Collections / Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver -Spatial Transcriptomics

Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver -Spatial Transcriptomics

ADAR1 is thought to be an immune suppressor maintaining self-tolerance to endogenous nucleic acids. Lack of ADAR1 results in MDA5 (Ifih1) activation and MDA5 deletion rescues ADAR1 null embryonic lethality. We generated liver specific ADAR1; MDA5 double KO mice and performed high throughput sequencing to investigate hepatic inflammation in these mice. Spatial transcriptomics (Visium, 10x Genomics) was performed on FFPE mice liver tissues. Constructed libraries were sequenced on the Novaseq 6000 platform. Over 250 million pairs of mappable reads for each sample were obtained.

Datasets9
Size~337 MB
AssayVisium
Samplemouse · liver
KindComparison
PMID:38935501 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse228195")
coll.ordered_artifacts.df()                 # the 9 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 · 9
Open in Vitessce
Visium
Mouse liver
GSM7116322
mouse liver 53 MB 4,538 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size53 MB
Obs4,538
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM7116328
mouse liver 30 MB 2,736 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size30 MB
Obs2,736
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM7116324
mouse liver 32 MB 2,737 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size32 MB
Obs2,737
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM7116326
mouse liver 31 MB 2,868 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size31 MB
Obs2,868
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM7116329
mouse liver 32 MB 2,741 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size32 MB
Obs2,741
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM7116325
mouse liver 32 MB 2,928 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size32 MB
Obs2,928
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM7116323
mouse liver 43 MB 4,579 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size43 MB
Obs4,579
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM7116327
mouse liver 33 MB 2,868 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size33 MB
Obs2,868
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM7116321
mouse liver 50 MB 4,198 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size50 MB
Obs4,198
silver H&E Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.