Collections / Spatial transcriptomics of cellular niches in pulmonary granuloma of chronic sarcoidosis patients

Spatial transcriptomics of cellular niches in pulmonary granuloma of chronic sarcoidosis patients

Spatial Transcriptomics using the 10x Genomics Visium technology was performed in lung tissues from 9 patients with chronic sarcoidosis

Datasets9
Size~2.7 GB
AssayVisium
Samplehuman · lung
KindOther
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www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE288607 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse288607")
cohort.members        # the 9 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-gse288607")
coll.ordered_artifacts.to_dataframe()   # the 9 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-gse288607 --dest data/
Install (Python 3.12+) Docs →

Licenses: 9 NCBI GEO policy

Member datasets · 9
Open in Vitessce
Visium
Human lung
GSM8770958
human lung sarcoidosis 13.7 MB 4,991 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuelung
Conditionsarcoidosis
Size13.7 MB
Spots4,991
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8770954
human lung sarcoidosis 865 MB 4,992 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuelung
Conditionsarcoidosis
Size865 MB
Spots4,992
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8770961
human lung sarcoidosis 701 MB 4,992 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuelung
Conditionsarcoidosis
Size701 MB
Spots4,992
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8770956
human lung sarcoidosis 37.0 MB 4,992 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuelung
Conditionsarcoidosis
Size37.0 MB
Spots4,992
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8770959
human lung sarcoidosis 85.3 MB 4,991 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuelung
Conditionsarcoidosis
Size85.3 MB
Spots4,991
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8770962
human lung sarcoidosis 759 MB 4,992 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuelung
Conditionsarcoidosis
Size759 MB
Spots4,992
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8770957
human lung sarcoidosis 38.2 MB 4,992 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuelung
Conditionsarcoidosis
Size38.2 MB
Spots4,992
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8770960
human lung sarcoidosis 138 MB 4,992 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuelung
Conditionsarcoidosis
Size138 MB
Spots4,992
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8770955
human lung sarcoidosis 52.9 MB 4,992 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuelung
Conditionsarcoidosis
Size52.9 MB
Spots4,992
silver H&E NCBI GEO policy Open in Vitessce

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