Collections / Single cell- Cluster-RNA seq and Spatial Transcriptomics from the trunk of mouse embryos of different genotypes (wild type, Pax2-GFP, Pax2-GFP; Gata3 knockout) and developmental stages (E8.75, E9.5, E11.5) [Spatial Transcriptomics]

Single cell- Cluster-RNA seq and Spatial Transcriptomics from the trunk of mouse embryos of different genotypes (wild type, Pax2-GFP, Pax2-GFP; Gata3 knockout) and developmental stages (E8.75, E9.5, E11.5) [Spatial Transcriptomics]

To study cell heterogeneity and state transitions in the developing urinary tract we performed spatial transcriptomics from the trunk of E9.5 Pax2GFP mouse embryos using the 10X Genomics Visium Spatial Gene Expression protocol

Datasets4
Size~17.1 MB
AssayVisium
Samplemouse · trunk
KindOther
Flag a data issue
PMID:33976190 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse160137")
cohort.members        # the 4 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/")
Install (Python 3.12+) Docs →
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-gse160137")
coll.ordered_artifacts.to_dataframe()   # the 4 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
Install (Python 3.12+) Docs →
Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse160137 --dest data/
Install (Python 3.12+) Docs →

Licenses: 4 NCBI GEO policy

Member datasets · 4
Open in Vitessce
Visium
Mouse trunk
GSM4861203
mouse trunk 4.4 MB 222 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuetrunk
Size4.4 MB
Spots222
Magnificationother · 3.574 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse trunk
GSM4861205
mouse trunk 3.6 MB 178 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuetrunk
Size3.6 MB
Spots178
Magnificationother · 3.557 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse trunk
GSM4861204
mouse trunk 4.0 MB 192 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuetrunk
Size4.0 MB
Spots192
Magnificationother · 3.552 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse trunk
GSM4861202
mouse trunk 5.1 MB 198 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuetrunk
Size5.1 MB
Spots198
Magnificationother · 3.602 µm/px
bronze H&E NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.1038/s41467-021-22931-5 ↗
BibTeX 
@article{Sanchez_Ferras_2021,
  title = {A coordinated progression of progenitor cell states initiates urinary tract development},
  volume = {12},
  ISSN = {2041-1723},
  url = {http://dx.doi.org/10.1038/s41467-021-22931-5},
  DOI = {10.1038/s41467-021-22931-5},
  number = {1},
  journal = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  author = {Sanchez-Ferras, Oraly and Pacis, Alain and Sotiropoulou, Maria and Zhang, Yuhong and Wang, Yu Chang and Bourgey, Mathieu and Bourque, Guillaume and Ragoussis, Jiannis and Bouchard, Maxime},
  year = {2021},
  month = May
}