Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson’s disease patients – 10x snATAC-seq
Output Details
Description
This dataset consists of raw sequencing snATAC-seq data (10x Genomics Chromium Next GEM Single Cell ATAC v2). The data is part of an overall set of samples derived from postmortem midbrain (n=140), cingulate cortex (n=190) and motor cortex (n=4) of healthy donors (n=114), patients with Parkinson's disease (n=75) or patients with other neurological disorder (n=1). The protocol followed to isolate nuclei from postmortem brain samples and to prepare sequencing libraries can be found here: https://www.protocols.io/view/nuclei-isolation-from-brain-tissue-for-single-cell-14egnrb7ql5d/v1. To increase throughput and to decrease batch effects, several donors have been pooled together into a single sequencing library. To computationally demultiplex the nuclei to their corresponding donors, cellsnp-lite (version commit: aad18644adcde853c313362a856a24245c9b91f7) followed by vireo (https://github.com/single-cell-genetics/vireo/pull/108 ) has been used. The population VCF with the donor genotypes derived from whole genome sequencing data has been used to assign nuclei back to their donors.
Identifier (DOI)
10.5281/zenodo.18988730
