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~383 MB
AssayVisium
Samplemouse · multiple
KindComparison
Flag a data issue
PMID:35021063 ↗
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Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse192741")
cohort.members        # the 15 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/")
Install (Python 3.12+) Docs →
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-gse192741")
coll.ordered_artifacts.to_dataframe()   # the 15 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
Install (Python 3.12+) Docs →
Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse192741 --dest data/
Install (Python 3.12+) Docs →

Licenses: 15 NCBI GEO policy

Member datasets · 15
Open in Vitessce
Visium
Mouse liver
GSM5764424
mouse liver fatty liver disease 14.8 MB 1,248 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Conditionfatty liver disease
Size14.8 MB
Spots1,248
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764421
mouse liver metabolic dysfunction-associated steatotic liver disease 36.1 MB 2,076 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Conditionmetabolic dysfunction-associated steatotic liver disease
Size36.1 MB
Spots2,076
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764420
mouse liver metabolic dysfunction-associated steatotic liver disease 42.2 MB 2,348 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Conditionmetabolic dysfunction-associated steatotic liver disease
Size42.2 MB
Spots2,348
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764417
mouse liver 38.1 MB 2,286 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Size38.1 MB
Spots2,286
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764426
mouse liver 32.9 MB 2,501 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Size32.9 MB
Spots2,501
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764425
mouse liver fatty liver disease 8.7 MB 532 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Conditionfatty liver disease
Size8.7 MB
Spots532
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764416
mouse liver 25.6 MB 1,604 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Size25.6 MB
Spots1,604
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764427
mouse liver fatty liver disease 16.5 MB 1,185 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Conditionfatty liver disease
Size16.5 MB
Spots1,185
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764428
mouse liver 16.1 MB 1,423 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Size16.1 MB
Spots1,423
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse capsule of liver
GSM5764418
mouse capsule of liver 8.9 MB 438 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuecapsule of liver
Size8.9 MB
Spots438
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764423
mouse liver 22.9 MB 1,708 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Size22.9 MB
Spots1,708
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764414
mouse liver 27.9 MB 1,646 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Size27.9 MB
Spots1,646
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764415
mouse liver 27.6 MB 1,651 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Size27.6 MB
Spots1,651
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764419
mouse liver 24.8 MB 1,279 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Size24.8 MB
Spots1,279
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse liver
GSM5764422
mouse liver metabolic dysfunction-associated steatotic liver disease 40.2 MB 2,254 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueliver
Conditionmetabolic dysfunction-associated steatotic liver disease
Size40.2 MB
Spots2,254
silver H&E NCBI GEO policy Open in Vitessce

Cite this collection

No linked publication found — please cite the data source.