Collections / Spatial transcriptomic analysis of developing hearts at embryonic and neonatal stages

Spatial transcriptomic analysis of developing hearts at embryonic and neonatal stages

Cd1 wildetype mice, Wt1-CreER;Rosa-mTmG mice, and Wt1-CreER;Rosa-DTA mice derived hearts were isolated and directly embeded. The hearts were then sectioned for spatial transcriptomic analysis.

Datasets8
Size~117 MB
AssayVisium
Samplemouse · heart
KindOther
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PMID:42141139 ↗
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Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse282547")
cohort.members        # the 8 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-gse282547")
coll.ordered_artifacts.to_dataframe()   # the 8 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-gse282547 --dest data/
Install (Python 3.12+) Docs →

Licenses: 8 NCBI GEO policy

Member datasets · 8
Open in Vitessce
Visium
Mouse heart
GSM8645799
mouse heart 12.1 MB 456 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Size12.1 MB
Spots456
Magnificationother · 3.767 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM8645796
mouse heart 15.1 MB 664 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Size15.1 MB
Spots664
Magnificationother · 3.509 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM8645794
mouse heart 14.1 MB 621 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Size14.1 MB
Spots621
Magnificationother · 3.504 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM8645800
mouse heart 7.1 MB 243 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Size7.1 MB
Spots243
Magnificationother · 3.763 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM8645795
mouse heart 24.3 MB 1,293 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Size24.3 MB
Spots1,293
Magnificationother · 3.515 µm/px
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM8645798
mouse heart 14.1 MB 849 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Size14.1 MB
Spots849
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM8645793
mouse heart 15.8 MB 741 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Size15.8 MB
Spots741
bronze H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse heart
GSM8645797
mouse heart 14.8 MB 708 spots bronze H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueheart
Size14.8 MB
Spots708
Magnificationother · 3.770 µm/px
bronze H&E NCBI GEO policy Open in Vitessce

Cite this collection

doi.org/10.1038/s42003-026-10259-z ↗
BibTeX 
@article{Hu_2026,
  title = {Spatial transcriptomic profiling of developing mouse hearts reveals a spatially patterned signaling environment},
  volume = {9},
  ISSN = {2399-3642},
  url = {http://dx.doi.org/10.1038/s42003-026-10259-z},
  DOI = {10.1038/s42003-026-10259-z},
  number = {1},
  journal = {Communications Biology},
  publisher = {Springer Science and Business Media LLC},
  author = {Hu, Junqi and He, Haoting and Xu, Juan and MacDonald, William A. and He, Yuanhang and Liu, Tianhao and Chen, Wei and Li, Guang},
  year = {2026},
  month = May
}