Collections / Single Nuclei and Spatial Transcriptomic Datasets in Brain Metastases

Single Nuclei and Spatial Transcriptomic Datasets in Brain Metastases

We performed single nuclei and spatial transcriptomic sequencing on a cohort of solid tumor human brain metastasis specimens resected at Duke University Medical Center from 1998 to 2022. This includes 23 single nuclei specimens, 12 Visium standard specimens, and 4 Xenium specimens. These samples encompass metastases from lung cancer, breast cancer, melanoma, and sarcoma primaries. Analysis of these data revealed novel tumor-microenvironment cell-cell interactions associated with patient survival.

Datasets12
Size~449 MB
AssayVisium
Samplehuman · brain
KindComparison
www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE325196 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse325196")
coll.ordered_artifacts.df()                 # the 12 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 · 12
Visium
Human brain
GSM9597736
human brain metastatic malignant neoplasm 46 MB 2,921 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionmetastatic malignant neoplasm
Size46 MB
Obs2,921
silver H&E
Open in Vitessce
Visium
Human brain
GSM9597732
human brain metastatic malignant neoplasm 18 MB 1,151 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionmetastatic malignant neoplasm
Size18 MB
Obs1,151
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM9597735
human brain metastatic malignant neoplasm 11 MB 1,033 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionmetastatic malignant neoplasm
Size11 MB
Obs1,033
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM9597727
human brain metastatic malignant neoplasm 45 MB 4,569 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionmetastatic malignant neoplasm
Size45 MB
Obs4,569
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM9597731
human brain metastatic malignant neoplasm 48 MB 4,436 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionmetastatic malignant neoplasm
Size48 MB
Obs4,436
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM9597729
human brain metastatic malignant neoplasm 8.0 MB 330 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionmetastatic malignant neoplasm
Size8.0 MB
Obs330
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM9597726
human brain metastatic malignant neoplasm 32 MB 2,671 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionmetastatic malignant neoplasm
Size32 MB
Obs2,671
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM9597733
human brain metastatic malignant neoplasm 71 MB 3,735 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionmetastatic malignant neoplasm
Size71 MB
Obs3,735
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM9597734
human brain metastatic malignant neoplasm 11 MB 911 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionmetastatic malignant neoplasm
Size11 MB
Obs911
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM9597730
human brain metastatic malignant neoplasm 84 MB 4,607 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionmetastatic malignant neoplasm
Size84 MB
Obs4,607
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM9597728
human brain metastatic malignant neoplasm 67 MB 3,876 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionmetastatic malignant neoplasm
Size67 MB
Obs3,876
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM9597725
human brain metastatic malignant neoplasm 6.7 MB 996 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionmetastatic malignant neoplasm
Size6.7 MB
Obs996
silver H&E Open in Vitessce

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