Collections / A single cell and spatial atlas of preinvasive breast cancer [Visium ST]

A single cell and spatial atlas of preinvasive breast cancer [Visium ST]

Ductal carcinoma in situ (DCIS) is the most common preinvasive breast cancer, however our knowledge of the DCIS tumor microenvironment (TME) remains limited. We constructed a comprehensive atlas of the TME in estrogen-receptor positive DCIS using fresh samples collected from normal breast tissues, DCIS and invasive breast cancers. This Series is only for the Visium samples, see GSE348584 for the Xenium samples.

Datasets11
Size~425 MB
AssayVisium
Samplehuman · breast
KindOther
www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE348919 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse348919")
coll.ordered_artifacts.df()                 # the 11 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 · 11
Open in Vitessce
Visium
Human breast
GSM10083693
human breast ductal breast carcinoma in situ 73 MB 3,756 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditionductal breast carcinoma in situ
Size73 MB
Obs3,756
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM10083685
human breast ductal breast carcinoma in situ 55 MB 4,623 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditionductal breast carcinoma in situ
Size55 MB
Obs4,623
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM10083688
human breast ductal breast carcinoma in situ 40 MB 2,800 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditionductal breast carcinoma in situ
Size40 MB
Obs2,800
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM10083687
human breast ductal breast carcinoma in situ 27 MB 1,567 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditionductal breast carcinoma in situ
Size27 MB
Obs1,567
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM10083686
human breast ductal breast carcinoma in situ 28 MB 3,164 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditionductal breast carcinoma in situ
Size28 MB
Obs3,164
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM10083696
human breast ductal breast carcinoma in situ 27 MB 3,585 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditionductal breast carcinoma in situ
Size27 MB
Obs3,585
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM10083692
human breast ductal breast carcinoma in situ 50 MB 2,952 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditionductal breast carcinoma in situ
Size50 MB
Obs2,952
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM10083690
human breast ductal breast carcinoma in situ 30 MB 2,063 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditionductal breast carcinoma in situ
Size30 MB
Obs2,063
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM10083689
human breast ductal breast carcinoma in situ 21 MB 1,818 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditionductal breast carcinoma in situ
Size21 MB
Obs1,818
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM10083694
human breast ductal breast carcinoma in situ 35 MB 2,773 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditionductal breast carcinoma in situ
Size35 MB
Obs2,773
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM10083691
human breast ductal breast carcinoma in situ 40 MB 2,510 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditionductal breast carcinoma in situ
Size40 MB
Obs2,510
silver H&E Open in Vitessce

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