infrapatellar fat pad during knee osteoarthritis},
volume = {84},
ISSN = {0003-4967},
url = {http://dx.doi.org/10.1136/ard-2024-225928},
DOI = {10.1136/ard-2024-225928},
number = {2},
journal = {Annals of the Rheumatic Diseases},
publisher = {Elsevier BV},
author = {Peters, Hayley and Potla, Pratibha and Rockel, Jason S. and Tockovska, Teodora and Pastrello, Chiara and Jurisica, Igor and Delos Santos, Keemo and Vohra, Shabana and Fine, Noah and Lively, Starlee and Perry, Kim and Looby, Nikita and Li, Sheng Han and Chandran, Vinod and Hueniken, Katrina and Kaur, Paramvir and Perruccio, Anthony V. and Mahomed, Nizar N. and Rampersaud, Raja and Syed, Khalid and Gracey, Eric and Krawetz, Roman and Buechler, Matthew B. and Gandhi, Rajiv and Kapoor, Mohit},
year = {2025},
month = Feb,
pages = {351–367}
}