Collections / Spatial transcriptomical analysis of livers from patients with COVID19

Spatial transcriptomical analysis of livers from patients with COVID19

In this study, we stained liver tissues from COVID-19 cases with abnormal liver functions, and found viral proteins were detectable from dead or severe cases, but not from moderate patients. We then conducted spatial transcriptomics to analyze effects of SARS-COV-2 on livers.

Datasets3
Size~141 MB
AssayVisium
Samplehuman · liver
KindComparison
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PMID:39709771 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse279405")
cohort.members        # the 3 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-gse279405")
coll.ordered_artifacts.to_dataframe()   # the 3 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-gse279405 --dest data/
Install (Python 3.12+) Docs →

Licenses: 3 NCBI GEO policy

Member datasets · 3
Open in Vitessce
Visium
Human liver
GSM8569297
human liver COVID-19 22.5 MB 4,991 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueliver
ConditionCOVID-19
Size22.5 MB
Spots4,991
Magnificationother · 6.722 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Human liver
GSM8569295
human liver COVID-19 106 MB 4,992 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueliver
ConditionCOVID-19
Size106 MB
Spots4,992
Magnificationother · 5.492 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Visium
Human liver
GSM8569296
human liver COVID-19 12.9 MB 4,778 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismhuman
Tissueliver
ConditionCOVID-19
Size12.9 MB
Spots4,778
bronze H&E NCBI GEO policy

Cite this collection

doi.org/10.1016/j.ebiom.2024.105517 ↗
BibTeX 
@article{Chen_2025,
  title = {Combination of spatial transcriptomics analysis and retrospective study reveals liver infection of SARS-COV-2 is associated with clinical outcomes of COVID-19},
  volume = {111},
  ISSN = {2352-3964},
  url = {http://dx.doi.org/10.1016/j.ebiom.2024.105517},
  DOI = {10.1016/j.ebiom.2024.105517},
  journal = {eBioMedicine},
  publisher = {Elsevier BV},
  author = {Chen, Shiqi and Zhang, Yi and Ashuo, Asha and Song, Shu and Yuan, Lunzhi and Wang, Weixia and Wang, Cong and Du, Zunguo and Wu, Yangtao and Tan, Dan and Huang, Chenlu and Chen, Jingna and Li, Yaming and Bai, Jinjin and Guo, Huilin and Huang, Zehong and Guan, Yi and Xia, Ningshao and Yuan, Zhenghong and Zhang, Jiming and Yuan, Quan and Fang, Zhong},
  year = {2025},
  month = Jan,
  pages = {105517}
}