ASAP Human Postmortem-Derived Brain Sequencing Collection (PMDBS): Mapping to the Whole Human Brain (WHB) and Seattle Alzheimer’s Disease Brain Cell Atlas (SEA-AD) Taxonomies#

We run the Allen Institute’s MapMyCell tool over the ASAP-PMDBS data to provide cell type insight to the PMDBS dataset.

MapMyCells(RRID: SCR_024672) transforms cell types from a concept in publications to a tool for public research. Scientists worldwide can discover what cell types their transcriptomics and spatial data corresponds with by comparing their data to massive, high-quality reference datasets using multiple mapping methods. Currently available taxonomies include 10X whole mouse brain taxonomy, 10X whole human brain taxonomy and 10X Human MTG SEA-AD taxonomy. Available algorithms include correlation mapping (flatmap), hierarchical correlation mapping and a deep generative model-based algorithm.

We mapped the approximately 3 million cells of PMDBS to the 10X whole human brain taxonomy (Siletti et. al.) and the SEA-AD taxonomy using the hierarchical correlation mapping method where assignments are first made at the top level of the taxonomy using mean gene expression profiles of the reference dataset and pre-selected set of marker genes to distinguish cluster from its sibling. For robustness, the process is repeated 100 times, using 50% of the marker genes each time. A cell is assigned the class that receives the plurality of votes, a probability and correlation score. This process is repeated down the taxonomy until the last finest level.

The mappings to the Whole Human Brain (WHB) and SEA-AD taxonomies are available on S3:

Component

Current Version

Size

Taxonomy

s3://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/metadata/ASAP-PMDBS-taxonomy/20250331/

2 GB

Data is being shared under the CC BY 4.0 license.

Related resources:

  • Overview of the ~3 million cell ASAP-PMDBS, harmonized dataset (ASAP-PMDBS-10X)

Associated notebooks: