Collections / scRNA-seq, snATAC-seq, and spatial transcriptomics analysis of mammary glands of aged female mice

scRNA-seq, snATAC-seq, and spatial transcriptomics analysis of mammary glands of aged female mice

Aging results in changes in mammary gland cell proportions, gene expression, and chromatin accessibility. Cell types captured include epithelial, immune, and stromal cell types.

Datasets4
Size~263 MB
AssayVisium
Samplemouse · mammary gland
KindTime course
PMID:39587369 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse216542")
coll.ordered_artifacts.df()                 # the 4 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()}
Open in Vitessce
Visium
Mouse mammary gland
GSM8155366
mouse mammary gland breast neoplasm 76 MB 4,403 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuemammary gland
Conditionbreast neoplasm
Size76 MB
Obs4,403
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse mammary gland
GSM7837730
mouse mammary gland breast neoplasm 59 MB 6,597 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuemammary gland
Conditionbreast neoplasm
Size59 MB
Obs6,597
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse mammary gland
GSM8155367
mouse mammary gland breast neoplasm 64 MB 4,070 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuemammary gland
Conditionbreast neoplasm
Size64 MB
Obs4,070
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse mammary gland
GSM7837731
mouse mammary gland breast neoplasm 64 MB 9,745 obs silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuemammary gland
Conditionbreast neoplasm
Size64 MB
Obs9,745
silver H&E NCBI GEO policy Open in Vitessce

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