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~461 MB
AssayVisium
Samplehuman · spleen
KindComparison
Flag a data issue
www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE332563 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse332563")
cohort.members        # the 12 datasets as a table

print(cohort.licenses())              # check the terms before you download

sdatas = cohort.to_dict()             # {uid: SpatialData}, cached locally
# or keep the .zarr files in a folder of your choice:
# sdatas = cohort.to_dict(dest="data/")
Install (Python 3.12+) Docs →
Python · lamindb

Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.

import lamindb as ln

db = ln.DB("scverse/spatialdata-db")
coll = db.Collection.get(key="geo-gse332563")
coll.ordered_artifacts.to_dataframe()   # the 12 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
Install (Python 3.12+) Docs →
Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse332563 --dest data/
Install (Python 3.12+) Docs →

Licenses: 12 NCBI GEO policy

Member datasets · 12
Open in Vitessce
Visium
Human spleen
GSM9750810
human spleen 30.6 MB 4,988 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuespleen
Size30.6 MB
Spots4,988
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750819
human spleen myelofibrosis 43.1 MB 4,905 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuespleen
Conditionmyelofibrosis
Size43.1 MB
Spots4,905
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750811
human spleen myelofibrosis 57.2 MB 4,992 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuespleen
Conditionmyelofibrosis
Size57.2 MB
Spots4,992
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750817
human spleen myelofibrosis 33.2 MB 4,663 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuespleen
Conditionmyelofibrosis
Size33.2 MB
Spots4,663
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750808
human spleen 29.3 MB 4,571 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuespleen
Size29.3 MB
Spots4,571
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750812
human spleen myelofibrosis 74.2 MB 4,896 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuespleen
Conditionmyelofibrosis
Size74.2 MB
Spots4,896
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750815
human spleen myelofibrosis 37.2 MB 4,873 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuespleen
Conditionmyelofibrosis
Size37.2 MB
Spots4,873
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750818
human spleen myelofibrosis 31.9 MB 4,948 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuespleen
Conditionmyelofibrosis
Size31.9 MB
Spots4,948
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750816
human spleen myelofibrosis 31.0 MB 4,992 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuespleen
Conditionmyelofibrosis
Size31.0 MB
Spots4,992
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750814
human spleen myelofibrosis 22.3 MB 4,979 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuespleen
Conditionmyelofibrosis
Size22.3 MB
Spots4,979
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750809
human spleen 26.8 MB 4,963 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuespleen
Size26.8 MB
Spots4,963
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human spleen
GSM9750813
human spleen myelofibrosis 44.0 MB 4,867 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissuespleen
Conditionmyelofibrosis
Size44.0 MB
Spots4,867
silver H&E NCBI GEO policy Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.