Collections / Spatial RNA-sequencing of day7 and day 21 post-LCMV Cl13 infection following transient CD4+ T cell depletion (Visium)

Spatial RNA-sequencing of day7 and day 21 post-LCMV Cl13 infection following transient CD4+ T cell depletion (Visium)

CD4+ T cells play a critical role in sustaining the effector function of CD8+ T cells during chronic viral infection. When CD4+ T cell “help” is absent, CD8+ T cells enter a dysfunctional state, losing their capacity for viral control. Here, we applied spatial transcriptomics to explore cellular localization and potential interaction between key immune cell subsets during chronic LCMV Clone 13 infection.

Datasets8
Size~275 MB
AssayVisium
Samplemouse · spleen
KindTime course
PMID:36450262 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse200720")
coll.ordered_artifacts.df()                 # the 8 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 · 8
Open in Vitessce
Visium
Mouse spleen
GSM6042732
mouse spleen lymphocytic choriomeningitis 38 MB 3,018 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuespleen
Conditionlymphocytic choriomeningitis
Size38 MB
Obs3,018
Magnificationother · 3.960 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse spleen
GSM6042729
mouse spleen lymphocytic choriomeningitis 33 MB 2,495 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuespleen
Conditionlymphocytic choriomeningitis
Size33 MB
Obs2,495
Magnificationother · 3.617 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse spleen
GSM6042727
mouse spleen lymphocytic choriomeningitis 35 MB 2,177 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuespleen
Conditionlymphocytic choriomeningitis
Size35 MB
Obs2,177
Magnificationother · 3.513 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse spleen
GSM6042730
mouse spleen lymphocytic choriomeningitis 30 MB 2,254 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuespleen
Conditionlymphocytic choriomeningitis
Size30 MB
Obs2,254
Magnificationother · 3.961 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse spleen
GSM6042728
mouse spleen lymphocytic choriomeningitis 35 MB 2,659 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuespleen
Conditionlymphocytic choriomeningitis
Size35 MB
Obs2,659
Magnificationother · 3.505 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse spleen
GSM6042733
mouse spleen lymphocytic choriomeningitis 23 MB 1,669 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuespleen
Conditionlymphocytic choriomeningitis
Size23 MB
Obs1,669
Magnificationother · 3.975 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse spleen
GSM6042731
mouse spleen lymphocytic choriomeningitis 44 MB 2,714 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuespleen
Conditionlymphocytic choriomeningitis
Size44 MB
Obs2,714
Magnificationother · 3.962 µm/px
bronze H&E Open in Vitessce
Open in Vitessce
Visium
Mouse spleen
GSM6042726
mouse spleen lymphocytic choriomeningitis 37 MB 2,774 obs bronze H&E
TechnologyVisium
Organismmouse
Tissuespleen
Conditionlymphocytic choriomeningitis
Size37 MB
Obs2,774
Magnificationother · 3.930 µm/px
bronze H&E Open in Vitessce

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