Collections / Spatial transcriptomics of triple negative breast cancer

Spatial transcriptomics of triple negative breast cancer

Triple negative breast cancer (TNBC) is an aggressive and clinically challenging subtype of breast cancer. TNBC disporportionately affects African-American (AA) women, but the biological basis of this disparity is not understood. To gain a better understanding of TNBC, particularly in AA patients, we applied spatial transcriptomics to thoroughly characterize gene expression and tissue architecture in TNBC. Our cohort consisted of 22 patients, 15 of whom were AA, and 7 who were Caucasian. We obtained 2 sections from each patient's tumor (except for patient 19) for a total of 43 samples.

Datasets43
Size~1.1 GB
AssayVisium
Samplehuman · breast
KindOther
PMID:36283023 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse210616")
coll.ordered_artifacts.df()                 # the 43 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 · 43
Open in Vitessce
Visium
Human breast
GSM6433604
human breast triple-negative breast carcinoma 13 MB 1,111 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size13 MB
Obs1,111
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433608
human breast triple-negative breast carcinoma 42 MB 3,116 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size42 MB
Obs3,116
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433625
human breast triple-negative breast carcinoma 13 MB 635 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size13 MB
Obs635
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433619
human breast triple-negative breast carcinoma 27 MB 2,196 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size27 MB
Obs2,196
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433595
human breast triple-negative breast carcinoma 36 MB 1,264 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size36 MB
Obs1,264
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433585
human breast triple-negative breast carcinoma 33 MB 1,289 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size33 MB
Obs1,289
Magnificationother · 3.880 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433611
human breast triple-negative breast carcinoma 22 MB 1,359 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size22 MB
Obs1,359
Magnificationother · 3.295 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433620
human breast triple-negative breast carcinoma 18 MB 926 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size18 MB
Obs926
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433600
human breast triple-negative breast carcinoma 20 MB 754 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size20 MB
Obs754
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433624
human breast triple-negative breast carcinoma 14 MB 1,266 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size14 MB
Obs1,266
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433590
human breast triple-negative breast carcinoma 29 MB 1,532 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size29 MB
Obs1,532
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433626
human breast triple-negative breast carcinoma 15 MB 897 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size15 MB
Obs897
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433586
human breast triple-negative breast carcinoma 30 MB 1,376 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size30 MB
Obs1,376
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433613
human breast triple-negative breast carcinoma 29 MB 1,868 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size29 MB
Obs1,868
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433602
human breast triple-negative breast carcinoma 39 MB 1,554 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size39 MB
Obs1,554
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433589
human breast triple-negative breast carcinoma 43 MB 2,117 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size43 MB
Obs2,117
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433617
human breast triple-negative breast carcinoma 11 MB 554 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size11 MB
Obs554
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433599
human breast triple-negative breast carcinoma 45 MB 1,949 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size45 MB
Obs1,949
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433610
human breast triple-negative breast carcinoma 20 MB 1,511 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size20 MB
Obs1,511
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433622
human breast triple-negative breast carcinoma 22 MB 1,298 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size22 MB
Obs1,298
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433597
human breast triple-negative breast carcinoma 25 MB 1,109 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size25 MB
Obs1,109
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433605
human breast triple-negative breast carcinoma 15 MB 558 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size15 MB
Obs558
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433614
human breast triple-negative breast carcinoma 27 MB 1,199 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size27 MB
Obs1,199
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433603
human breast triple-negative breast carcinoma 28 MB 1,127 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size28 MB
Obs1,127
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433612
human breast triple-negative breast carcinoma 14 MB 844 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size14 MB
Obs844
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433609
human breast triple-negative breast carcinoma 25 MB 1,518 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size25 MB
Obs1,518
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433621
human breast triple-negative breast carcinoma 16 MB 821 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size16 MB
Obs821
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433618
human breast triple-negative breast carcinoma 34 MB 2,207 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size34 MB
Obs2,207
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433623
human breast triple-negative breast carcinoma 12 MB 901 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size12 MB
Obs901
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433591
human breast triple-negative breast carcinoma 20 MB 772 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size20 MB
Obs772
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433587
human breast triple-negative breast carcinoma 31 MB 1,654 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size31 MB
Obs1,654
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433592
human breast triple-negative breast carcinoma 29 MB 1,325 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size29 MB
Obs1,325
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433606
human breast triple-negative breast carcinoma 17 MB 850 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size17 MB
Obs850
Magnificationother · 3.285 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433594
human breast triple-negative breast carcinoma 38 MB 1,391 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size38 MB
Obs1,391
Magnificationother · 3.600 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433615
human breast triple-negative breast carcinoma 18 MB 1,048 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size18 MB
Obs1,048
Magnificationother · 3.636 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433588
human breast triple-negative breast carcinoma 30 MB 1,178 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size30 MB
Obs1,178
Magnificationother · 3.785 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433593
human breast triple-negative breast carcinoma 43 MB 1,542 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size43 MB
Obs1,542
Magnificationother · 3.601 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433596
human breast triple-negative breast carcinoma 32 MB 1,167 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size32 MB
Obs1,167
Magnificationother · 3.604 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433607
human breast triple-negative breast carcinoma 30 MB 2,088 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size30 MB
Obs2,088
Magnificationother · 3.276 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433598
human breast triple-negative breast carcinoma 27 MB 1,058 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size27 MB
Obs1,058
Magnificationother · 3.288 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433627
human breast triple-negative breast carcinoma 16 MB 1,124 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size16 MB
Obs1,124
Magnificationother · 3.649 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433616
human breast triple-negative breast carcinoma 17 MB 921 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size17 MB
Obs921
Magnificationother · 3.636 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human breast
GSM6433601
human breast triple-negative breast carcinoma 24 MB 1,593 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebreast
Conditiontriple-negative breast carcinoma
Size24 MB
Obs1,593
Magnificationother · 3.267 µm/px
bronze H&E Open in Vitessce

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