The ABC Atlas has been updated with new data!
We are proud to share new data produced by Aligning Science Across Parkinson’s (ASAP) researchers. The ASAP initiative, Allen Institute, and 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.
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) integrated with cell type taxonomies using the Allen Institute’s MapMyCells tool.
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 million 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.
Learn more about the data here, including documentation of the data curation process ASAP CRN Cloud PMDBS snRNAseq Quality Control Dimension Reduction.
Explore this data now in the ABC Atlas!
As always, thank you for being part of the AIBS community. Please let us know how we can improve the ABC Atlas to better serve your needs.