Collections / Identification of perturbation-responsive regions and genes in comparative spatial transcriptomics atlases

Identification of perturbation-responsive regions and genes in comparative spatial transcriptomics atlases

This submission is a dataset of single-nucleus transcriptomics in the spinal cords of mice. The single-nuclei transcriptomics data is harvested and profiled using Visium Spatial Gene Expression.

Datasets7
Size~277 MB
AssayVisium
Samplemouse · spinal cord
KindComparison
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www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE268779 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse268779")
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-gse268779")
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-gse268779 --dest data/
Install (Python 3.12+) Docs →

Licenses: 7 NCBI GEO policy

Member datasets · 7
Open in Vitessce
Visium
Mouse spinal cord
GSM8299021
mouse spinal cord 33.2 MB 2,448 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuespinal cord
Size33.2 MB
Spots2,448
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse spinal cord
GSM8299016
mouse spinal cord 27.2 MB 4,243 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuespinal cord
Size27.2 MB
Spots4,243
Magnificationother · 3.289 µm/px
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse spinal cord
GSM8299017
mouse spinal cord 36.3 MB 3,842 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuespinal cord
Size36.3 MB
Spots3,842
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse spinal cord
GSM8299015
mouse spinal cord 51.1 MB 3,746 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuespinal cord
Size51.1 MB
Spots3,746
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse spinal cord
GSM8299020
mouse spinal cord 48.2 MB 3,578 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuespinal cord
Size48.2 MB
Spots3,578
silver H&E NCBI GEO policy Open in Vitessce
Visium
Mouse spinal cord
GSM8299018
mouse spinal cord 45.8 MB 3,985 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuespinal cord
Size45.8 MB
Spots3,985
silver H&E NCBI GEO policy
Open in Vitessce
Visium
Mouse spinal cord
GSM8299019
mouse spinal cord 35.5 MB 3,291 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuespinal cord
Size35.5 MB
Spots3,291
silver H&E NCBI GEO policy Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.