spatial ATAC-RNA-seq
Mouse brain
GSM9248997
silver Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'tissue_hires': DataArray[cyx] (3, 3145, 3154)
├── Shapes
│ ├── 'epi_spots': GeoDataFrame shape: (10000, 1) (2D shapes)
│ └── 'epi_spots_for_vitessce': GeoDataFrame shape: (10000, 2) (2D shapes)
└── Tables
├── 'epigenome_atac': AnnData (10000, 545114)
└── 'table': AnnData (7794, 31889)
with coordinate systems:
▸ 'global', with elements:
tissue_hires (Images), epi_spots (Shapes), epi_spots_for_vitessce (Shapes) Python · sddb client
from sddb import Catalog
ds = Catalog().dataset("5CjJqsXejE1oCMzv0000")
ds.elements() # inspect without downloading
sdata = ds.to_sdata() # cached locally, reused
print(sdata) 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")
artifact = db.Artifact.get("5CjJqsXejE1oCMzv") # stem uid: Lamin resolves it to the latest version
sdata = artifact.load() # cache, then load into memory
group = artifact.open() # stream without downloading
path = artifact.cache() # sync into the local cache, returns the path Shell
# sddb client: download the .zarr into data/
sddb-cli download 5CjJqsXejE1oCMzv0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/5CjJqsXejE1oCMzv
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid 5CjJqsXejE1oCMzvLicense: NCBI GEO policy
Metadata
- Technology
- spatial ATAC-RNA-seq
- Organism
- mouse
- Tissue
- brain
- Modality
- RNA · Epigenomics
- Observations (pixels)
- 7,794
- Tier
- silver
- Resolution
- 3,154 × 3,145 px
- Size
- 458 MB
- Sample ID
- GSM9248997
- License
- NCBI GEO policy
- Published
- Sep 19, 2025
Cite this dataset
doi.org/10.1038/s41586-025-09663-y ↗ BibTeX
@article{geo:GSE308599,
doi = {10.1038/s41586-025-09663-y},
title = {GSM9248996},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB