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~9.5 GB
Assay10x Xenium
Samplemouse · bone element
KindComparison
www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE329415 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse329415")
coll.ordered_artifacts.df()                 # the 6 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]

# …or load each straight into memory as a SpatialData object:
sdatas = {a.key: sd.read_zarr(a.cache()) for a in coll.ordered_artifacts.all()}
Member datasets · 6
Open in Vitessce
10x Xenium
Mouse bone element
GSM9703599
mouse bone element melanoma 906 MB 77,166 obs silver
Technology10x Xenium
Organismmouse
Tissuebone element
Conditionmelanoma
Size906 MB
Obs77,166
silver Open in Vitessce
Open in Vitessce
10x Xenium
Mouse bone element
GSM9703603
mouse bone element 1.4 GB 182,887 obs silver
Technology10x Xenium
Organismmouse
Tissuebone element
Size1.4 GB
Obs182,887
silver Open in Vitessce
Open in Vitessce
10x Xenium
Mouse bone element
GSM9703602
mouse bone element melanoma 2.4 GB 119,458 obs silver
Technology10x Xenium
Organismmouse
Tissuebone element
Conditionmelanoma
Size2.4 GB
Obs119,458
silver Open in Vitessce
Open in Vitessce
10x Xenium
Mouse bone element
GSM9703604
mouse bone element 1.4 GB 169,216 obs silver
Technology10x Xenium
Organismmouse
Tissuebone element
Size1.4 GB
Obs169,216
silver Open in Vitessce
Open in Vitessce
10x Xenium
Mouse bone element
GSM9703601
mouse bone element melanoma 2.6 GB 140,716 obs silver
Technology10x Xenium
Organismmouse
Tissuebone element
Conditionmelanoma
Size2.6 GB
Obs140,716
silver Open in Vitessce
Open in Vitessce
10x Xenium
Mouse bone element
GSM9703600
mouse bone element melanoma 813 MB 65,456 obs silver
Technology10x Xenium
Organismmouse
Tissuebone element
Conditionmelanoma
Size813 MB
Obs65,456
silver Open in Vitessce

Cite this collection

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