Collections / Conserved principles of spatial biology define tumor heterogeneity and immunotherapy sensitivity

Conserved principles of spatial biology define tumor heterogeneity and immunotherapy sensitivity

Spatial transcriptomics experiments were performed on human patient pre-treatment biopsies for patients with either NSCLC or DLBCL. This was part of a larger study on pan-tumor spatial biology organization.

Datasets18
Size~2.4 GB
AssayVisium
Samplehuman · multiple
KindTime course
PMID:42664957 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse292299")
coll.ordered_artifacts.df()                 # the 18 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
Human brain
GSM8855712
human brain non-small cell lung carcinoma 179 MB 8,862 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionnon-small cell lung carcinoma
Size179 MB
Obs8,862
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human cheek
GSM8855715
human cheek non-small cell lung carcinoma 172 MB 5,247 obs silver H&E
TechnologyVisium
Organismhuman
Tissuecheek
Conditionnon-small cell lung carcinoma
Size172 MB
Obs5,247
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pleura
GSM8855718
human pleura non-small cell lung carcinoma 63 MB 5,351 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepleura
Conditionnon-small cell lung carcinoma
Size63 MB
Obs5,351
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8855714
human lung non-small cell lung carcinoma 43 MB 2,131 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionnon-small cell lung carcinoma
Size43 MB
Obs2,131
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM8855704
human brain non-small cell lung carcinoma 111 MB 6,907 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionnon-small cell lung carcinoma
Size111 MB
Obs6,907
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lymph node
GSM8855720
human lymph node diffuse large B-cell lymphoma 110 MB 13,713 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelymph node
Conditiondiffuse large B-cell lymphoma
Size110 MB
Obs13,713
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human pleura
GSM8855716
human pleura non-small cell lung carcinoma 28 MB 1,862 obs silver H&E
TechnologyVisium
Organismhuman
Tissuepleura
Conditionnon-small cell lung carcinoma
Size28 MB
Obs1,862
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM8855709
human brain non-small cell lung carcinoma 109 MB 5,705 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionnon-small cell lung carcinoma
Size109 MB
Obs5,705
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8855717
human lung non-small cell lung carcinoma 195 MB 13,002 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionnon-small cell lung carcinoma
Size195 MB
Obs13,002
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8855707
human lung non-small cell lung carcinoma 58 MB 5,388 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionnon-small cell lung carcinoma
Size58 MB
Obs5,388
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lymph node
GSM8855705
human lymph node non-small cell lung carcinoma 117 MB 9,158 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelymph node
Conditionnon-small cell lung carcinoma
Size117 MB
Obs9,158
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lung
GSM8855710
human lung non-small cell lung carcinoma 61 MB 5,218 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelung
Conditionnon-small cell lung carcinoma
Size61 MB
Obs5,218
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM8855706
human brain non-small cell lung carcinoma 110 MB 9,516 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionnon-small cell lung carcinoma
Size110 MB
Obs9,516
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM8855711
human brain non-small cell lung carcinoma 228 MB 12,242 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionnon-small cell lung carcinoma
Size228 MB
Obs12,242
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM8855703
human brain non-small cell lung carcinoma 129 MB 8,458 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionnon-small cell lung carcinoma
Size129 MB
Obs8,458
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM8855708
human brain non-small cell lung carcinoma 221 MB 10,078 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionnon-small cell lung carcinoma
Size221 MB
Obs10,078
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lymph node
GSM8855719
human lymph node diffuse large B-cell lymphoma 130 MB 12,413 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelymph node
Conditiondiffuse large B-cell lymphoma
Size130 MB
Obs12,413
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human brain
GSM8855713
human brain non-small cell lung carcinoma 362 MB 13,202 obs silver H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionnon-small cell lung carcinoma
Size362 MB
Obs13,202
silver H&E Open in Vitessce

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