Collections / Spatial RNA sequencing of bleomycin-treated young and old mice lungs at day 14 and day 28 post injection

Spatial RNA sequencing of bleomycin-treated young and old mice lungs at day 14 and day 28 post injection

We monitored lung fibrosis formation and resolution in young and old mice by generating a series of spatial transcriptomics datasets using the 10x Genomics Visium platform

Datasets8
Size~148 MB
AssayVisium
Samplemouse · lung
KindTime course
Flag a data issue
PMID:40769983 ↗
Python · sddb client
from sddb import Catalog

cohort = Catalog().collection("geo-gse234198")
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/")
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-gse234198")
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()]
Shell
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse234198 --dest data/

Licenses: 8 NCBI GEO policy

Open in Vitessce
Visium
Mouse lung
GSM7454047
mouse lung pulmonary fibrosis 7.4 MB 1,134 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuelung
Conditionpulmonary fibrosis
Size7.4 MB
Spots1,134
silver H&E NCBI GEO policy Open in Vitessce
Visium
Mouse lung
GSM7454048
mouse lung pulmonary fibrosis 27.1 MB 2,383 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuelung
Conditionpulmonary fibrosis
Size27.1 MB
Spots2,383
silver H&E NCBI GEO policy
Open in Vitessce
Visium
Mouse lung
GSM7454045
mouse lung pulmonary fibrosis 19.2 MB 1,734 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuelung
Conditionpulmonary fibrosis
Size19.2 MB
Spots1,734
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse lung
GSM7454043
mouse lung pulmonary fibrosis 9.3 MB 1,303 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuelung
Conditionpulmonary fibrosis
Size9.3 MB
Spots1,303
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse lung
GSM7454049
mouse lung pulmonary fibrosis 14.7 MB 1,449 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuelung
Conditionpulmonary fibrosis
Size14.7 MB
Spots1,449
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse lung
GSM7454046
mouse lung pulmonary fibrosis 26.7 MB 2,135 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuelung
Conditionpulmonary fibrosis
Size26.7 MB
Spots2,135
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse lung
GSM7454044
mouse lung pulmonary fibrosis 30.0 MB 2,400 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuelung
Conditionpulmonary fibrosis
Size30.0 MB
Spots2,400
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse lung
GSM7454042
mouse lung pulmonary fibrosis 13.9 MB 1,254 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuelung
Conditionpulmonary fibrosis
Size13.9 MB
Spots1,254
silver H&E NCBI GEO policy Open in Vitessce

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