Collections / geo-gse137986

geo-gse137986

Datasets7
Size~80.8 MB
AssayDBiT-seq
Samplemouse · embryo
KindPublication
Flag a data issue
10.1016/j.cell.2020.10.026 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse137986")
cohort.members        # the 7 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-gse137986")
coll.ordered_artifacts.to_dataframe()   # the 7 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-gse137986 --dest data/
Install (Python 3.12+) Docs →

Licenses: 7 NCBI GEO policy

About the study

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue.

Read the abstract at the source →
Member datasets · 7
Open in Vitessce
DBiT-seq
Mouse embryo
GSM4096261
mouse embryo 20.1 MB 2,500 pixels silver NCBI GEO policy
TechnologyDBiT-seq
Organismmouse
Tissueembryo
Size20.1 MB
Pixels2,500
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
DBiT-seq
Mouse embryo
GSM4364242
mouse embryo 10.0 MB 1,837 pixels silver NCBI GEO policy
TechnologyDBiT-seq
Organismmouse
Tissueembryo
Size10.0 MB
Pixels1,837
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
DBiT-seq
Mouse embryo
GSM4364245
mouse embryo 6.8 MB 2,109 pixels silver NCBI GEO policy
TechnologyDBiT-seq
Organismmouse
Tissueembryo
Size6.8 MB
Pixels2,109
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
DBiT-seq
Mouse embryo
GSM4364244
mouse embryo 6.4 MB 1,840 pixels silver NCBI GEO policy
TechnologyDBiT-seq
Organismmouse
Tissueembryo
Size6.4 MB
Pixels1,840
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
DBiT-seq
Mouse embryo
GSM4364243
mouse embryo 13.5 MB 1,662 pixels silver NCBI GEO policy
TechnologyDBiT-seq
Organismmouse
Tissueembryo
Size13.5 MB
Pixels1,662
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
DBiT-seq
Mouse embryo
GSM4189611
mouse embryo 11.6 MB 902 pixels silver NCBI GEO policy
TechnologyDBiT-seq
Organismmouse
Tissueembryo
Size11.6 MB
Pixels902
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
DBiT-seq
Mouse embryo
GSM4189612
mouse embryo 12.4 MB 1,667 pixels silver NCBI GEO policy
TechnologyDBiT-seq
Organismmouse
Tissueembryo
Size12.4 MB
Pixels1,667
silver NCBI GEO policy Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.