Single nuclei sequencing of brain regions from healthy and Parkinson's Disease individuals

We performed single nuclei RNA sequencing of postmortem PD and control brain tissue of four different brain regions (substantia nigra, putamen, amygdala, and prefrontal cortex). Briefly, 8500 nuclei were FACS sorted from approximately 2 mm3 of tissue. Single nuclei RNAseq libraries were prepared using 10X genomics platform for single cell 3' sequencing. Sequencing libraries are prepared by fragmentation, end repair and a tailing followed by sample index PCR. To process the data, FASTQ files were processed using Cell Ranger, aligning and quantifying for hg38. Intronic reads were also quantified. 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 Version bump from 2.0 to 2.1 The updated Datasets fix inconsistencies in the ASAP assigned `ASAP_subject_id` and `ASAP_sample_id` for these previously released PMDBS Datasets. These erroneously included the string "PMBDS", now replaced with "PMDBS". This change does not affect the underlying data files, but does update the metadata to be consistent with the naming convention used for all other PMDBS Datasets and the corresponding CDEs.