Collections / Spatial transcriptomics of human plastic and non-plastic breast cancer subtypes

Spatial transcriptomics of human plastic and non-plastic breast cancer subtypes

Cellular plasticity is a hallmark of rare Claudin-low (CL) and metaplastic (MBC) breast cancer subtypes, with a documented overlap whose exact extent is yet unknown, and which are associated to resistance and poor survival. We used spatial transcriptomics to further characterise these plastic subtypes, respectively defined molecularly and histopathologically. We identified 3 putative CL tumours (CL-like) and 4 genomically unstable TNBC samples via molecular analyses, combined with 4 MBCs identified by a breast pathologist. High resolution images are available on Zenodo https://zenodo.org/records/20727406

Datasets14
Size~360 MB
AssayVisium
Samplehuman · breast
KindComparison
PMID:37813278 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse213688")
coll.ordered_artifacts.df()                 # the 14 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 · 14
Open in Vitessce
Visium
Human breast
GSM6592055
human breast triple-negative breast carcinoma 15 MB 1,055 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size15 MB
Obs1,055
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6592057
human breast triple-negative breast carcinoma 5.8 MB 370 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size5.8 MB
Obs370
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6592051
human breast triple-negative breast carcinoma 20 MB 1,564 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size20 MB
Obs1,564
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6592059
human breast triple-negative breast carcinoma 44 MB 2,657 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size44 MB
Obs2,657
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6592060
human breast triple-negative breast carcinoma 22 MB 1,295 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size22 MB
Obs1,295
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6592061
human breast triple-negative breast carcinoma 53 MB 3,037 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size53 MB
Obs3,037
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6592062
human breast triple-negative breast carcinoma 44 MB 2,700 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size44 MB
Obs2,700
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6592049
human breast triple-negative breast carcinoma 24 MB 1,848 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size24 MB
Obs1,848
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6592050
human breast triple-negative breast carcinoma 30 MB 2,417 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size30 MB
Obs2,417
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6592054
human breast triple-negative breast carcinoma 15 MB 1,596 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size15 MB
Obs1,596
Magnificationother · 3.419 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6592058
human breast triple-negative breast carcinoma 22 MB 1,405 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size22 MB
Obs1,405
Magnificationother · 3.314 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6592053
human breast triple-negative breast carcinoma 29 MB 1,731 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size29 MB
Obs1,731
Magnificationother · 3.350 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6592052
human breast triple-negative breast carcinoma 25 MB 2,104 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size25 MB
Obs2,104
Magnificationother · 3.419 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6592056
human breast triple-negative breast carcinoma 10 MB 1,258 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size10 MB
Obs1,258
Magnificationother · 3.342 µm/px
bronze H&E Open in Vitessce

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