spatial CUT&Tag
Mouse embryo
GSM8189704
bronze Interactive viewer H&E ✓ Verified publication
print(sdata)
SpatialData object
├── Images
│ └── 'tissue_hires': DataArray[cyx] (3, 1776, 1776)
├── Shapes
│ ├── 'epi_spots': GeoDataFrame shape: (2500, 1) (2D shapes)
│ └── 'epi_spots_for_vitessce': GeoDataFrame shape: (2500, 2) (2D shapes)
└── Tables
├── 'epigenome_h3k27me3': AnnData (2500, 545114)
└── 'table': AnnData (2500, 545114)
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("im5mUjTrigIYsQIr0000")
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("im5mUjTrigIYsQIr") # 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 im5mUjTrigIYsQIr0000 --dest data/
# or lamin: cache the dataset and print its local path
lamin load https://lamin.ai/scverse/spatialdata-db/artifact/im5mUjTrigIYsQIr
# or connect once, then load by uid
lamin connect scverse/spatialdata-db
lamin load artifact --uid im5mUjTrigIYsQIrLicense: NCBI GEO policy
Metadata
- Technology
- spatial CUT&Tag
- Organism
- mouse
- Tissue
- embryo
- Modality
- Epigenomics
- Observations (pixels)
- 2,500
- Tier
- bronze
- Resolution
- 1,776 × 1,776 px
- mpp
- 50.000 µm/px
- Size
- 240 MB
- Sample ID
- GSM8189704
- License
- NCBI GEO policy
- Published
- Oct 22, 2024
Cite this dataset
doi.org/10.1038/s41592-024-02576-0 ↗ BibTeX
@article{geo:GSE263333,
doi = {10.1038/s41592-024-02576-0},
title = {GSM8189705},
year = {2025}
}Source: NCBI GEO ↗ · License: NCBI GEO policy ↗ · Reprocessed to SpatialData by SpatialData-DB