Collections / Comprehensive spatial profiling of the spleen in human myelofibrosis [ST_Visium]

Comprehensive spatial profiling of the spleen in human myelofibrosis [ST_Visium]

Splenomegaly is a defining feature of myelofibrosis, yet the contribution of splenic mesenchymal stroma to disease progression remains unclear. We combined spatial and single-nucleus transcriptomics of patient spleens to map extramedullary hematopoiesis niches. Activated red pulp reticular cells localize near hematopoietic stem and progenitor cells, and early disease shows marginal zone disruption with lymphoid depletion preceding stromal remodeling. Macrophage- and megakaryocyte-derived signals activate complement and induce TNFα, TGF-β, extracellular matrix, and Thbs1 programs in reticular cells.

Datasets12
Size~440 MB
AssayVisium
Samplehuman · spleen
KindComparison
www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE332563 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse332563")
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
Open in Vitessce
Visium
Human spleen
GSM9750810
human spleen 29 MB 4,988 obs silver H&E
TechnologyVisium
Organismhuman
Tissuespleen
Size29 MB
Obs4,988
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750819
human spleen myelofibrosis 41 MB 4,905 obs silver H&E
TechnologyVisium
Organismhuman
Tissuespleen
Conditionmyelofibrosis
Size41 MB
Obs4,905
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750811
human spleen myelofibrosis 55 MB 4,992 obs silver H&E
TechnologyVisium
Organismhuman
Tissuespleen
Conditionmyelofibrosis
Size55 MB
Obs4,992
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750817
human spleen myelofibrosis 32 MB 4,663 obs silver H&E
TechnologyVisium
Organismhuman
Tissuespleen
Conditionmyelofibrosis
Size32 MB
Obs4,663
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750808
human spleen 28 MB 4,571 obs silver H&E
TechnologyVisium
Organismhuman
Tissuespleen
Size28 MB
Obs4,571
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750812
human spleen myelofibrosis 71 MB 4,896 obs silver H&E
TechnologyVisium
Organismhuman
Tissuespleen
Conditionmyelofibrosis
Size71 MB
Obs4,896
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750815
human spleen myelofibrosis 35 MB 4,873 obs silver H&E
TechnologyVisium
Organismhuman
Tissuespleen
Conditionmyelofibrosis
Size35 MB
Obs4,873
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750818
human spleen myelofibrosis 30 MB 4,948 obs silver H&E
TechnologyVisium
Organismhuman
Tissuespleen
Conditionmyelofibrosis
Size30 MB
Obs4,948
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750816
human spleen myelofibrosis 30 MB 4,992 obs silver H&E
TechnologyVisium
Organismhuman
Tissuespleen
Conditionmyelofibrosis
Size30 MB
Obs4,992
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750814
human spleen myelofibrosis 21 MB 4,979 obs silver H&E
TechnologyVisium
Organismhuman
Tissuespleen
Conditionmyelofibrosis
Size21 MB
Obs4,979
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750809
human spleen 26 MB 4,963 obs silver H&E
TechnologyVisium
Organismhuman
Tissuespleen
Size26 MB
Obs4,963
silver H&E Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750813
human spleen myelofibrosis 42 MB 4,867 obs silver H&E
TechnologyVisium
Organismhuman
Tissuespleen
Conditionmyelofibrosis
Size42 MB
Obs4,867
silver H&E Open in Vitessce

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