Collections / Spatial transcriptomic sequencing data of human small cell lung cancer

Spatial transcriptomic sequencing data of human small cell lung cancer

Small cell lung cancer is a lung tumor with extremely poor prognosis, and its tumor heterogeneity and unique microenvironment remain unclear. This study aimed to reveal the early tumorigenesis and microenvironment of small cell lung cancer by performing idle transcriptomic sequencing of patients' small cell lung cancer tissues.

Datasets4
Size~184 MB
AssayVisium
Samplehuman · lung
KindOther
Flag a data issue
www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE263196 ↗
Python · sddb client
from sddb import Catalog

cohort = Catalog().collection("geo-gse263196")
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-gse263196")
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-gse263196 --dest data/

Licenses: 4 NCBI GEO policy

Open in Vitessce
Visium
Human lung
GSM8187469
human lung small cell lung carcinoma 48.5 MB 3,860 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuelung
Conditionsmall cell lung carcinoma
Size48.5 MB
Spots3,860
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8187472
human lung small cell lung carcinoma 71.2 MB 3,520 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuelung
Conditionsmall cell lung carcinoma
Size71.2 MB
Spots3,520
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8187473
human lung small cell lung carcinoma 20.3 MB 2,655 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuelung
Conditionsmall cell lung carcinoma
Size20.3 MB
Spots2,655
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8187470
human lung small cell lung carcinoma 44.4 MB 2,709 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuelung
Conditionsmall cell lung carcinoma
Size44.4 MB
Spots2,709
silver H&E NCBI GEO policy Open in Vitessce

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