DBiT-seq
Mouse embryo
GSM9742826
mouse embryo 12.6 MB 1,628 pixels bronze NCBI GEO policy
TechnologyDBiT-seq
Organismmouse
Tissueembryo
Pixels1,628
bronze NCBI GEO policy
Collections / geo-gse331262
geo-gse331262
Datasets2
Size~21.5 MB
AssayDBiT-seq
Samplemouse · embryo
KindPublication
Download the whole collection
Python · sddb client
from sddb import Catalog
cohort = Catalog().collection("geo-gse331262")
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/") 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-gse331262")
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()] Shell
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse331262 --dest data/Licenses: 2 NCBI GEO policy
About the study
Mapping Embryonic Mouse Lung Development Using Enhanced Spatial Transcriptomics.
The mature mammalian lung contains ∼50 different cell types that are located in precise positions along and around the airway epithelial tree. Here, we apply spatial transcriptomics to early embryonic mouse lungs to investigate how these spatial patterns are progressively established during development. Specifically, we optimized a microfluidics-enabled, deterministic barcoding-based sequencing (DBiT-seq) workflow to achieve sensitive spatial mapping of tissue sections, resulting in up to a twofold increase in average transcript recovery compared with previous implementations. Spatial mapping of epithelial populations revealed that Sox9<sup>+</sup> epithelial progenitors are located throughout the epithelial tree at early stages before becoming confined to the distal ends. Moreover, we describe a previously unrecognized mesenchymal cluster that exhibits consistent spatial position, expresses high levels of extracellular matrix proteins, and appears to promote embryonic lung innervation. These findings provide new insights into the spatial organization and cellular dynamics underlying early lung development, and demonstrate the power of spatial transcriptomics to uncover hidden patterns and populations of cells.
Member datasets · 2
DBiT-seq
Mouse embryo
GSM9742827
mouse embryo 9.0 MB 1,545 pixels bronze NCBI GEO policy
TechnologyDBiT-seq
Organismmouse
Tissueembryo
Pixels1,545
bronze NCBI GEO policy
Cite this collection
No linked publication found — please cite the data source.