ASAP Human Postmortem-Derived Brain Sequencing Collection (PMDBS): Data Overview#

Aligning Science Across Parkinson’s (ASAP), The Michael J. Fox Foundation for Parkinson’s Research (MJFF), and the Allen Institute for Brain Science (AIBS) are teaming up to further the mission of the ASAP Collaborative Research Network (CRN) program, to accelerate discoveries in the Parkinson’s disease (PD) and neurodegenerative disease research communities. Together we will annotate, enhance and add knowledge to the growing data catalog in the ASAP CRN Cloud through integration of cell type taxonomies using the Allen Institute’s MapMyCells tool and visualization through the Allen Brain Cell (ABC) Atlas web application. This integration of data and knowledge will allow users to visualize and explore the changes in gene expression of specific, highly resolved brain cell types in the context of a large PD cohort of donors.

This initial collaboration focuses on the Human Postmortem-derived Brain Sequencing Collection (PMDBS), a harmonized repository comprised of single nucleus and PolyA RNA-seq data contributed by five ASAP CRN teams (Hafler, Lee, Jakobsson, Scherzer, Hardy). Sequencing data were uniformly aligned to the GRCh38.p13 reference genome (Gencode V32), quality control was performed and low-quality cells were filtered out. A set of highly variable genes were identified and the scVI workflow resulted in an integrated latent variable representation, 2D UMAP coordinates and a set of 30 clusters. Currently, the repository spans roughly 3 millions cells obtained from 9 brain regions and 211 donors with various pathologies (including healthy control). For more details on this dataset and to access the raw data used in its preparation, please visit the ASAP CRN Cloud webpage.

The simplified data created by AIBS in the form of expression matrices and associated metadata are hosted on AWS S3 bucket as a AWS Public Dataset:

Component

Current Version

Size

Expression Matrices

s3://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/expression_matrices/ASAP-PMDBS-10X/20250331/

29 GB

Cell and gene metadata

s3://allen-brain-cell-atlas.s3.us-west-2.amazonaws.com/metadata/ASAP-PMDBS-10X/20250331/

660 MB

Data is being shared under the CC BY 4.0 license.

Related resources:

  • Results of running mapping the ~3 million ASAP-PMDBS cells into the WHB and SEA-AD taxonomies (ASAP-PMDBS-MapMyCells)

Associated notebooks: