Visium Human palatine tonsil
GSM8500542
human palatine tonsil 122 MB 4,923 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuepalatine tonsil
Obs4,923
Magnificationother · 3.038 µm/px
bronze H&E
Collections / Spatial transcriptomics characterization of ecosystems in the immune tumor microenvironment of diffuse large B-cell lymphoma
Spatial transcriptomics characterization of ecosystems in the immune tumor microenvironment of diffuse large B-cell lymphoma
This dataset comprises spatial transcriptomic profiles from 10 tissue samples of Diffuse Large B-cell Lymphoma (DLBCL) the most common subtype of non-Hodgkin’s lymphoma and secondary lymphoid organ controls (SLO). The diffuse nature of DLBCL challenges the analysis of cellular organization within the immune tumor microenvironment (TME). We employed spatial transcriptomics to map spatially-resolved gene expression patterns. The analysis led to the identification of six cellular ecosystems (Cell-Eco) that differ in cellular composition, functional patterns, and neighborhood characteristics. The spatially-resolved Cell-Eco signatures provided prognostic scores that stratified patients with different overall survival rates. We also found that C1q+ tumor-associated macrophages are the primary cells interacting with malignant B cells and influencing the spatial architecture of the TME. This resource offers valuable insights into the spatial complexity of the DLBCL microenvironment and its potential prognostic significance.
Datasets9
Size~672 MB
AssayVisium
Samplehuman · multiple
KindOther
Download the whole collection
Python · lamindb
import lamindb as ln
import spatialdata as sd
coll = ln.Collection.get(key="geo-gse276542")
coll.ordered_artifacts.df() # the 9 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 · 9
Visium 
Visium Human lymph node
GSM8500537
human lymph node diffuse large B-cell lymphoma 45 MB 1,723 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelymph node
Conditiondiffuse large B-cell lymphoma
Obs1,723
Magnificationother · 2.752 µm/px
bronze H&E
Visium Human palatine tonsil
GSM8500535
human palatine tonsil 74 MB 3,318 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuepalatine tonsil
Obs3,318
Magnificationother · 3.658 µm/px
bronze H&E
Visium Human lymph node
GSM8500534
human lymph node 35 MB 3,384 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelymph node
Obs3,384
Magnificationother · 3.655 µm/px
bronze H&E
Visium Human lymph node
GSM8500540
human lymph node diffuse large B-cell lymphoma 112 MB 4,992 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelymph node
Conditiondiffuse large B-cell lymphoma
Obs4,992
Magnificationother · 3.083 µm/px
bronze H&E
Visium Human lymph node
GSM8500538
human lymph node diffuse large B-cell lymphoma 44 MB 1,827 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelymph node
Conditiondiffuse large B-cell lymphoma
Obs1,827
Magnificationother · 3.002 µm/px
bronze H&E
Visium Human lymph node
GSM8500539
human lymph node diffuse large B-cell lymphoma 117 MB 4,992 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelymph node
Conditiondiffuse large B-cell lymphoma
Obs4,992
bronze H&E
Visium Human lymph node
GSM8500536
human lymph node diffuse large B-cell lymphoma 24 MB 1,197 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelymph node
Conditiondiffuse large B-cell lymphoma
Obs1,197
bronze H&E
Visium Human lymph node
GSM8500541
human lymph node 100 MB 4,674 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuelymph node
Obs4,674
bronze H&E
Cite this collection
No linked publication found — please cite the data source.