Collections / Activated Interferon Signaling Suppresses Age-Dependent Liver Cancer [MERFISH]

Activated Interferon Signaling Suppresses Age-Dependent Liver Cancer [MERFISH]

MERFISH data from two young and two old WT C57BL/6J mouse livers, using a custom 500-gene panel targeted at aging and cancer-associated genes.

Datasets10
Size~7.0 GB
AssayVizgen MERSCOPE
Samplemouse · liver
KindTime course
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www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE313704 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse313704")
cohort.members        # the 10 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-gse313704")
coll.ordered_artifacts.to_dataframe()   # the 10 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-gse313704 --dest data/
Install (Python 3.12+) Docs →

Licenses: 10 NCBI GEO policy

Member datasets · 10
Open in Vitessce
Vizgen MERSCOPE
Mouse liver
GSM9372790
mouse liver 836 MB 163,186 cells silver NCBI GEO policy
TechnologyVizgen MERSCOPE
Organismmouse
Tissueliver
Size836 MB
Cells163,186
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
Vizgen MERSCOPE
Mouse liver
GSM9372788
mouse liver 1.4 GB 140,698 cells silver NCBI GEO policy
TechnologyVizgen MERSCOPE
Organismmouse
Tissueliver
Size1.4 GB
Cells140,698
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
Vizgen MERSCOPE
Mouse liver
GSM9372795
mouse liver 312 MB 105,825 cells silver NCBI GEO policy
TechnologyVizgen MERSCOPE
Organismmouse
Tissueliver
Size312 MB
Cells105,825
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
Vizgen MERSCOPE
Mouse liver
GSM9372789
mouse liver 749 MB 73,904 cells silver NCBI GEO policy
TechnologyVizgen MERSCOPE
Organismmouse
Tissueliver
Size749 MB
Cells73,904
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
Vizgen MERSCOPE
Mouse liver
GSM9372796
mouse liver 127 MB 114,324 cells silver NCBI GEO policy
TechnologyVizgen MERSCOPE
Organismmouse
Tissueliver
Size127 MB
Cells114,324
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
Vizgen MERSCOPE
Mouse liver
GSM9372794
mouse liver 600 MB 243,863 cells silver NCBI GEO policy
TechnologyVizgen MERSCOPE
Organismmouse
Tissueliver
Size600 MB
Cells243,863
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
Vizgen MERSCOPE
Mouse liver
GSM9372791
mouse liver 1.7 GB 177,494 cells silver NCBI GEO policy
TechnologyVizgen MERSCOPE
Organismmouse
Tissueliver
Size1.7 GB
Cells177,494
silver NCBI GEO policy Open in Vitessce
Vizgen MERSCOPE
Mouse liver
GSM9372797
mouse liver 239 MB 141,524 cells silver NCBI GEO policy
TechnologyVizgen MERSCOPE
Organismmouse
Tissueliver
Size239 MB
Cells141,524
silver NCBI GEO policy
Open in Vitessce
Vizgen MERSCOPE
Mouse liver
GSM9372793
mouse liver 938 MB 237,950 cells silver NCBI GEO policy
TechnologyVizgen MERSCOPE
Organismmouse
Tissueliver
Size938 MB
Cells237,950
silver NCBI GEO policy Open in Vitessce
Open in Vitessce
Vizgen MERSCOPE
Mouse liver
GSM9372792
mouse liver 88.7 MB 54,197 cells silver NCBI GEO policy
TechnologyVizgen MERSCOPE
Organismmouse
Tissueliver
Size88.7 MB
Cells54,197
silver NCBI GEO policy Open in Vitessce

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