DBiT-seq
Chicken lung
GSM9771951
chicken lung 6.9 MB 1,091 pixels bronze NCBI GEO policy
TechnologyDBiT-seq
Organismchicken
Tissuelung
Pixels1,091
bronze NCBI GEO policy
Collections / geo-gse333735
geo-gse333735
Datasets3
Size~26.6 MB
AssayDBiT-seq
Samplechicken · lung
KindPublication
Download the whole collection
Python · sddb client
from sddb import Catalog
cohort = Catalog().collection("geo-gse333735")
cohort.members # the 3 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/") Python · lamindb
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-gse333735")
coll.ordered_artifacts.to_dataframe() # the 3 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()] Shell
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse333735 --dest data/Licenses: 3 NCBI GEO policy
About the study
TGFβ determines epithelial tissue spacing by regulating mesenchymal condensation.
The branched structure of the vertebrate lung provides a high surface area-to-volume ratio that enhances diffusion-driven gas exchange. Generating this structure requires that epithelial branches avoid contacting one another during development, but the underlying mechanisms remain elusive. Using the embryonic chicken lung as a model system, we found that branch spacing is regulated primarily by signaling to the mesenchyme through transforming growth factor β (TGFβ). Although proliferation decreases in epithelial cells that are located in close proximity to an adjacent branch, these patterns emerge after regular branch spacing has been established. Instead, we find that TGFβ promotes the directed migration of mesenchymal cells, which form a condensation that physically displaces the adjacent epithelium and tunes branch spacing. Continuous disruption of TGFβ signaling prevents mesenchymal condensation and eventually results in contact between adjacent branches. These data suggest that the spacing between epithelial branches results from mesenchymal cell dynamics rather than from epithelial-intrinsic self-avoidance.
Member datasets · 3
DBiT-seq
Chicken lung
GSM9771950
chicken lung 7.7 MB 1,018 pixels bronze NCBI GEO policy
TechnologyDBiT-seq
Organismchicken
Tissuelung
Pixels1,018
bronze NCBI GEO policy
DBiT-seq
Chicken lung
GSM9771952
chicken lung 12.0 MB 1,421 pixels bronze NCBI GEO policy
TechnologyDBiT-seq
Organismchicken
Tissuelung
Pixels1,421
bronze NCBI GEO policy
Cite this collection
No linked publication found — please cite the data source.