Single nuclei ATAC sequencing of postmortem cingulate cortex and midbrain of healthy donors and Parkinson's disease patients – Scale-ATAC + 10x Genomics.

This Zenodo deposit contains a publicly available description of the Dataset: Title: "Single nuclei ATAC sequencing of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson's disease patients – Scale-ATAC + 10x Genomics.". Description: This dataset consists of raw sequencing ATAC-seq data (Scale-ATAC pre-indexing followed by 10x Genomics snATAC 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://dx.doi.org/10.17504/protocols.io.14egnrb7ql5d/v1, https://dx.doi.org/10.17504/protocols.io.4r3l2z24ql1y/v1, https://cdn.10xgenomics.com/image/upload/v1666737555/support-documents/CG000496_Chromium_NextGEM_SingleCell_ATAC_ReagentKits_v2_UserGuide_RevB.pdf. 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. This dataset is made available to researchers via the ASAP CRN Cloud: cloud.parkinsonsroadmap.org. Instructions for how to request access can be found in the User Manual. This research was funded by the Aligning Science Across Parkinson's Collaborative Research Network (ASAP CRN), through the Michael J. Fox Foundation for Parkinson's Research (MJFF). This Zenodo deposit was created by the ASAP CRN Cloud staff on behalf of the dataset authors. It provides a citable reference for a CRN Cloud Dataset