Visium HD
Human lung
GSM9021740
human lung 5.9 GB 263,684 bins bronze H&E NCBI GEO policy
TechnologyVisium HD
Organismhuman
Tissuelung
Bins263,684
Magnification40x · 0.221 µm/px
bronze H&E NCBI GEO policy
Collections / geo-gse266680
geo-gse266680
Datasets1
Size~5.9 GB
TechnologyVisium HD
Samplehuman · lung
KindPublication
Download the whole collection
Python · sddb client
from sddb import Catalog
cohort = Catalog().collection("geo-gse266680")
cohort.members # the 1 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/") 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-gse266680")
coll.ordered_artifacts.to_dataframe() # the 1 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()] Shell
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse266680 --dest data/Licenses: 1 NCBI GEO policy
About the study
Architecture of the neutrophil compartment.
Neutrophils exhibit remarkable phenotypic and functional diversity across tissues and diseases<sup>1,2</sup>, yet the lack of understanding of how this immune compartment is globally organized challenges translation to the clinic. Here we performed single-cell transcriptional profiling of neutrophils spanning 47 anatomical, physiological and pathological scenarios to generate an integrated map of the global neutrophil compartment in mice, which we refer to as NeuMap. NeuMap integrates and expands existing models<sup>3,4</sup> to generate fundamental new insights; it reveals that neutrophils organize in a finite number of functional hubs that distribute sequentially during maturation to then branch out into interferon-responsive and immunosuppressive states, as well as a functionally silent state that dominates in the healthy circulation. Computational modelling and timestamp analyses identify prototypical trajectories that connect these hubs, and reveal that the dynamics and preferred paths vary during health, inflammation and cancer. We show that TGFβ, IFNβ and GM-CSF push neutrophils along the different trajectories, and projection of chromatin accessibility sites onto NeuMap reveals that the transcription factor JUNB controls angiogenic and immunosuppressive states and promotes tissue revascularization. The architecture of NeuMap appears to be conserved across sex, environmental and genetic backgrounds, as well as in humans. Finally, we show that NeuMap enables inference of the pathophysiological state of the host by profiling blood neutrophils. Our study delineates the global architecture of the neutrophil compartment and establishes a framework for exploration and exploitation of neutrophil biology.
Member datasets · 1
Cite this collection
No linked publication found — please cite the data source.