Collections / Patient-derived lymphomoids preserve the tumor architecture and allow testing response to therapies in lymphoma [Spatial Transcriptomics]

Patient-derived lymphomoids preserve the tumor architecture and allow testing response to therapies in lymphoma [Spatial Transcriptomics]

We designed an ex vivo system to culture tissue explants from lymphoma tissue. To characterize the spatial and molecular structure of human lymphomoids and their tissue of origin, we performed spatial transcriptomics analyses on original tissues and lymphomoids obtained from 2 patients using the 10x Genomics Visium technology.

Datasets5
Size~57 MB
AssayVisium
Samplehuman · lymph node
KindComparison
PMID:39653701 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse269695")
coll.ordered_artifacts.df()                 # the 5 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 · 5
Open in Vitessce
Visium
Human lymph node
GSM8324907
human lymph node diffuse large B-cell lymphoma 13 MB 378 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelymph node
Conditiondiffuse large B-cell lymphoma
Size13 MB
Obs378
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lymph node
GSM8324909
human lymph node diffuse large B-cell lymphoma 7.7 MB 191 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelymph node
Conditiondiffuse large B-cell lymphoma
Size7.7 MB
Obs191
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lymph node
GSM8324908
human lymph node diffuse large B-cell lymphoma 6.7 MB 135 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelymph node
Conditiondiffuse large B-cell lymphoma
Size6.7 MB
Obs135
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lymph node
GSM8324905
human lymph node 18 MB 1,001 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelymph node
Size18 MB
Obs1,001
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human lymph node
GSM8324906
human lymph node diffuse large B-cell lymphoma 12 MB 349 obs silver H&E
TechnologyVisium
Organismhuman
Tissuelymph node
Conditiondiffuse large B-cell lymphoma
Size12 MB
Obs349
silver H&E Open in Vitessce

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