Collections / Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in Desmoplastic Small Round Cell Tumors [Visium: Spatial transcriptomics]

Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in Desmoplastic Small Round Cell Tumors [Visium: Spatial transcriptomics]

Desmoplastic Small Round Cell Tumor (DSRCT) is a rare, aggressive sarcoma driven by the EWSR1-WT1 chimeric transcription factor. Despite this unique oncogenic driver, DSRCT displays a polyphenotypic differentiation of unknown causality. Using single-cell multi-omics on samples from patients, we find that DSRCT tumor cells cluster into consistant subpopulations with partially overlapping lineage- and metabolism-related transcriptional programs.

Datasets6
Size~271 MB
AssayVisium
Samplehuman · peritoneum
KindOther
PMID:38781959 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse267806")
coll.ordered_artifacts.df()                 # the 6 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 · 6
Open in Vitessce
Visium
Human peritoneum
GSM8279107
human peritoneum desmoplastic small round cell tumor 50 MB 4,240 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditiondesmoplastic small round cell tumor
Size50 MB
Obs4,240
Magnificationother · 3.351 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8279110
human peritoneum desmoplastic small round cell tumor 41 MB 3,537 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditiondesmoplastic small round cell tumor
Size41 MB
Obs3,537
Magnificationother · 3.434 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8279109
human peritoneum desmoplastic small round cell tumor 34 MB 3,583 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditiondesmoplastic small round cell tumor
Size34 MB
Obs3,583
Magnificationother · 3.461 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8279111
human peritoneum desmoplastic small round cell tumor 28 MB 3,215 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditiondesmoplastic small round cell tumor
Size28 MB
Obs3,215
Magnificationother · 3.432 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8279108
human peritoneum desmoplastic small round cell tumor 55 MB 3,452 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditiondesmoplastic small round cell tumor
Size55 MB
Obs3,452
Magnificationother · 3.381 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Human peritoneum
GSM8279112
human peritoneum desmoplastic small round cell tumor 64 MB 3,697 obs bronze H&E
TechnologyVisium
Organismhuman
Tissueperitoneum
Conditiondesmoplastic small round cell tumor
Size64 MB
Obs3,697
Magnificationother · 3.642 µm/px
bronze H&E Open in Vitessce

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