SEA-AD - Caudate Nucleus taxonomy

SEA-AD - Caudate Nucleus taxonomy#

The caudate nucleus (Ca) is a “C”-shaped subcortical structure that pairs with the putamen to form the striatum, a component of the basal ganglia. Beyond its role in motor control, the caudate participates in cognitive processes such as procedural memory and associative learning, and it is implicated in several neurodegenerative diseases, including Parkinson’s, Huntington’s, and Alzheimer’s. In Alzheimer’s specifically, the presence of amyloid-\(\beta\) plaques in the head of the caudate partly defines Thal stage III. Here we introduce the SEA-AD Caudate Head Atlas, a cellular-resolution view of Alzheimer’s disease pathology in the caudate head of human donors.

This dataset comprises ~800,000 single cells from a 42-donor subset of the original 84-donor SEA-AD cohort, selected to minimize comorbidities with other known brain diseases. Disease progression is quantified with a continuous pseudo-progression score (CPS), derived from a biophysical model of disease progression fit to quantitative neuropathology from the region. Standard staging measures are also included: overall AD neuropathologic change (ADNC), Braak, and Thal. To annotate the data, we integrated two references — the Human and Mammalian Brain Atlas (HMBA) of the basal ganglia and the SEA-AD middle temporal gyrus (MTG) atlas — merging overlapping classes into the SEA-AD taxonomy. Quality control was performed after integration: for each cluster, thresholds were set on standard metrics including Genes Detected, Doublet score, and Fraction mitochondrial UMIs.

The notebooks presented here demonstrate how to access and visualize taxonomy annotations, cell type metadata, donor information, brain region annotations, and AD-associated cellular changes from the SEA-AD CaH dataset. These examples focus on precomputed metadata accessible through the Allen Brain Cell Atlas Access package. Additional data, including links to raw sequencing, spatial transcriptomic, and neuropathology data, are available at SEA-AD.org.

All associated metadata is publicly available as an AWS Public Dataset hosted on Amazon S3 and through the Allen Brain Cell Atlass Access (abc_atlas_access) package.

The associated metadata is hosted on AWS S3 bucket as a AWS Public Dataset:

Component

Current Version

Size

Cell taxonomy metadata

s3://allen-brain-cell-atlas/metadata/SEA-AD-CaH-taxonomy/20260711/

79.3 MB

Data is being shared under the CC BY NC 4.0 license.

Related resources:

Associated notebooks: