from sddb import Catalog
cohort = Catalog().collection("geo-gse264425")
cohort.members # the 2 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-gse264425")
coll.ordered_artifacts.to_dataframe() # the 2 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-gse264425 --dest data/Licenses: 2 NCBI GEO policy
Studying human fetal lungs can inform how developmental defects and disease states alter the function of the lungs. Here, we sequenced >150,000 single cells from 19 healthy human pseudoglandular fetal lung tissues ranging between gestational weeks 10-19. We capture dynamic developmental trajectories from progenitor cells that express abundant levels of the cystic fibrosis conductance transmembrane regulator (CFTR). These cells give rise to multiple specialized epithelial cell types. Combined with spatial transcriptomics, we show temporal regulation of key signalling pathways that may drive the temporal and spatial emergence of specialized epithelial cells including ciliated and pulmonary neuroendocrine cells. Finally, we show that human pluripotent stem cell-derived fetal lung models contain CFTR-expressing progenitor cells that capture similar lineage developmental trajectories as identified in the native tissue. Overall, this study provides a comprehensive single-cell atlas of the developing human lung, outlining the temporal and spatial complexities of cell lineage development and benchmarks fetal lung cultures from human pluripotent stem cell differentiations to similar developmental window.
@article{Quach_2024,
title = {Early human fetal lung atlas reveals the temporal dynamics of epithelial cell plasticity},
volume = {15},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-024-50281-5},
DOI = {10.1038/s41467-024-50281-5},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Quach, Henry and Farrell, Spencer and Wu, Ming Jia Michael and Kanagarajah, Kayshani and Leung, Joseph Wai-Hin and Xu, Xiaoqiao and Kallurkar, Prajkta and Turinsky, Andrei L. and Bear, Christine E. and Ratjen, Felix and Kalish, Brian and Goyal, Sidhartha and Moraes, Theo J. and Wong, Amy P.},
year = {2024},
month = July
}