spatial-ATAC-seq
Human thymus
GSM8831039
human thymus 2.3 GB bronze H&E NCBI GEO policy
Technologyspatial-ATAC-seq
Organismhuman
Tissuethymus
bronze H&E NCBI GEO policy
Collections / geo-gse278007
geo-gse278007
Datasets1
Size~2.3 GB
Technologyspatial-ATAC-seq
Samplehuman · thymus
KindPublication
Download the whole collection
Python · sddb client
from sddb import Catalog
cohort = Catalog().collection("geo-gse278007")
cohort.members # the 1 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/") 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-gse278007")
coll.ordered_artifacts.to_dataframe() # the 1 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()] Shell
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse278007 --dest data/Licenses: 1 NCBI GEO policy
About the study
Spatial profiling of chromatin accessibility in formalin-fixed paraffin-embedded tissues.
Formalin-fixed paraffin-embedded (FFPE) samples represent a vast, untapped resource for epigenomic research, yet molecular tools for deep analysis of these specimens remain limited. We introduce spatial FFPE-ATAC-seq, an approach for in situ profiling chromatin accessibility within archived tissues. This approach overcomes formalin-induced crosslinking challenges, allowing high-resolution mapping of chromatin landscapes while preserving tissue architecture. Applying spatial FFPE-ATAC-seq to mouse and human tissues, including brain and thymus, reveals intricate spatial organization and distinct cell types in alignment with tissue morphology. Integration with single-cell RNA sequencing validates the precision of our chromatin profiles in identifying key cell types and regulatory elements. We further apply this method to human melanoma, comprehensively characterizing chromatin accessibility across both tumor and non-tumor regions. This method significantly expands the toolkit for epigenomic research, unlocking the potential of an extensive collection of archived FFPE samples for studying gene regulation and disease mechanisms with spatial context.
Member datasets · 1
Cite this collection
No linked publication found — please cite the data source.