Collections / geo-gse213264

geo-gse213264

Datasets8
Size~54.6 MB
Assayspatial-CITE-seq
Samplemultiple · multiple
KindPublication
Flag a data issue
10.1038/s41587-023-01676-0 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse213264")
cohort.members        # the 8 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-gse213264")
coll.ordered_artifacts.to_dataframe()   # the 8 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-gse213264 --dest data/
Install (Python 3.12+) Docs →

Licenses: 8 NCBI GEO policy

About the study

High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq.

In this study, we extended co-indexing of transcriptomes and epitopes (CITE) to the spatial dimension and demonstrated high-plex protein and whole transcriptome co-mapping. We profiled 189 proteins and whole transcriptome in multiple mouse tissue types with spatial CITE sequencing and then further applied the method to measure 273 proteins and transcriptome in human tissues, revealing spatially distinct germinal center reactions in tonsil and early immune activation in skin at the Coronavirus Disease 2019 mRNA vaccine injection site.

Member datasets · 8
Open in Vitessce
spatial-CITE-seq
Mouse colon
GSM6578059
mouse colon 2.7 MB 2,037 pixels bronze NCBI GEO policy
Technologyspatial-CITE-seq
Organismmouse
Tissuecolon
Size2.7 MB
Pixels2,037
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
spatial-CITE-seq
Mouse intestine
GSM6578060
mouse intestine 1.2 MB 902 pixels bronze NCBI GEO policy
Technologyspatial-CITE-seq
Organismmouse
Tissueintestine
Size1.2 MB
Pixels902
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
spatial-CITE-seq
Mouse kidney
GSM6578061
mouse kidney 10.9 MB 2,419 pixels bronze NCBI GEO policy
Technologyspatial-CITE-seq
Organismmouse
Tissuekidney
Size10.9 MB
Pixels2,419
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
spatial-CITE-seq
Human skin of body
GSM6578065
human skin of body 2.9 MB 1,691 pixels bronze NCBI GEO policy
Technologyspatial-CITE-seq
Organismhuman
Tissueskin of body
Size2.9 MB
Pixels1,691
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
spatial-CITE-seq
Human tonsil
GSM6578062
human tonsil 16.4 MB 2,492 pixels bronze NCBI GEO policy
Technologyspatial-CITE-seq
Organismhuman
Tissuetonsil
Size16.4 MB
Pixels2,492
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
spatial-CITE-seq
Human thymus
GSM6578064
human thymus 13.2 MB 2,500 pixels bronze NCBI GEO policy
Technologyspatial-CITE-seq
Organismhuman
Tissuethymus
Size13.2 MB
Pixels2,500
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
spatial-CITE-seq
Mouse spleen
GSM6578058
mouse spleen 5.3 MB 1,303 pixels bronze NCBI GEO policy
Technologyspatial-CITE-seq
Organismmouse
Tissuespleen
Size5.3 MB
Pixels1,303
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
spatial-CITE-seq
Human spleen
GSM6578063
human spleen 2.1 MB 2,494 pixels bronze NCBI GEO policy
Technologyspatial-CITE-seq
Organismhuman
Tissuespleen
Size2.1 MB
Pixels2,494
bronze NCBI GEO policy Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.