Single nuclei RNA sequencing (10x) of postmortem cingulate cortex,midbrain and motor cortex of healthy donors and Parkinson’s disease patients – 10x snRNA-seq
Output Details
Description
This dataset consists of raw sequencing snRNA-seq data (10x Genomics Chromium Next GEM Single Cell 3ʹ). 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.5qpvo1rddg4o/v1, https://www.10xgenomics.com/support/universal-three-prime-gene-expression/documentation/steps/library-prep/chromium-single-cell-3-reagent-kits-user-guide-v-3-1-chemistry-dual-index. 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.18988769
