Spatiotemporal single-cell profiling of T cell clonal dynamics in human graft-versus-host disease (gut, Visium HD).
from sddb import Catalog
cohort = Catalog().collection("geo-gse307215-gvhd-gut")
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-gse307215-gvhd-gut")
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-gse307215-gvhd-gut --dest data/Licenses: 8 NCBI GEO policy
@article{Shi_2026,
title = {Spatiotemporal single-cell profiling reveals T cell clonal dynamics and phenotypic plasticity in human graft-versus-host disease},
volume = {27},
ISSN = {1529-2916},
url = {http://dx.doi.org/10.1038/s41590-026-02631-2},
DOI = {10.1038/s41590-026-02631-2},
number = {10},
journal = {Nature Immunology},
publisher = {Springer Science and Business Media LLC},
author = {Shi, Lingting and Uzuni, Ajna and Wang, Ximi K. and Pressler, Michael and Harle, David W. and Chakrabarti, Shami and Macedo, Rodney and Belay, Kirubel and Gordillo, Christian A. and McMahon-Skates, Thomas and Raps, Erik and Zhang, Jia Yi Ady and Nazaret, Achille and Fan, Joy L. and Jin, Yinuo and Shen, Xumin and Fuller, Joshua S. and Azad, Tamjeed and Huang, Jessie and Chainani, Pranik and Nima, Jose Pomarino and Abrams, Julian A. and Del Portillo, Armando and Mapara, Markus Y. and Alhamar, Mohamed and Sykes, Megan and McFaline-Figueroa, José L. and Azizi, Elham and Reshef, Ran},
year = {2026},
month = Sept,
pages = {2156–2171}
}