ASAP Human Postmortem-Derived Brain Sequencing Collection
The Aligning Science Across Parkinson’s (ASAP) initiative, Allen Institute, and the Michael J. Fox Foundation are teaming up to help researchers unlock deeper insights into how cell types, brain anatomy, and diseases like Parkinson’s are connected.
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 allows users to visualize and explore the changes in gene expression of specific, highly resolved brain cell types in the context of a large Parkinson’s disease cohort of donors.
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About the data
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 collection description on the ASAP CRN Cloud webpage.
ASAP-PMDBS cells were mapped to the whole human brain (WHB) taxonomy (Siletti et al., 2023), which is hierarchical taxonomy of ~3.3 million cells (neurons and non-neuronal cells) with 31 superclusters, 461 clusters, and 3,313 subclusters spanning 105 anatomical dissections across the whole human brain. The 30 ASAP clusters were mapped at the WHB supercluster, cluster, and subcluster levels. Click the button below to view the datasets side-by-side.
Additional Resources