Collections / Spatial transcriptomics of bone taken from two PRF1-/- B16F10-injected and one PRF1-/- healthy control- bone tissues using Xenium

Spatial transcriptomics of bone taken from two PRF1-/- B16F10-injected and one PRF1-/- healthy control- bone tissues using Xenium

Spatial transcriptomic profiling was performed on bone tissue from perforin-deficient (Prf1⁻/⁻) mice following bone injection and from Prf1⁻/⁻ uninjected control bone tissue using the 10x Genomics Xenium platform. The study aimed to characterize spatially resolved gene expression changes associated with tumor or cell injection in the absence of perforin-mediated cytotoxic immunity.

Datasets6
Size~10.2 GB
Assay10x Xenium
Samplemouse · bone element
KindComparison
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www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE329415 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse329415")
cohort.members        # the 6 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-gse329415")
coll.ordered_artifacts.to_dataframe()   # the 6 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-gse329415 --dest data/
Install (Python 3.12+) Docs →

Licenses: 6 NCBI GEO policy

Member datasets · 6
Open in Vitessce
10x Xenium
Mouse bone element
GSM9703599
mouse bone element melanoma 950 MB 77,166 cells silver NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuebone element
Conditionmelanoma
Size950 MB
Cells77,166
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse bone element
GSM9703603
mouse bone element 1.5 GB 182,887 cells silver NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuebone element
Size1.5 GB
Cells182,887
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse bone element
GSM9703602
mouse bone element melanoma 2.6 GB 119,458 cells silver NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuebone element
Conditionmelanoma
Size2.6 GB
Cells119,458
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse bone element
GSM9703604
mouse bone element 1.5 GB 169,216 cells silver NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuebone element
Size1.5 GB
Cells169,216
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse bone element
GSM9703601
mouse bone element melanoma 2.8 GB 140,716 cells silver NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuebone element
Conditionmelanoma
Size2.8 GB
Cells140,716
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
10x Xenium
Mouse bone element
GSM9703600
mouse bone element melanoma 852 MB 65,456 cells silver NCBI GEO policy
Technology10x Xenium
Organismmouse
Tissuebone element
Conditionmelanoma
Size852 MB
Cells65,456
silver NCBI GEO policy Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.