Collections / Spatial sequencing of young and aged lungs following influenza A virus infection

Spatial sequencing of young and aged lungs following influenza A virus infection

Aging is known to alter the host repsonse to influenza infection. Here, we use 10x Visium spatial sequencing to identify spatial changes in mRNA expression of left lungs of young (16-week-old) and aged (80-week-old) mice following influenza infection.

Datasets6
Size~181 MB
AssayVisium
Samplemouse · lung
KindTime course
PMID:37852965 ↗
Python · lamindb
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse202322")
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()}
Open in Vitessce
Visium
Mouse lung
GSM6108349
mouse lung influenza 28 MB 2,520 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuelung
Conditioninfluenza
Size28 MB
Obs2,520
Magnificationother · 4.311 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse lung
GSM6108351
mouse lung influenza 36 MB 2,969 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuelung
Conditioninfluenza
Size36 MB
Obs2,969
Magnificationother · 3.984 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse lung
GSM6108350
mouse lung influenza 39 MB 2,847 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuelung
Conditioninfluenza
Size39 MB
Obs2,847
Magnificationother · 3.980 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse lung
GSM6108348
mouse lung influenza 32 MB 2,486 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuelung
Conditioninfluenza
Size32 MB
Obs2,486
Magnificationother · 4.322 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse lung
GSM6108346
mouse lung 23 MB 1,986 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuelung
Size23 MB
Obs1,986
Magnificationother · 4.004 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse lung
GSM6108347
mouse lung 22 MB 2,218 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuelung
Size22 MB
Obs2,218
Magnificationother · 3.989 µm/px
bronze H&E Open in Vitessce

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