Collections / Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches (spatial)

Spatial proteogenomics reveals distinct and evolutionarily-conserved hepatic macrophage niches (spatial)

Analysis of CITE-seq data , Nuclei RNA-seq data and single cell RNA-seq data on CD45+ and CD45- cells isolated from the livers of mice fed a standard diet (SD) or western diet (WD; fat, cholesterol and sugar), from healthy and steatotic human livers, from hamster liver, pig liver, chicken liver, monkey liver and zebrafish liver. We also performed Spatial Transcriptomics analysis on heatlhy mouse livers, NAFLD mouse livers, healthy human livers and steatotic human livers.

Datasets15
Size~365 MB
AssayVisium
Samplemouse · multiple
KindComparison
PMID:35021063 ↗
Download the whole collection
Python · lamindb 
import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse192741")
coll.ordered_artifacts.df()                 # the 15 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 · 15
Open in Vitessce
Visium
Mouse liver
GSM5764424
mouse liver fatty liver disease 14 MB 1,248 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Conditionfatty liver disease
Size14 MB
Obs1,248
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764421
mouse liver metabolic dysfunction-associated steatotic liver disease 34 MB 2,076 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Conditionmetabolic dysfunction-associated steatotic liver disease
Size34 MB
Obs2,076
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764420
mouse liver metabolic dysfunction-associated steatotic liver disease 40 MB 2,348 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Conditionmetabolic dysfunction-associated steatotic liver disease
Size40 MB
Obs2,348
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764417
mouse liver 36 MB 2,286 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size36 MB
Obs2,286
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764426
mouse liver 31 MB 2,501 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size31 MB
Obs2,501
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764425
mouse liver fatty liver disease 8.3 MB 532 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Conditionfatty liver disease
Size8.3 MB
Obs532
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764416
mouse liver 24 MB 1,604 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size24 MB
Obs1,604
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764427
mouse liver fatty liver disease 16 MB 1,185 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Conditionfatty liver disease
Size16 MB
Obs1,185
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764428
mouse liver 15 MB 1,423 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size15 MB
Obs1,423
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse capsule of liver
GSM5764418
mouse capsule of liver 8.4 MB 438 obs silver H&E
TechnologyVisium
Organismmouse
Tissuecapsule of liver
Size8.4 MB
Obs438
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764423
mouse liver 22 MB 1,708 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size22 MB
Obs1,708
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764414
mouse liver 27 MB 1,646 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size27 MB
Obs1,646
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764415
mouse liver 26 MB 1,651 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size26 MB
Obs1,651
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764419
mouse liver 24 MB 1,279 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Size24 MB
Obs1,279
silver H&E Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764422
mouse liver metabolic dysfunction-associated steatotic liver disease 38 MB 2,254 obs silver H&E
TechnologyVisium
Organismmouse
Tissueliver
Conditionmetabolic dysfunction-associated steatotic liver disease
Size38 MB
Obs2,254
silver H&E Open in Vitessce

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