We present the first spatially-resolved transcriptomics and single-nucleus RNA-sequencing integrated dataset from the entorhinal cortex (ERC) of postmortem human brain donors. ERC is implicated in early progression of Alzheimer’s Disease (AD) and we chose this brain region to study gene expression changes associated with AD risk by comparing APOE E2 and E4 allele carriers. Donors with no AD diagnosis or widespread neurodegeneration were exclusively selected. As AD risk is increased in African Ancestry in contrast to European Ancestry backgrounds, and AD risk is also increased in women compared to men, our dataset included donors from these different backgrounds. We identified a pre-myleinating oligodendrocyte sub-cluster with transcriptomic changes strongly associated with APOE E4 carriers. These changes were present in both ancestry backgrounds, although they were more pronounced in African Ancestry donors. To facilitate future studies based on this dataset, we provided the raw and processed data, and created interactive web applications.
from sddb import Catalog
cohort = Catalog().collection("geo-gse307990")
cohort.members # the 31 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/")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-gse307990")
coll.ordered_artifacts.to_dataframe() # the 31 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse307990 --dest data/Licenses: 31 NCBI GEO policy
@article{Huuki_Myers_2025,
title = {<i>APOE</i>
E4 Alzheimer’s Risk Converges on an Oligodendrocyte Subtype in the Human Entorhinal Cortex},
url = {http://dx.doi.org/10.1101/2025.11.20.689483},
DOI = {10.1101/2025.11.20.689483},
publisher = {openRxiv},
author = {Huuki-Myers, Louise A. and Divecha, Heena R. and Bach, Svitlana V. and Valentine, Madeline R. and Eagles, Nicholas J. and Mulvey, Bernard and Bharadwaj, Rahul A. and Zhang, Ruth and Evans, James R. and Grant-Peters, Melissa and Miller, Ryan A. and Kleinman, Joel E. and Han, Shizhong and Hyde, Thomas M. and Page, Stephanie C. and Weinberger, Daniel R. and Martinowich, Keri and Ryten, Mina and Maynard, Kristen R. and Collado-Torres, Leonardo},
year = {2025},
month = Nov
}