Collections / Spatial transcriptomics reveals C10 tumor transcriptomic changes generated by Smarta cell transfer

Spatial transcriptomics reveals C10 tumor transcriptomic changes generated by Smarta cell transfer

To elucidate how antigen-specific CD4 T cells indirectly repress tumor growth independently of other lymphocytes, we first sought to gain insight into the changes they induced in the tumor micro-environment (TME) using the 10x Genomics Visium technology

Datasets2
Size~292 MB
AssayVisium
Samplemouse · lung
KindOther
Flag a data issue
PMID:42313973 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse254861")
cohort.members        # the 2 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-gse254861")
coll.ordered_artifacts.to_dataframe()   # the 2 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-gse254861 --dest data/
Install (Python 3.12+) Docs →

Licenses: 2 NCBI GEO policy

Member datasets · 2
Open in Vitessce
Visium
Mouse lung
GSM8059173
mouse lung 188 MB 7,088 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuelung
Size188 MB
Spots7,088
Magnificationother · 6.397 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse lung
GSM8059174
mouse lung 104 MB 3,480 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissuelung
Size104 MB
Spots3,480
Magnificationother · 5.941 µm/px
bronze H&E NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.1126/science.ads7910 ↗
BibTeX 
@article{Lian_2026,
  title = {CD4
                    <sup>+</sup>
                    T cells impair tumor growth through IL-3 and TNF-dependent vascular damage},
  volume = {392},
  ISSN = {1095-9203},
  url = {http://dx.doi.org/10.1126/science.ads7910},
  DOI = {10.1126/science.ads7910},
  number = {6804},
  journal = {Science},
  publisher = {American Association for the Advancement of Science (AAAS)},
  author = {Lian, Qiaoshi and Nie, Jia and Singh, Jatinder and Chen, Qiang and Matta, Jennifer and Chan, Waipan and Balmaceno-Criss, Mariah and Vacchio, Melanie S. and Yu, Weiming and Clark, Alexander D. and Edmondson, Elijah and Kelly, Michael C. and Germain, Ronald N. and Bosselut, Rémy},
  year = {2026},
  month = June
}