Collections / Characterizing Neonatal Heart Maturation, Regeneration, and Scar Resolution Using Spatial Transcriptomics [spatial]

Characterizing Neonatal Heart Maturation, Regeneration, and Scar Resolution Using Spatial Transcriptomics [spatial]

We use spatial transcriptomics to establish regional transcriptional profile of neonatal heart tissue obtained at indicated timpoints after apical resection surgery.

Datasets4
Size~112 MB
AssayVisium
Samplemouse · heart
KindTime course
Flag a data issue
PMID:35050211 ↗
Python · sddb client
from sddb import Catalog

cohort = Catalog().collection("geo-gse188888")
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/")
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-gse188888")
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()]
Shell
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse188888 --dest data/

Licenses: 4 NCBI GEO policy

Open in Vitessce
Visium
Mouse heart
GSM5691527
mouse heart 28.4 MB 1,374 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Size28.4 MB
Spots1,374
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM5691526
mouse heart 17.1 MB 959 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Size17.1 MB
Spots959
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM5691528
mouse heart 36.2 MB 1,722 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Size36.2 MB
Spots1,722
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM5691529
mouse heart 30.0 MB 2,095 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Size30.0 MB
Spots2,095
silver H&E NCBI GEO policy Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.