Desmoplastic Small Round Cell Tumor (DSRCT) is a rare, aggressive sarcoma driven by the EWSR1-WT1 chimeric transcription factor. Despite this unique oncogenic driver, DSRCT displays a polyphenotypic differentiation of unknown causality. Using single-cell multi-omics on samples from patients, we find that DSRCT tumor cells cluster into consistant subpopulations with partially overlapping lineage- and metabolism-related transcriptional programs.
from sddb import Catalog
cohort = Catalog().collection("geo-gse267806")
cohort.members # the 6 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-gse267806")
coll.ordered_artifacts.to_dataframe() # the 6 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-gse267806 --dest data/Licenses: 6 NCBI GEO policy
@article{Henon_2024,
title = {Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in DSRCTs},
volume = {5},
ISSN = {2666-3791},
url = {http://dx.doi.org/10.1016/j.xcrm.2024.101582},
DOI = {10.1016/j.xcrm.2024.101582},
number = {6},
journal = {Cell Reports Medicine},
publisher = {Elsevier BV},
author = {Henon, Clémence and Vibert, Julien and Eychenne, Thomas and Gruel, Nadège and Colmet-Daage, Léo and Ngo, Carine and Garrido, Marlène and Dorvault, Nicolas and Marques Da Costa, Maria Eugenia and Marty, Virginie and Signolle, Nicolas and Marchais, Antonin and Herbel, Noé and Kawai-Kawachi, Asuka and Lenormand, Madison and Astier, Clémence and Chabanon, Roman and Verret, Benjamin and Bahleda, Rastislav and Le Cesne, Axel and Mechta-Grigoriou, Fatima and Faron, Matthieu and Honoré, Charles and Delattre, Olivier and Waterfall, Joshua J. and Watson, Sarah and Postel-Vinay, Sophie},
year = {2024},
month = June,
pages = {101582}
}