from sddb import Catalog
cohort = Catalog().collection("doi-10-1016-j-cell-2020-05-039")
cohort.members # the 16 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="doi-10.1016/j.cell.2020.05.039")
coll.ordered_artifacts.to_dataframe() # the 16 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 doi-10-1016-j-cell-2020-05-039 --dest data/Licenses: 16 CC BY-NC-SA 4.0
To define the cellular composition and architecture of cutaneous squamous cell carcinoma (cSCC), we combined single-cell RNA sequencing with spatial transcriptomics and multiplexed ion beam imaging from a series of human cSCCs and matched normal skin. cSCC exhibited four tumor subpopulations, three recapitulating normal epidermal states, and a tumor-specific keratinocyte (TSK) population unique to cancer, which localized to a fibrovascular niche. Integration of single-cell and spatial data mapped ligand-receptor networks to specific cell types, revealing TSK cells as a hub for intercellular communication. Multiple features of potential immunosuppression were observed, including T regulatory cell (Treg) co-localization with CD8 T cells in compartmentalized tumor stroma. Finally, single-cell characterization of human tumor xenografts and in vivo CRISPR screens identified essential roles for specific tumor subpopulation-enriched gene networks in tumorigenesis. These data define cSCC tumor and stromal cell subpopulations, the spatial niches where they interact, and the communicating gene networks that they engage in cancer.
@article{Ji_2020,
title = {Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma},
volume = {182},
ISSN = {0092-8674},
url = {http://dx.doi.org/10.1016/j.cell.2020.05.039},
DOI = {10.1016/j.cell.2020.05.039},
number = {2},
journal = {Cell},
publisher = {Elsevier BV},
author = {Ji, Andrew L. and Rubin, Adam J. and Thrane, Kim and Jiang, Sizun and Reynolds, David L. and Meyers, Robin M. and Guo, Margaret G. and George, Benson M. and Mollbrink, Annelie and Bergenstråhle, Joseph and Larsson, Ludvig and Bai, Yunhao and Zhu, Bokai and Bhaduri, Aparna and Meyers, Jordan M. and Rovira-Clavé, Xavier and Hollmig, S. Tyler and Aasi, Sumaira Z. and Nolan, Garry P. and Lundeberg, Joakim and Khavari, Paul A.},
year = {2020},
month = July,
pages = {497–514.e22}
}