Mouse brain
GSM9618494
mouse brain breast cancer 70.5 MB 3,406 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditionbreast cancer
Spots3,406
bronze H&E NCBI GEO policy
Collections / Interleukin-34 induced Arg1+ macrophages play a key role in breast cancer brain metastasis
Interleukin-34 induced Arg1+ macrophages play a key role in breast cancer brain metastasis
We use 10x Genomics to perform the visium RNA sequencing on two tumor tissue, which showed cell type clusters and whole genome profiling in each cell clusters. Visium CytAssist Spatial Gene Expression kit was used for FFPE (Mouse Transcriptome, 6.5 mm, 4 rxns, PN-1000521,10x Genomics).
Datasets2
Size~155 MB
AssayVisium
Samplemouse · brain
KindOther
Download the whole collection
Python · sddb client
from sddb import Catalog
cohort = Catalog().collection("geo-gse325996")
cohort.members # the 2 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-gse325996")
coll.ordered_artifacts.to_dataframe() # the 2 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-gse325996 --dest data/Licenses: 2 NCBI GEO policy
Member datasets · 2
Mouse brain
GSM9618495
mouse brain breast cancer 84.0 MB 4,017 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuebrain
Conditionbreast cancer
Spots4,017
bronze H&E NCBI GEO policy
Cite this collection
No linked publication found — please cite the data source.