Collections / A spatiotemporal atlas of orchiectomy-induced modulation of cellular composition and gene expression in the mouse prostate

A spatiotemporal atlas of orchiectomy-induced modulation of cellular composition and gene expression in the mouse prostate

Mice models are commonly used to further our understanding of the function of the prostate and response to androgen depletion. We used both spatial transcriptomics and single cell transcriptomics to determine how the mouse prostate degrades after castration. We identified changes in each of the prostate lobes that couuld be tracked over time as well as changes in the immune profile and of the composition of fibroblasts within the prostate. In addition to several previously identified fibroblast subtypes that we were able to show were altered in response to androgen depletion, we identified a novel fibroblast subtype present only in the castrated prostate.

Datasets8
Size~354 MB
AssayVisium
Samplemouse · prostate gland
KindComparison
PMID:40974890 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse295043")
coll.ordered_artifacts.df()                 # the 8 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 · 8
Open in Vitessce
Visium
Mouse prostate gland
GSM8941070
mouse prostate gland 48 MB 2,385 obs bronze H&E
TechnologyVisium
Organismmouse
Tissueprostate gland
Size48 MB
Obs2,385
Magnificationother · 4.019 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse prostate gland
GSM8941074
mouse prostate gland 47 MB 2,222 obs bronze H&E
TechnologyVisium
Organismmouse
Tissueprostate gland
Size47 MB
Obs2,222
Magnificationother · 3.970 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse prostate gland
GSM8941075
mouse prostate gland 39 MB 1,693 obs bronze H&E
TechnologyVisium
Organismmouse
Tissueprostate gland
Size39 MB
Obs1,693
Magnificationother · 4.101 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse prostate gland
GSM8941071
mouse prostate gland 51 MB 2,363 obs bronze H&E
TechnologyVisium
Organismmouse
Tissueprostate gland
Size51 MB
Obs2,363
Magnificationother · 4.062 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse prostate gland
GSM8941069
mouse prostate gland 44 MB 1,980 obs bronze H&E
TechnologyVisium
Organismmouse
Tissueprostate gland
Size44 MB
Obs1,980
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse prostate gland
GSM8941076
mouse prostate gland 43 MB 1,860 obs bronze H&E
TechnologyVisium
Organismmouse
Tissueprostate gland
Size43 MB
Obs1,860
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse prostate gland
GSM8941073
mouse prostate gland 28 MB 1,185 obs bronze H&E
TechnologyVisium
Organismmouse
Tissueprostate gland
Size28 MB
Obs1,185
Magnificationother · 4.082 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse prostate gland
GSM8941072
mouse prostate gland 54 MB 2,558 obs bronze H&E
TechnologyVisium
Organismmouse
Tissueprostate gland
Size54 MB
Obs2,558
bronze H&E Open in Vitessce

Cite this collection

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