Collections / Spatial Transcriptomics of Human Fetal Lungs

Spatial Transcriptomics of Human Fetal Lungs

Spatial transcriptomic profiles were generated using lung tissue sections obtained from twelve prenatal human lung samples ranging in gestational age from 13 – 20 weeks, of which four were diagnosed with Trisomy 21, with defined hypoplasia.

Datasets12

Size~738 MB

AssayVisium

Samplehuman · lung

KindTime course

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PMID:41484334 ↗

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Client Lamin CLI

Python · sddb client

from sddb import Catalog

cohort = Catalog().collection("geo-gse310610")
cohort.members        # the 12 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-gse310610")
coll.ordered_artifacts.to_dataframe()   # the 12 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-gse310610 --dest data/

Install (Python 3.12+) Docs →

Licenses: 12 NCBI GEO policy

Member datasets · 12

Visium

Human lung

GSM9304479

human lung 27.1 MB 4,251 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuelung

Size27.1 MB

Spots4,251

bronze H&E NCBI GEO policy

Visium

Human lung

GSM9304476

human lung 98.9 MB 4,411 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuelung

Size98.9 MB

Spots4,411

bronze H&E NCBI GEO policy

Visium

Human lung

GSM9304484

human lung 70.0 MB 4,399 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuelung

Size70.0 MB

Spots4,399

bronze H&E NCBI GEO policy

Visium

Human lung

GSM9304480

human lung 95.5 MB 4,146 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuelung

Size95.5 MB

Spots4,146

bronze H&E NCBI GEO policy

Visium

Human lung

GSM9304477

human lung 76.5 MB 3,190 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuelung

Size76.5 MB

Spots3,190

bronze H&E NCBI GEO policy

Visium

Human lung

GSM9304483

human lung 117 MB 4,558 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuelung

Size117 MB

Spots4,558

bronze H&E NCBI GEO policy

Visium

Human lung

GSM9304481

human lung 11.5 MB 3,130 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuelung

Size11.5 MB

Spots3,130

bronze H&E NCBI GEO policy

Visium

Human lung

GSM9304482

human lung 29.6 MB 3,251 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuelung

Size29.6 MB

Spots3,251

bronze H&E NCBI GEO policy

Visium

Human lung

GSM9304473

human lung 8.1 MB 838 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuelung

Size8.1 MB

Spots838

bronze H&E NCBI GEO policy

Visium

Human lung

GSM9304474

human lung 27.4 MB 3,792 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuelung

Size27.4 MB

Spots3,792

bronze H&E NCBI GEO policy

Visium

Human lung

GSM9304478

human lung 101 MB 4,198 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuelung

Size101 MB

Spots4,198

bronze H&E NCBI GEO policy

Visium

Human lung

GSM9304475

human lung 75.4 MB 3,271 spots bronze H&E NCBI GEO policy

TechnologyVisium

Organismhuman

Tissuelung

Size75.4 MB

Spots3,271

bronze H&E NCBI GEO policy

Cite this collection

No linked publication found — please cite the data source.