Collections / Spatial and single cell transcriptomics in the human Entorhinal Cortex across diverse risk of Alzheimer’s disease [Visium]

Spatial and single cell transcriptomics in the human Entorhinal Cortex across diverse risk of Alzheimer’s disease [Visium]

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.

Datasets31

Size~943 MB

AssayVisium

Samplehuman · entorhinal cortex

KindOther

PMID:41332786 ↗

Download the whole collection

Python · lamindb

import lamindb as ln
import spatialdata as sd

coll = ln.Collection.get(key="geo-gse307990")
coll.ordered_artifacts.df()                 # the 31 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]

# …or load each straight into memory as a SpatialData object:
sdatas = {a.key: sd.read_zarr(a.cache()) for a in coll.ordered_artifacts.all()}

Member datasets · 31

Visium

Human entorhinal cortex

GSM9235051

human entorhinal cortex 40 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size40 MB

Obs4,992

Magnificationother · 4.186 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235059

human entorhinal cortex 30 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size30 MB

Obs4,992

Magnificationother · 4.084 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235055

human entorhinal cortex 31 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size31 MB

Obs4,992

Magnificationother · 3.774 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235054

human entorhinal cortex 34 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size34 MB

Obs4,992

Magnificationother · 4.117 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235045

human entorhinal cortex 16 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size16 MB

Obs4,992

Magnificationother · 4.359 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235057

human entorhinal cortex 12 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size12 MB

Obs4,992

Magnificationother · 3.942 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235031

human entorhinal cortex 41 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size41 MB

Obs4,992

Magnificationother · 4.120 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235038

human entorhinal cortex 33 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size33 MB

Obs4,992

Magnificationother · 4.271 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235058

human entorhinal cortex 17 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size17 MB

Obs4,992

Magnificationother · 4.085 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235037

human entorhinal cortex 31 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size31 MB

Obs4,992

Magnificationother · 4.274 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235046

human entorhinal cortex 30 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size30 MB

Obs4,992

Magnificationother · 4.220 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235053

human entorhinal cortex 38 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size38 MB

Obs4,992

Magnificationother · 4.186 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235060

human entorhinal cortex 15 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size15 MB

Obs4,992

Magnificationother · 4.089 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235044

human entorhinal cortex 22 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size22 MB

Obs4,992

Magnificationother · 4.361 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235036

human entorhinal cortex 29 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size29 MB

Obs4,992

Magnificationother · 4.274 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235056

human entorhinal cortex 28 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size28 MB

Obs4,992

Magnificationother · 3.945 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235050

human entorhinal cortex 43 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size43 MB

Obs4,992

Magnificationother · 4.190 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235041

human entorhinal cortex 40 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size40 MB

Obs4,992

Magnificationother · 4.447 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235043

human entorhinal cortex 20 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size20 MB

Obs4,992

Magnificationother · 4.357 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235048

human entorhinal cortex 21 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size21 MB

Obs4,992

Magnificationother · 4.220 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235061

human entorhinal cortex 29 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size29 MB

Obs4,992

Magnificationother · 4.085 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235034

human entorhinal cortex 51 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size51 MB

Obs4,992

Magnificationother · 4.114 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235039

human entorhinal cortex 41 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size41 MB

Obs4,992

Magnificationother · 4.449 µm/px

bronze H&E

Visium

Human entorhinal cortex

GSM9235033

human entorhinal cortex 30 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size30 MB

Obs4,992

bronze H&E

Visium

Human entorhinal cortex

GSM9235049

human entorhinal cortex 31 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size31 MB

Obs4,992

bronze H&E

Visium

Human entorhinal cortex

GSM9235035

human entorhinal cortex 33 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size33 MB

Obs4,992

bronze H&E

Visium

Human entorhinal cortex

GSM9235047

human entorhinal cortex 31 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size31 MB

Obs4,992

bronze H&E

Visium

Human entorhinal cortex

GSM9235042

human entorhinal cortex 17 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size17 MB

Obs4,992

bronze H&E

Visium

Human entorhinal cortex

GSM9235040

human entorhinal cortex 33 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size33 MB

Obs4,992

bronze H&E

Visium

Human entorhinal cortex

GSM9235052

human entorhinal cortex 29 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size29 MB

Obs4,992

bronze H&E

Visium

Human entorhinal cortex

GSM9235032

human entorhinal cortex 46 MB 4,992 obs bronze H&E

TechnologyVisium

Organismhuman

Tissueentorhinal cortex

Size46 MB

Obs4,992

bronze H&E

Cite this collection

No linked publication found — please cite the data source.